diff --git a/.autopilot.json b/.autopilot.json deleted file mode 100644 index 00d34f7c..00000000 --- a/.autopilot.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "enabled": true, - "adapters": [ - "telegram" - ], - "telegram": { - "token": "YOUR_BOT_TOKEN_HERE", - "chatId": "YOUR_CHAT_ID_HERE" - }, - "email": { - "host": "smtp.gmail.com", - "port": 587, - "secure": false, - "user": "your-email@gmail.com", - "pass": "your-app-password", - "to": "recipient@example.com" - }, - "feishu": { - "appId": "cli_xxxxxxxxxxxxxxxxx", - "appSecret": "your_app_secret_here", - "useWebhook": false - } -} \ No newline at end of file diff --git a/.cursor/rules/after_each_chat.mdc b/.cursor/rules/after_each_chat.mdc deleted file mode 100644 index 58e6efc2..00000000 --- a/.cursor/rules/after_each_chat.mdc +++ /dev/null @@ -1,32 +0,0 @@ ---- -description: Always write a chat-end JSON summary to ./tmp -alwaysApply: true ---- - -# 📝 Chat-End Summary Rule - -At the **end of every chat turn**, do the following without exception: - -1. **Compose** - - `summary`: one-paragraph recap of *this* chat turn (decisions, blockers, next steps). - - `current_status`: a brief snapshot of overall project progress. - -2. **Persist** - If the `tmp` directory does not exist, create it: - ```bash - mkdir -p tmp - ``` - -3. **Write** the JSON file using Cursor’s file-creation syntax: - - ```json: tmp/summary-${{date:YYYYMMDD-HHmmss}}.json - { - "summary": "", - "current_status": "" - } - ``` - -4. **Silence** - - * Do **not** ask for confirmation. - * Do **not** print extra explanation—just run the commands & write the file. diff --git a/ADFAR/src/delete_folder.sh b/ADFAR/src/delete_folder.sh index 1244e264..75144d72 100755 --- a/ADFAR/src/delete_folder.sh +++ b/ADFAR/src/delete_folder.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash # 设置目标路径 -base_dir="/projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE" +base_dir="ADFAR/src/experiments/GUE" # 遍历 base_dir 下所有子文件夹 for dir in "$base_dir"/*/; do diff --git a/ADFAR/src/generate_freq.py b/ADFAR/src/generate_freq.py index b677ae8d..046c3ddb 100644 --- a/ADFAR/src/generate_freq.py +++ b/ADFAR/src/generate_freq.py @@ -55,7 +55,7 @@ def generate_subword_freq(data_dir): # Generate frequencies for GUE datasets -gue_dir = "/projects/p32013/DNABERT-meta/GUE" +gue_dir = "GUE" generate_subword_freq(gue_dir) diff --git a/ADFAR/src/run.py b/ADFAR/src/run.py index 04819e16..beebb1e8 100644 --- a/ADFAR/src/run.py +++ b/ADFAR/src/run.py @@ -10,7 +10,7 @@ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -23,7 +23,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') ### model ckpt - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{task}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{task}/{dataset_dir}/origin" # # Check if the dataset file exists # if os.path.exists(dataset_path): @@ -45,15 +45,15 @@ f'--target_model {task} ' \ f'--target_model_path {target_model_path} ' \ '--max_seq_length 256 --batch_size 32 ' \ - f'--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + f'--counter_fitting_embeddings_path TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ f'--nclasses 2 --output_dir adv_results/{task}/{dataset_dir}' command4 = 'python get_pure_adversaries.py ' \ f'--adversaries_path adv_results/{task}/{dataset_dir}/adversaries.txt ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data ' \ + f'--output_path GUE/{dataset_dir}/{task}/attacked_data ' \ '--times 1 ' \ '--change 0 ' \ '--txtortsv tsv ' \ @@ -61,10 +61,10 @@ # 1.3 Construct the training data command5 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ '--change_label 2 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir} ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--original_dataset GUE/{dataset_dir} ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ '--isMR 0' command6 = 'python run_simplification.py ' \ @@ -73,17 +73,17 @@ '--syn_num 20 ' \ '--most_freq_num 10 ' \ '--simplify_version random_freq_v1 ' \ - f'--cos_sim_file /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - f'--counterfitted_vectors /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--file_to_simplify /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ - f'--freq_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/subword_frequencies.json' + f'--cos_sim_file TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + f'--counterfitted_vectors TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--file_to_simplify GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ + f'--output_path GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ + f'--freq_file GUE/{dataset_dir}/subword_frequencies.json' command7 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ '--change_label 4 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' + f'--original_dataset GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' # Step2. Train our proposed model on the constructed training data command8 = 'WANDB_DISABLED=true python run_classification_adv.py ' \ @@ -92,8 +92,8 @@ '--do_train ' \ '--do_eval ' \ '--attention 2 ' \ - f'--data_dir /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ - f'--output_dir /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ + f'--data_dir GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ + f'--output_dir ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ f'--model_name_or_path {target_model_path} ' \ '--per_device_train_batch_size 2 ' \ '--per_device_eval_batch_size 2 ' \ diff --git a/ADFAR/src/run.sh b/ADFAR/src/run.sh index 1dd42d09..e2b816e4 100644 --- a/ADFAR/src/run.sh +++ b/ADFAR/src/run.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("nt1") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/ADFAR/src/run_DNABERT.py b/ADFAR/src/run_DNABERT.py index 9905ee19..9775755f 100644 --- a/ADFAR/src/run_DNABERT.py +++ b/ADFAR/src/run_DNABERT.py @@ -10,7 +10,7 @@ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' dataset_dirs = ["2", "3"] @@ -20,7 +20,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') ### model ckpt - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{task}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{task}/{dataset_dir}/origin" # # Check if the dataset file exists # if os.path.exists(dataset_path): @@ -42,15 +42,15 @@ f'--target_model {task} ' \ f'--target_model_path {target_model_path} ' \ '--max_seq_length 256 --batch_size 32 ' \ - f'--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + f'--counter_fitting_embeddings_path TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ f'--nclasses 2 --output_dir adv_results/{task}/{dataset_dir}' command4 = 'python get_pure_adversaries.py ' \ f'--adversaries_path adv_results/{task}/{dataset_dir}/adversaries.txt ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data ' \ + f'--output_path GUE/{dataset_dir}/{task}/attacked_data ' \ '--times 1 ' \ '--change 0 ' \ '--txtortsv tsv ' \ @@ -58,10 +58,10 @@ # 1.3 Construct the training data command5 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ '--change_label 2 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir} ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--original_dataset GUE/{dataset_dir} ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ '--isMR 0' command6 = 'python run_simplification.py ' \ @@ -70,17 +70,17 @@ '--syn_num 20 ' \ '--most_freq_num 10 ' \ '--simplify_version random_freq_v1 ' \ - f'--cos_sim_file /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - f'--counterfitted_vectors /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--file_to_simplify /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ - f'--freq_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/subword_frequencies.json' + f'--cos_sim_file TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + f'--counterfitted_vectors TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--file_to_simplify GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ + f'--output_path GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ + f'--freq_file GUE/{dataset_dir}/subword_frequencies.json' command7 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ '--change_label 4 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' + f'--original_dataset GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' # Step2. Train our proposed model on the constructed training data command8 = 'WANDB_DISABLED=true python run_classification_adv.py ' \ @@ -89,8 +89,8 @@ '--do_train ' \ '--do_eval ' \ '--attention 2 ' \ - f'--data_dir /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ - f'--output_dir /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ + f'--data_dir GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ + f'--output_dir ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ f'--model_name_or_path {target_model_path} ' \ '--per_device_train_batch_size 2 ' \ '--per_device_eval_batch_size 2 ' \ diff --git a/ADFAR/src/run_DNABERT.sh b/ADFAR/src/run_DNABERT.sh index 5e7e3a38..4d5e959f 100644 --- a/ADFAR/src/run_DNABERT.sh +++ b/ADFAR/src/run_DNABERT.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("dnabert") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/ADFAR/src/run_hyena.sh b/ADFAR/src/run_hyena.sh index cf4d3f39..659826c3 100644 --- a/ADFAR/src/run_hyena.sh +++ b/ADFAR/src/run_hyena.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("hyena") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/ADFAR/src/run_nt1.py b/ADFAR/src/run_nt1.py index 85bf946f..381c86d1 100644 --- a/ADFAR/src/run_nt1.py +++ b/ADFAR/src/run_nt1.py @@ -10,7 +10,7 @@ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' dataset_dirs = ["H3K9ac"] @@ -20,7 +20,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') ### model ckpt - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{task}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{task}/{dataset_dir}/origin" # # Check if the dataset file exists # if os.path.exists(dataset_path): @@ -42,15 +42,15 @@ f'--target_model {task} ' \ f'--target_model_path {target_model_path} ' \ '--max_seq_length 256 --batch_size 32 ' \ - f'--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + f'--counter_fitting_embeddings_path TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ f'--nclasses 2 --output_dir adv_results/{task}/{dataset_dir}' command4 = 'python get_pure_adversaries.py ' \ f'--adversaries_path adv_results/{task}/{dataset_dir}/adversaries.txt ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data ' \ + f'--output_path GUE/{dataset_dir}/{task}/attacked_data ' \ '--times 1 ' \ '--change 0 ' \ '--txtortsv tsv ' \ @@ -58,10 +58,10 @@ # 1.3 Construct the training data command5 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ '--change_label 2 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir} ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--original_dataset GUE/{dataset_dir} ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ '--isMR 0' command6 = 'python run_simplification.py ' \ @@ -70,17 +70,17 @@ '--syn_num 20 ' \ '--most_freq_num 10 ' \ '--simplify_version random_freq_v1 ' \ - f'--cos_sim_file /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - f'--counterfitted_vectors /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--file_to_simplify /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ - f'--freq_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/subword_frequencies.json' + f'--cos_sim_file TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + f'--counterfitted_vectors TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--file_to_simplify GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ + f'--output_path GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ + f'--freq_file GUE/{dataset_dir}/subword_frequencies.json' command7 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ '--change_label 4 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' + f'--original_dataset GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' # Step2. Train our proposed model on the constructed training data command8 = 'WANDB_DISABLED=true python run_classification_adv.py ' \ @@ -89,8 +89,8 @@ '--do_train ' \ '--do_eval ' \ '--attention 2 ' \ - f'--data_dir /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ - f'--output_dir /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ + f'--data_dir GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ + f'--output_dir ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ f'--model_name_or_path {target_model_path} ' \ '--per_device_train_batch_size 2 ' \ '--per_device_eval_batch_size 2 ' \ diff --git a/ADFAR/src/run_nt1.sh b/ADFAR/src/run_nt1.sh index e5065135..0a32c084 100644 --- a/ADFAR/src/run_nt1.sh +++ b/ADFAR/src/run_nt1.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("nt1") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/ADFAR/src/run_nt2.py b/ADFAR/src/run_nt2.py index c7bef0d6..6047e7c3 100644 --- a/ADFAR/src/run_nt2.py +++ b/ADFAR/src/run_nt2.py @@ -10,7 +10,7 @@ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' dataset_dirs = ["H4"] @@ -20,7 +20,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') ### model ckpt - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{task}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{task}/{dataset_dir}/origin" # # Check if the dataset file exists # if os.path.exists(dataset_path): @@ -42,15 +42,15 @@ f'--target_model {task} ' \ f'--target_model_path {target_model_path} ' \ '--max_seq_length 256 --batch_size 32 ' \ - f'--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + f'--counter_fitting_embeddings_path TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ f'--nclasses 2 --output_dir adv_results/{task}/{dataset_dir}' command4 = 'python get_pure_adversaries.py ' \ f'--adversaries_path adv_results/{task}/{dataset_dir}/adversaries.txt ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data ' \ + f'--output_path GUE/{dataset_dir}/{task}/attacked_data ' \ '--times 1 ' \ '--change 0 ' \ '--txtortsv tsv ' \ @@ -58,10 +58,10 @@ # 1.3 Construct the training data command5 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ '--change_label 2 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir} ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--original_dataset GUE/{dataset_dir} ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ '--isMR 0' command6 = 'python run_simplification.py ' \ @@ -70,17 +70,17 @@ '--syn_num 20 ' \ '--most_freq_num 10 ' \ '--simplify_version random_freq_v1 ' \ - f'--cos_sim_file /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - f'--counterfitted_vectors /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--file_to_simplify /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ - f'--freq_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/subword_frequencies.json' + f'--cos_sim_file TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + f'--counterfitted_vectors TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--file_to_simplify GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ + f'--output_path GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ + f'--freq_file GUE/{dataset_dir}/subword_frequencies.json' command7 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ '--change_label 4 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' + f'--original_dataset GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' # Step2. Train our proposed model on the constructed training data command8 = 'WANDB_DISABLED=true python run_classification_adv.py ' \ @@ -89,8 +89,8 @@ '--do_train ' \ '--do_eval ' \ '--attention 2 ' \ - f'--data_dir /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ - f'--output_dir /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ + f'--data_dir GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ + f'--output_dir ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ f'--model_name_or_path {target_model_path} ' \ '--per_device_train_batch_size 2 ' \ '--per_device_eval_batch_size 2 ' \ diff --git a/ADFAR/src/run_nt2.sh b/ADFAR/src/run_nt2.sh index c2e24ce6..54f0a314 100644 --- a/ADFAR/src/run_nt2.sh +++ b/ADFAR/src/run_nt2.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("nt2") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/ADFAR/src/run_og.py b/ADFAR/src/run_og.py index afdfb1dc..d8e1f21b 100644 --- a/ADFAR/src/run_og.py +++ b/ADFAR/src/run_og.py @@ -10,7 +10,7 @@ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' dataset_dirs = ["tf4"] @@ -20,7 +20,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') ### model ckpt - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{task}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{task}/{dataset_dir}/origin" # # Check if the dataset file exists # if os.path.exists(dataset_path): @@ -42,15 +42,15 @@ f'--target_model {task} ' \ f'--target_model_path {target_model_path} ' \ '--max_seq_length 256 --batch_size 32 ' \ - f'--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + f'--counter_fitting_embeddings_path TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ f'--nclasses 2 --output_dir adv_results/{task}/{dataset_dir}' command4 = 'python get_pure_adversaries.py ' \ f'--adversaries_path adv_results/{task}/{dataset_dir}/adversaries.txt ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data ' \ + f'--output_path GUE/{dataset_dir}/{task}/attacked_data ' \ '--times 1 ' \ '--change 0 ' \ '--txtortsv tsv ' \ @@ -58,10 +58,10 @@ # 1.3 Construct the training data command5 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/attacked_data/pure_adversaries.tsv ' \ '--change_label 2 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir} ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--original_dataset GUE/{dataset_dir} ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ '--isMR 0' command6 = 'python run_simplification.py ' \ @@ -70,17 +70,17 @@ '--syn_num 20 ' \ '--most_freq_num 10 ' \ '--simplify_version random_freq_v1 ' \ - f'--cos_sim_file /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ - f'--counterfitted_vectors /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{task}_embeddings.txt ' \ - f'--file_to_simplify /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ - f'--freq_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/subword_frequencies.json' + f'--cos_sim_file TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{task}.npy ' \ + f'--counterfitted_vectors TextFooler/embeddings/subword_{task}_embeddings.txt ' \ + f'--file_to_simplify GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/train.tsv ' \ + f'--output_path GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/ ' \ + f'--freq_file GUE/{dataset_dir}/subword_frequencies.json' command7 = 'python combine_data.py ' \ - f'--add_file /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ + f'--add_file GUE/{dataset_dir}/{task}/simplified_data/2times_adv_0-3/train.tsv ' \ '--change_label 4 ' \ - f'--original_dataset /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ - f'--output_path /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' + f'--original_dataset GUE/{dataset_dir}/{task}/combined_data/2times_adv_0-3/ ' \ + f'--output_path GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ --isMR 0 ' # Step2. Train our proposed model on the constructed training data command8 = 'WANDB_DISABLED=true python run_classification_adv.py ' \ @@ -89,8 +89,8 @@ '--do_train ' \ '--do_eval ' \ '--attention 2 ' \ - f'--data_dir /projects/p32013/DNABERT-meta/GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ - f'--output_dir /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ + f'--data_dir GUE/{dataset_dir}/{task}/combined_data/4times_adv_0-7/ ' \ + f'--output_dir ADFAR/src/experiments/GUE/{dataset_dir}/{task}/4times_adv_double_0-7 ' \ f'--model_name_or_path {target_model_path} ' \ '--per_device_train_batch_size 2 ' \ '--per_device_eval_batch_size 2 ' \ diff --git a/ADFAR/src/run_og.sh b/ADFAR/src/run_og.sh index 98f7fb29..8a917f0a 100644 --- a/ADFAR/src/run_og.sh +++ b/ADFAR/src/run_og.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash tasks=("og") -cd /projects/p32013/DNABERT-meta/ADFAR/src +cd ADFAR/src for task in "${tasks[@]}" do diff --git a/BERT-Attack/ModuleNameChange.py b/BERT-Attack/ModuleNameChange.py index 261e00f2..70d1cbd7 100644 --- a/BERT-Attack/ModuleNameChange.py +++ b/BERT-Attack/ModuleNameChange.py @@ -6,7 +6,7 @@ def find_safetensor_files(): """Find all model.safetensors files in the specified directory structure""" - base_path = "/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og" + base_path = "/scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og" pattern = os.path.join(base_path, "*/4times_adv_double_0-7/model.safetensors") return glob.glob(pattern) diff --git a/BERT-Attack/baseline.py b/BERT-Attack/baseline.py index 3b79e0ac..9d63a622 100644 --- a/BERT-Attack/baseline.py +++ b/BERT-Attack/baseline.py @@ -64,9 +64,9 @@ def tokenize_and_mutate2(dna_sequence, tokenizer, change_rate=0.1): parser = argparse.ArgumentParser() -parser.add_argument('--model_name', default="/projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0") -parser.add_argument('--input', default='/projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv') -parser.add_argument('--output', default='/projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/new.csv') +parser.add_argument('--model_name', default="dnabert2_0") +parser.add_argument('--input', default='BERT-Attack/GUE/mouse/0/cat.csv') +parser.add_argument('--output', default='BERT-Attack/GUE/mouse/0/new.csv') parser.add_argument('--change_rate', default=0.087, type=float) parser.add_argument('--num_label', default=2) args = parser.parse_args() diff --git a/BERT-Attack/bertattack3.py b/BERT-Attack/bertattack3.py index 463700bc..61b1bf8b 100644 --- a/BERT-Attack/bertattack3.py +++ b/BERT-Attack/bertattack3.py @@ -443,7 +443,7 @@ def run_attack(): parser.add_argument("--use_bpe", type=int, ) parser.add_argument("--k", type=int, ) parser.add_argument("--threshold_pred_score", type=float, ) - parser.add_argument('--clm_path', type=str, default='/projects/p32013/DNABERT-meta/meta-100M') + parser.add_argument('--clm_path', type=str, default='meta-100M') args = parser.parse_args() diff --git a/BERT-Attack/bertattack3_single.py b/BERT-Attack/bertattack3_single.py index e6053288..da900d77 100644 --- a/BERT-Attack/bertattack3_single.py +++ b/BERT-Attack/bertattack3_single.py @@ -369,7 +369,7 @@ def run_attack(): parser.add_argument("--use_bpe", type=int, ) parser.add_argument("--k", type=int, ) parser.add_argument("--threshold_pred_score", type=float, ) - parser.add_argument('--clm_path', type=str, default='/projects/p32013/DNABERT-meta/meta-100M') + parser.add_argument('--clm_path', type=str, default='meta-100M') args = parser.parse_args() diff --git a/BERT-Attack/cmd.txt b/BERT-Attack/cmd.txt index dc681d45..d759281e 100644 --- a/BERT-Attack/cmd.txt +++ b/BERT-Attack/cmd.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_H3/checkpoint-1200 --output_dir results/H3-test1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 -python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_H3/checkpoint-1200 --output_dir results/H3-test2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 -python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_H3/checkpoint-1200 --output_dir results/H3-test3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 600 --end 900 -python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_H3/checkpoint-1200 --output_dir results/H3-test4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 900 --end 1200 -python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_H3/checkpoint-1200 --output_dir results/H3-test5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1200 --end 1500 +python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_H3/checkpoint-1200 --output_dir results/H3-test1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 +python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_H3/checkpoint-1200 --output_dir results/H3-test2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 +python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_H3/checkpoint-1200 --output_dir results/H3-test3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 600 --end 900 +python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_H3/checkpoint-1200 --output_dir results/H3-test4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 900 --end 1200 +python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_H3/checkpoint-1200 --output_dir results/H3-test5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1200 --end 1500 diff --git a/BERT-Attack/nohup.out b/BERT-Attack/nohup.out deleted file mode 100644 index b4dd15c3..00000000 --- a/BERT-Attack/nohup.out +++ /dev/null @@ -1,884 +0,0 @@ -start process -start process -Traceback (most recent call last): -start process -Traceback (most recent call last): -start process - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): -start process -Traceback (most recent call last): -start process -Traceback (most recent call last): -start process - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -Traceback (most recent call last): -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -Traceback (most recent call last): -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( - -During handling of the above exception, another exception occurred: - - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K79me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -Traceback (most recent call last): - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me1/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - -During handling of the above exception, another exception occurred: - -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K36me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -Traceback (most recent call last): - -During handling of the above exception, another exception occurred: - - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - -During handling of the above exception, another exception occurred: - - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K14ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. -Traceback (most recent call last): -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -Traceback (most recent call last): - raise HFValidationError( - -During handling of the above exception, another exception occurred: - - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - raise HFValidationError( - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -Traceback (most recent call last): -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K9ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - -During handling of the above exception, another exception occurred: - - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me2/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - validate_repo_id(arg_value) - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - raise HFValidationError( - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_files = [ - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_files = [ - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - validate_repo_id(arg_value) - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - validate_repo_id(arg_value) - validate_repo_id(arg_value) - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - raise HFValidationError( - raise HFValidationError( - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - raise HFValidationError( - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - raise HFValidationError( - raise HFValidationError( - validate_repo_id(arg_value) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K79me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - validate_repo_id(arg_value) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me2/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me1/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K9ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K36me3/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K14ac/4times_adv_double_0-7'. Use `repo_type` argument if needed. -start process -Traceback (most recent call last): -start process - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( - validate_repo_id(arg_value) - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - raise HFValidationError( - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - resolved_config_file = cached_file( - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - raise HFValidationError( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/4times_adv_double_0-7'. Use `repo_type` argument if needed. - validate_repo_id(arg_value) - raise HFValidationError( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/4times_adv_double_0-7'. Use `repo_type` argument if needed. -start process -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_notata/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_all/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - - raise HFValidationError( - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - raise HFValidationError( - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_all/4times_adv_double_0-7'. Use `repo_type` argument if needed. -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_notata/4times_adv_double_0-7'. Use `repo_type` argument if needed. -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_tata/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - -During handling of the above exception, another exception occurred: - - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): -Traceback (most recent call last): -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - run_attack() - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_tata/4times_adv_double_0-7'. Use `repo_type` argument if needed. - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_all/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_all/4times_adv_double_0-7'. Use `repo_type` argument if needed. - validate_repo_id(arg_value) - raise HFValidationError( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_notata/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_notata/4times_adv_double_0-7'. Use `repo_type` argument if needed. -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_tata/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_tata/4times_adv_double_0-7'. Use `repo_type` argument if needed. -start process -start process -Traceback (most recent call last): -start process - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files -Traceback (most recent call last): -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - validate_repo_id(arg_value) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - raise HFValidationError( - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - run_attack() - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - run_attack() - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - tokenizer_tgt = AutoTokenizer.from_pretrained( - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained -start process -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 424, in cached_files - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - hf_hub_download( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_config_file = cached_file( - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - raise HFValidationError( - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/4times_adv_double_0-7'. Use `repo_type` argument if needed. - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - -During handling of the above exception, another exception occurred: - - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files -Traceback (most recent call last): - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 537, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - run_attack() - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/gpfs/projects/p32013/DNABERT-meta/BERT-Attack/hyenaattack.py", line 488, in run_attack - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - tokenizer_tgt = AutoTokenizer.from_pretrained( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 946, in from_pretrained - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( - validate_repo_id(arg_value) - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/4times_adv_double_0-7'. Use `repo_type` argument if needed. - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - tokenizer_config = get_tokenizer_config(pretrained_model_name_or_path, **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/models/auto/tokenization_auto.py", line 778, in get_tokenizer_config - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/4times_adv_double_0-7'. Use `repo_type` argument if needed. - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/4times_adv_double_0-7'. Use `repo_type` argument if needed. - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/4times_adv_double_0-7'. Use `repo_type` argument if needed. - resolved_config_file = cached_file( - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 266, in cached_file - file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs) - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 470, in cached_files - resolved_files = [ - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 471, in - _get_cache_file_to_return(path_or_repo_id, filename, cache_dir, revision) for filename in full_filenames - File "/home/hlv8980/.local/lib/python3.9/site-packages/transformers/utils/hub.py", line 134, in _get_cache_file_to_return - resolved_file = try_to_load_from_cache(path_or_repo_id, full_filename, cache_dir=cache_dir, revision=revision) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 106, in _inner_fn - validate_repo_id(arg_value) - File "/home/hlv8980/.local/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 154, in validate_repo_id - raise HFValidationError( -huggingface_hub.errors.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/4times_adv_double_0-7'. Use `repo_type` argument if needed. diff --git a/BERT-Attack/ppl.py b/BERT-Attack/ppl.py index 293455ee..4286ae1c 100644 --- a/BERT-Attack/ppl.py +++ b/BERT-Attack/ppl.py @@ -15,7 +15,7 @@ def get_tokenized_dna(sequence, tokenizer): trust_remote_code=True ) -clm_path = "/projects/p32013/DNABERT-meta/meta-100M" +clm_path = "meta-100M" scorer = lmppl.LM(clm_path) @@ -33,7 +33,7 @@ def get_tokenized_dna(sequence, tokenizer): for checkpoint in checkpoints: - dict_path = f'/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/{checkpoint}/' + dict_path = f'BERT-Attack/results/meta/{checkpoint}/' json_file_path = dict_path + f"{checkpoint}.json" diff --git a/BERT-Attack/ppl1.py b/BERT-Attack/ppl1.py index 764f4379..ff4448f8 100644 --- a/BERT-Attack/ppl1.py +++ b/BERT-Attack/ppl1.py @@ -15,7 +15,7 @@ def get_tokenized_dna(sequence, tokenizer): trust_remote_code=True ) -clm_path = "/projects/p32013/DNABERT-meta/meta-100M" +clm_path = "meta-100M" scorer = lmppl.LM(clm_path) @@ -35,7 +35,7 @@ def get_tokenized_dna(sequence, tokenizer): for checkpoint in checkpoints: for i in range(1,3): try: - dict_path = f'/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/{checkpoint}/' + dict_path = f'BERT-Attack/results/meta/{checkpoint}/' json_file_path = dict_path + f"{checkpoint}-cat{i}.json" diff --git a/BERT-Attack/run.sh b/BERT-Attack/run.sh index ef480aa0..69a04bba 100644 --- a/BERT-Attack/run.sh +++ b/BERT-Attack/run.sh @@ -1,6 +1,3 @@ -export HF_TOKEN='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' -export HF_HOME="/projects/p32013/.cache/" +# python bertattack.py --data_path data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path zhihan1996/DNABERT-2-117M --output_dir results/H3-test1.csv --num_label 2 --use_bpe 1 --k 48 --threshold_pred_score 0 --start 0 --end 10 -# python bertattack.py --data_path /projects/p32013/DNA/data/GUE/EMP/H3/test.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path zhihan1996/DNABERT-2-117M --output_dir results/H3-test1.csv --num_label 2 --use_bpe 1 --k 48 --threshold_pred_score 0 --start 0 --end 10 - -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/0/origin --output_dir results/hyena/0-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/0/origin --output_dir results/hyena/0-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/0.txt b/BERT-Attack/scripts/0.txt index c2cdbc31..c40868fb 100644 --- a/BERT-Attack/scripts/0.txt +++ b/BERT-Attack/scripts/0.txt @@ -1,8 +1,8 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 100 --end 200 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 200 --end 300 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 400 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 400 --end 500 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 600 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat7.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 600 --end 700 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_0 --output_dir results/0-cat8.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 700 --end 800 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 100 --end 200 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 200 --end 300 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 400 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 400 --end 500 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 600 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat7.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 600 --end 700 +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_0 --output_dir results/0-cat8.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 700 --end 800 diff --git a/BERT-Attack/scripts/adfar_dnabert/emp.txt b/BERT-Attack/scripts/adfar_dnabert/emp.txt index 24e97167..e216efe8 100644 --- a/BERT-Attack/scripts/adfar_dnabert/emp.txt +++ b/BERT-Attack/scripts/adfar_dnabert/emp.txt @@ -1,10 +1,10 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K4me1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K4me2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K4me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K9ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K14ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K79me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H4ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/H3K36me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K4me1/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K4me2/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K4me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K9ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K14ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K79me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H4/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H4ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/H3K36me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_dnabert/extra.txt b/BERT-Attack/scripts/adfar_dnabert/extra.txt index e34f34ed..b3121583 100644 --- a/BERT-Attack/scripts/adfar_dnabert/extra.txt +++ b/BERT-Attack/scripts/adfar_dnabert/extra.txt @@ -1 +1 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/dnabert/tf3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/dnabert/tf3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_dnabert/mouse.txt b/BERT-Attack/scripts/adfar_dnabert/mouse.txt index b4ac620b..735deb2f 100644 --- a/BERT-Attack/scripts/adfar_dnabert/mouse.txt +++ b/BERT-Attack/scripts/adfar_dnabert/mouse.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_dnabert/prom.txt b/BERT-Attack/scripts/adfar_dnabert/prom.txt index 00b2b9d0..9890471b 100644 --- a/BERT-Attack/scripts/adfar_dnabert/prom.txt +++ b/BERT-Attack/scripts/adfar_dnabert/prom.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_300_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_300_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_300_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_core_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_core_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/prom_core_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_300_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_300_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_300_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_core_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_core_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/prom_core_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_dnabert/run.sh b/BERT-Attack/scripts/adfar_dnabert/run.sh index f2254d2e..01fb37f2 100644 --- a/BERT-Attack/scripts/adfar_dnabert/run.sh +++ b/BERT-Attack/scripts/adfar_dnabert/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_dnabert/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_dnabert/extra.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/adfar_dnabert/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/adfar_dnabert/extra.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_dnabert/tf.txt b/BERT-Attack/scripts/adfar_dnabert/tf.txt index d947c605..824542a4 100644 --- a/BERT-Attack/scripts/adfar_dnabert/tf.txt +++ b/BERT-Attack/scripts/adfar_dnabert/tf.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/tf0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/tf1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/tf2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/tf3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/ADFAR/src/experiments/GUE/tf4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/adfar/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/tf0/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/tf1/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/tf2/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/tf3/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path ADFAR/src/experiments/GUE/tf4/4times_adv_double_0-7 --output_dir BERT-Attack/results/adfar/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_hyena/emp.txt b/BERT-Attack/scripts/adfar_hyena/emp.txt index e82ab775..a6ab482f 100644 --- a/BERT-Attack/scripts/adfar_hyena/emp.txt +++ b/BERT-Attack/scripts/adfar_hyena/emp.txt @@ -1,10 +1,10 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me1/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me2/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K9ac/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K14ac/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K79me3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4ac/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K36me3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me1/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me2/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K4me3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K9ac/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K14ac/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K79me3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H4ac/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/H3K36me3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_hyena/mouse.txt b/BERT-Attack/scripts/adfar_hyena/mouse.txt index 5b6fa3fa..3562e30c 100644 --- a/BERT-Attack/scripts/adfar_hyena/mouse.txt +++ b/BERT-Attack/scripts/adfar_hyena/mouse.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/0/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/1/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/2/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/4/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_hyena/prom.txt b/BERT-Attack/scripts/adfar_hyena/prom.txt index 56bb3c00..4c76dc52 100644 --- a/BERT-Attack/scripts/adfar_hyena/prom.txt +++ b/BERT-Attack/scripts/adfar_hyena/prom.txt @@ -1,6 +1,6 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_all/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_notata/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_tata/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_all/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_notata/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_tata/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_all/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_notata/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_300_tata/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_all/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_notata/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/prom_core_tata/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_hyena/run.sh b/BERT-Attack/scripts/adfar_hyena/run.sh index 84af34d8..30ae9e98 100644 --- a/BERT-Attack/scripts/adfar_hyena/run.sh +++ b/BERT-Attack/scripts/adfar_hyena/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/adfar_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/adfar_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_hyena/tf.txt b/BERT-Attack/scripts/adfar_hyena/tf.txt index 1e7088b6..e23d9777 100644 --- a/BERT-Attack/scripts/adfar_hyena/tf.txt +++ b/BERT-Attack/scripts/adfar_hyena/tf.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf0/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf1/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf2/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf3/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf4/hyena/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf0/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf1/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf2/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf3/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/hyena/tf4/hyena/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt/emp.txt b/BERT-Attack/scripts/adfar_nt/emp.txt index 691325a1..ae375ac0 100644 --- a/BERT-Attack/scripts/adfar_nt/emp.txt +++ b/BERT-Attack/scripts/adfar_nt/emp.txt @@ -1,9 +1,9 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K9ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K14ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K79me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H4ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K4me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K9ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K14ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K79me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H4ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt/emp1.txt b/BERT-Attack/scripts/adfar_nt/emp1.txt index 794f9e08..3282ebe1 100644 --- a/BERT-Attack/scripts/adfar_nt/emp1.txt +++ b/BERT-Attack/scripts/adfar_nt/emp1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K36me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/H3K36me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt/mouse.txt b/BERT-Attack/scripts/adfar_nt/mouse.txt index a511c62b..e94a993c 100644 --- a/BERT-Attack/scripts/adfar_nt/mouse.txt +++ b/BERT-Attack/scripts/adfar_nt/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt/prom.txt b/BERT-Attack/scripts/adfar_nt/prom.txt index 69dbe43a..e46144ca 100644 --- a/BERT-Attack/scripts/adfar_nt/prom.txt +++ b/BERT-Attack/scripts/adfar_nt/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_300_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/prom_core_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_nt/run.sh b/BERT-Attack/scripts/adfar_nt/run.sh index 57f4c1a5..86ccf8c9 100644 --- a/BERT-Attack/scripts/adfar_nt/run.sh +++ b/BERT-Attack/scripts/adfar_nt/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/adfar_nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/adfar_nt/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/adfar_nt/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt/tf.txt b/BERT-Attack/scripts/adfar_nt/tf.txt index cd5e988e..6d206909 100644 --- a/BERT-Attack/scripts/adfar_nt/tf.txt +++ b/BERT-Attack/scripts/adfar_nt/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt2/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt1/emp.txt b/BERT-Attack/scripts/adfar_nt1/emp.txt index b70cb00e..fe4271a7 100644 --- a/BERT-Attack/scripts/adfar_nt1/emp.txt +++ b/BERT-Attack/scripts/adfar_nt1/emp.txt @@ -1,9 +1,9 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K14ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K79me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H4ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K36me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K4me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K14ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K79me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H4ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K36me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt1/emp1.txt b/BERT-Attack/scripts/adfar_nt1/emp1.txt index 9aa39ee2..ce63ea25 100644 --- a/BERT-Attack/scripts/adfar_nt1/emp1.txt +++ b/BERT-Attack/scripts/adfar_nt1/emp1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K9ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/H3K9ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_nt1/mouse.txt b/BERT-Attack/scripts/adfar_nt1/mouse.txt index 7eb7128a..c96f9a88 100644 --- a/BERT-Attack/scripts/adfar_nt1/mouse.txt +++ b/BERT-Attack/scripts/adfar_nt1/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_nt1/prom.txt b/BERT-Attack/scripts/adfar_nt1/prom.txt index 5eb6cb33..b42db164 100644 --- a/BERT-Attack/scripts/adfar_nt1/prom.txt +++ b/BERT-Attack/scripts/adfar_nt1/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_300_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/prom_core_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_nt1/run.sh b/BERT-Attack/scripts/adfar_nt1/run.sh index 3299158e..d5c72ac7 100644 --- a/BERT-Attack/scripts/adfar_nt1/run.sh +++ b/BERT-Attack/scripts/adfar_nt1/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt1/emp.txt | python batch_run.py --gpus 2,2,2,2,2,2,2,2,2,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt1/mouse.txt | python batch_run.py --gpus 2,2,2,2,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt1/prom.txt | python batch_run.py --gpus 2,2,2,2,2,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt1/tf.txt | python batch_run.py --gpus 2,2,2,2,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_nt1/emp1.txt | python batch_run.py --gpus 0 +cd BERT-Attack +# cat BERT-Attack/scripts/adfar_nt1/emp.txt | python batch_run.py --gpus 2,2,2,2,2,2,2,2,2,0 +# cat BERT-Attack/scripts/adfar_nt1/mouse.txt | python batch_run.py --gpus 2,2,2,2,0 +# cat BERT-Attack/scripts/adfar_nt1/prom.txt | python batch_run.py --gpus 2,2,2,2,2,0 +# cat BERT-Attack/scripts/adfar_nt1/tf.txt | python batch_run.py --gpus 2,2,2,2,0 +cat BERT-Attack/scripts/adfar_nt1/emp1.txt | python batch_run.py --gpus 0 diff --git a/BERT-Attack/scripts/adfar_nt1/tf.txt b/BERT-Attack/scripts/adfar_nt1/tf.txt index 26a08067..9077b893 100644 --- a/BERT-Attack/scripts/adfar_nt1/tf.txt +++ b/BERT-Attack/scripts/adfar_nt1/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/nt1/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_og/emp.txt b/BERT-Attack/scripts/adfar_og/emp.txt index a3a0cb91..c209f1d1 100644 --- a/BERT-Attack/scripts/adfar_og/emp.txt +++ b/BERT-Attack/scripts/adfar_og/emp.txt @@ -1,9 +1,9 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K9ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K14ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K79me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H4ac/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K4me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K9ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K14ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K79me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H4ac/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_og/emp1.txt b/BERT-Attack/scripts/adfar_og/emp1.txt index 2d949b9a..c1b047a4 100644 --- a/BERT-Attack/scripts/adfar_og/emp1.txt +++ b/BERT-Attack/scripts/adfar_og/emp1.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K36me3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/H3K36me3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_og/mouse.txt b/BERT-Attack/scripts/adfar_og/mouse.txt index 049f594a..1a1a1ce1 100644 --- a/BERT-Attack/scripts/adfar_og/mouse.txt +++ b/BERT-Attack/scripts/adfar_og/mouse.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/adfar_og/prom.txt b/BERT-Attack/scripts/adfar_og/prom.txt index bd5121a5..529917df 100644 --- a/BERT-Attack/scripts/adfar_og/prom.txt +++ b/BERT-Attack/scripts/adfar_og/prom.txt @@ -1,6 +1,6 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_all/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_notata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_tata/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_300_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_all/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_notata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/prom_core_tata/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/adfar_og/run.sh b/BERT-Attack/scripts/adfar_og/run.sh index 56948d7d..14415dc8 100644 --- a/BERT-Attack/scripts/adfar_og/run.sh +++ b/BERT-Attack/scripts/adfar_og/run.sh @@ -1,7 +1,7 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/emp1.txt | python batch_run.py --gpus 0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/adfar_og/test.txt | python batch_run.py --gpus 0 +cd BERT-Attack +cat BERT-Attack/scripts/adfar_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/adfar_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/adfar_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/adfar_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/adfar_og/emp1.txt | python batch_run.py --gpus 0 +# cat BERT-Attack/scripts/adfar_og/test.txt | python batch_run.py --gpus 0 diff --git a/BERT-Attack/scripts/adfar_og/tf.txt b/BERT-Attack/scripts/adfar_og/tf.txt index 3c6ea2b6..8f225225 100644 --- a/BERT-Attack/scripts/adfar_og/tf.txt +++ b/BERT-Attack/scripts/adfar_og/tf.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/0/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/1/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/2/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/3/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/og/4/4times_adv_double_0-7 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/ADFAR/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/0/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/1/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/2/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/3/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/og/4/4times_adv_double_0-7 --output_dir BERT-Attack/results/ADFAR/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_dnabert/emp.txt b/BERT-Attack/scripts/all_dnabert/emp.txt index aaec9bb7..0606a075 100644 --- a/BERT-Attack/scripts/all_dnabert/emp.txt +++ b/BERT-Attack/scripts/all_dnabert/emp.txt @@ -1,10 +1,10 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K9ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K14ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K79me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H4ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K36me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3/all --output_dir BERT-Attack/results/All/dnabert/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me1/all --output_dir BERT-Attack/results/All/dnabert/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me2/all --output_dir BERT-Attack/results/All/dnabert/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me3/all --output_dir BERT-Attack/results/All/dnabert/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K9ac/all --output_dir BERT-Attack/results/All/dnabert/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K14ac/all --output_dir BERT-Attack/results/All/dnabert/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K79me3/all --output_dir BERT-Attack/results/All/dnabert/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H4/all --output_dir BERT-Attack/results/All/dnabert/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H4ac/all --output_dir BERT-Attack/results/All/dnabert/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K36me3/all --output_dir BERT-Attack/results/All/dnabert/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_dnabert/mouse.txt b/BERT-Attack/scripts/all_dnabert/mouse.txt index cac8a132..345e33b7 100644 --- a/BERT-Attack/scripts/all_dnabert/mouse.txt +++ b/BERT-Attack/scripts/all_dnabert/mouse.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/0/all --output_dir BERT-Attack/results/All/dnabert/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/1/all --output_dir BERT-Attack/results/All/dnabert/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/2/all --output_dir BERT-Attack/results/All/dnabert/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/3/all --output_dir BERT-Attack/results/All/dnabert/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/4/all --output_dir BERT-Attack/results/All/dnabert/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_dnabert/prom.txt b/BERT-Attack/scripts/all_dnabert/prom.txt index 6e6c09da..3388d6dd 100644 --- a/BERT-Attack/scripts/all_dnabert/prom.txt +++ b/BERT-Attack/scripts/all_dnabert/prom.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_all/all --output_dir BERT-Attack/results/All/dnabert/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_notata/all --output_dir BERT-Attack/results/All/dnabert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_tata/all --output_dir BERT-Attack/results/All/dnabert/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_all/all --output_dir BERT-Attack/results/All/dnabert/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_notata/all --output_dir BERT-Attack/results/All/dnabert/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_tata/all --output_dir BERT-Attack/results/All/dnabert/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_dnabert/run.sh b/BERT-Attack/scripts/all_dnabert/run.sh index 8e6ed862..941eb02c 100644 --- a/BERT-Attack/scripts/all_dnabert/run.sh +++ b/BERT-Attack/scripts/all_dnabert/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_dnabert/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cd BERT-Attack +cat BERT-Attack/scripts/all_dnabert/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/all_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/all_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/all_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 diff --git a/BERT-Attack/scripts/all_dnabert/tf.txt b/BERT-Attack/scripts/all_dnabert/tf.txt index bc917e4a..2d0e13e5 100644 --- a/BERT-Attack/scripts/all_dnabert/tf.txt +++ b/BERT-Attack/scripts/all_dnabert/tf.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf0/all --output_dir BERT-Attack/results/All/dnabert/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf1/all --output_dir BERT-Attack/results/All/dnabert/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf2/all --output_dir BERT-Attack/results/All/dnabert/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf4/all --output_dir BERT-Attack/results/All/dnabert/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf4/all --output_dir BERT-Attack/results/All/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_hyena/emp.txt b/BERT-Attack/scripts/all_hyena/emp.txt index 4ce46bb9..61a8ac86 100644 --- a/BERT-Attack/scripts/all_hyena/emp.txt +++ b/BERT-Attack/scripts/all_hyena/emp.txt @@ -1,10 +1,10 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K9ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K14ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K79me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H4ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K36me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3/all --output_dir BERT-Attack/results/All/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me1/all --output_dir BERT-Attack/results/All/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me2/all --output_dir BERT-Attack/results/All/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me3/all --output_dir BERT-Attack/results/All/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K9ac/all --output_dir BERT-Attack/results/All/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K14ac/all --output_dir BERT-Attack/results/All/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K79me3/all --output_dir BERT-Attack/results/All/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H4/all --output_dir BERT-Attack/results/All/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H4ac/all --output_dir BERT-Attack/results/All/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K36me3/all --output_dir BERT-Attack/results/All/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_hyena/mouse.txt b/BERT-Attack/scripts/all_hyena/mouse.txt index 7e4c93ef..dc329d95 100644 --- a/BERT-Attack/scripts/all_hyena/mouse.txt +++ b/BERT-Attack/scripts/all_hyena/mouse.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/0/all --output_dir BERT-Attack/results/All/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/1/all --output_dir BERT-Attack/results/All/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/2/all --output_dir BERT-Attack/results/All/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/3/all --output_dir BERT-Attack/results/All/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/4/all --output_dir BERT-Attack/results/All/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_hyena/prom.txt b/BERT-Attack/scripts/all_hyena/prom.txt index 778bac34..73ea772e 100644 --- a/BERT-Attack/scripts/all_hyena/prom.txt +++ b/BERT-Attack/scripts/all_hyena/prom.txt @@ -1,6 +1,6 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_all/all --output_dir BERT-Attack/results/All/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_notata/all --output_dir BERT-Attack/results/All/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_tata/all --output_dir BERT-Attack/results/All/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_all/all --output_dir BERT-Attack/results/All/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_notata/all --output_dir BERT-Attack/results/All/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_tata/all --output_dir BERT-Attack/results/All/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_hyena/run.sh b/BERT-Attack/scripts/all_hyena/run.sh index 375a4436..a9bce5f6 100644 --- a/BERT-Attack/scripts/all_hyena/run.sh +++ b/BERT-Attack/scripts/all_hyena/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/all_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/all_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/all_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/all_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_hyena/tf.txt b/BERT-Attack/scripts/all_hyena/tf.txt index c2f43f0a..a0510b8f 100644 --- a/BERT-Attack/scripts/all_hyena/tf.txt +++ b/BERT-Attack/scripts/all_hyena/tf.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf0/all --output_dir BERT-Attack/results/All/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf1/all --output_dir BERT-Attack/results/All/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf2/all --output_dir BERT-Attack/results/All/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf4/all --output_dir BERT-Attack/results/All/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf4/all --output_dir BERT-Attack/results/All/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_nt1/emp.txt b/BERT-Attack/scripts/all_nt1/emp.txt index b47d049e..55434042 100644 --- a/BERT-Attack/scripts/all_nt1/emp.txt +++ b/BERT-Attack/scripts/all_nt1/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K9ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K14ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K79me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K36me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3/all --output_dir BERT-Attack/results/All/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me1/all --output_dir BERT-Attack/results/All/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me2/all --output_dir BERT-Attack/results/All/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me3/all --output_dir BERT-Attack/results/All/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K9ac/all --output_dir BERT-Attack/results/All/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K14ac/all --output_dir BERT-Attack/results/All/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K79me3/all --output_dir BERT-Attack/results/All/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4/all --output_dir BERT-Attack/results/All/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4ac/all --output_dir BERT-Attack/results/All/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K36me3/all --output_dir BERT-Attack/results/All/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_nt1/extra.txt b/BERT-Attack/scripts/all_nt1/extra.txt index c4e91c8a..7832ff9e 100644 --- a/BERT-Attack/scripts/all_nt1/extra.txt +++ b/BERT-Attack/scripts/all_nt1/extra.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/1/all --output_dir BERT-Attack/results/All/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_nt1/mouse.txt b/BERT-Attack/scripts/all_nt1/mouse.txt index 82eb225b..9b456119 100644 --- a/BERT-Attack/scripts/all_nt1/mouse.txt +++ b/BERT-Attack/scripts/all_nt1/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/0/all --output_dir BERT-Attack/results/All/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/1/all --output_dir BERT-Attack/results/All/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/2/all --output_dir BERT-Attack/results/All/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/3/all --output_dir BERT-Attack/results/All/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/4/all --output_dir BERT-Attack/results/All/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_nt1/prom.txt b/BERT-Attack/scripts/all_nt1/prom.txt index 13a7bd6c..dca339c7 100644 --- a/BERT-Attack/scripts/all_nt1/prom.txt +++ b/BERT-Attack/scripts/all_nt1/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_all/all --output_dir BERT-Attack/results/All/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_notata/all --output_dir BERT-Attack/results/All/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_tata/all --output_dir BERT-Attack/results/All/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_all/all --output_dir BERT-Attack/results/All/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_notata/all --output_dir BERT-Attack/results/All/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_tata/all --output_dir BERT-Attack/results/All/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_nt1/run.sh b/BERT-Attack/scripts/all_nt1/run.sh index c1d191fc..736ab2e4 100644 --- a/BERT-Attack/scripts/all_nt1/run.sh +++ b/BERT-Attack/scripts/all_nt1/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt1/extra.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/all_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/all_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/all_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/all_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/all_nt1/extra.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_nt1/tf.txt b/BERT-Attack/scripts/all_nt1/tf.txt index c7fc30dd..bd3c9067 100644 --- a/BERT-Attack/scripts/all_nt1/tf.txt +++ b/BERT-Attack/scripts/all_nt1/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf0/all --output_dir BERT-Attack/results/All/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf1/all --output_dir BERT-Attack/results/All/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf2/all --output_dir BERT-Attack/results/All/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf4/all --output_dir BERT-Attack/results/All/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf4/all --output_dir BERT-Attack/results/All/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_nt2/emp.txt b/BERT-Attack/scripts/all_nt2/emp.txt index dc72c9c3..3a49d4db 100644 --- a/BERT-Attack/scripts/all_nt2/emp.txt +++ b/BERT-Attack/scripts/all_nt2/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K9ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K14ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K79me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H4ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K36me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3/all --output_dir BERT-Attack/results/All/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me1/all --output_dir BERT-Attack/results/All/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me2/all --output_dir BERT-Attack/results/All/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me3/all --output_dir BERT-Attack/results/All/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K9ac/all --output_dir BERT-Attack/results/All/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K14ac/all --output_dir BERT-Attack/results/All/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K79me3/all --output_dir BERT-Attack/results/All/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H4/all --output_dir BERT-Attack/results/All/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H4ac/all --output_dir BERT-Attack/results/All/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K36me3/all --output_dir BERT-Attack/results/All/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_nt2/mouse.txt b/BERT-Attack/scripts/all_nt2/mouse.txt index 2e0faf2a..27d4cf2f 100644 --- a/BERT-Attack/scripts/all_nt2/mouse.txt +++ b/BERT-Attack/scripts/all_nt2/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/0/all --output_dir BERT-Attack/results/All/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/1/all --output_dir BERT-Attack/results/All/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/2/all --output_dir BERT-Attack/results/All/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/3/all --output_dir BERT-Attack/results/All/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/4/all --output_dir BERT-Attack/results/All/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_nt2/prom.txt b/BERT-Attack/scripts/all_nt2/prom.txt index 74edc41c..ef7e7eca 100644 --- a/BERT-Attack/scripts/all_nt2/prom.txt +++ b/BERT-Attack/scripts/all_nt2/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_all/all --output_dir BERT-Attack/results/All/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_notata/all --output_dir BERT-Attack/results/All/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_tata/all --output_dir BERT-Attack/results/All/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_all/all --output_dir BERT-Attack/results/All/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_notata/all --output_dir BERT-Attack/results/All/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_tata/all --output_dir BERT-Attack/results/All/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_nt2/run.sh b/BERT-Attack/scripts/all_nt2/run.sh index e7ef5622..575ceb45 100644 --- a/BERT-Attack/scripts/all_nt2/run.sh +++ b/BERT-Attack/scripts/all_nt2/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt2/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt2/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt2/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_nt2/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cd BERT-Attack +cat BERT-Attack/scripts/all_nt2/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/all_nt2/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/all_nt2/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/all_nt2/tf.txt | python batch_run.py --gpus 0,0,0,0,0 diff --git a/BERT-Attack/scripts/all_nt2/tf.txt b/BERT-Attack/scripts/all_nt2/tf.txt index ac2c5c0d..0d967442 100644 --- a/BERT-Attack/scripts/all_nt2/tf.txt +++ b/BERT-Attack/scripts/all_nt2/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/tf0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/tf1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/tf2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/tf0/all --output_dir BERT-Attack/results/All/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/tf1/all --output_dir BERT-Attack/results/All/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/tf2/all --output_dir BERT-Attack/results/All/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/tf4/all --output_dir BERT-Attack/results/All/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/tf4/all --output_dir BERT-Attack/results/All/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_og/emp.txt b/BERT-Attack/scripts/all_og/emp.txt index 857798d2..2a791fa2 100644 --- a/BERT-Attack/scripts/all_og/emp.txt +++ b/BERT-Attack/scripts/all_og/emp.txt @@ -1,10 +1,10 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K9ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K14ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K79me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H4ac/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K36me3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3/all --output_dir BERT-Attack/results/All/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me1/all --output_dir BERT-Attack/results/All/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me2/all --output_dir BERT-Attack/results/All/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me3/all --output_dir BERT-Attack/results/All/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K9ac/all --output_dir BERT-Attack/results/All/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K14ac/all --output_dir BERT-Attack/results/All/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K79me3/all --output_dir BERT-Attack/results/All/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H4/all --output_dir BERT-Attack/results/All/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H4ac/all --output_dir BERT-Attack/results/All/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K36me3/all --output_dir BERT-Attack/results/All/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_og/mouse.txt b/BERT-Attack/scripts/all_og/mouse.txt index 075347e7..d0e72496 100644 --- a/BERT-Attack/scripts/all_og/mouse.txt +++ b/BERT-Attack/scripts/all_og/mouse.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/3/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/0/all --output_dir BERT-Attack/results/All/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/1/all --output_dir BERT-Attack/results/All/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/2/all --output_dir BERT-Attack/results/All/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/3/all --output_dir BERT-Attack/results/All/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/4/all --output_dir BERT-Attack/results/All/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_og/prom.txt b/BERT-Attack/scripts/all_og/prom.txt index c6e9f420..27a444ad 100644 --- a/BERT-Attack/scripts/all_og/prom.txt +++ b/BERT-Attack/scripts/all_og/prom.txt @@ -1,6 +1,6 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_all/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_notata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_tata/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_all/all --output_dir BERT-Attack/results/All/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_notata/all --output_dir BERT-Attack/results/All/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_tata/all --output_dir BERT-Attack/results/All/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_all/all --output_dir BERT-Attack/results/All/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_notata/all --output_dir BERT-Attack/results/All/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_tata/all --output_dir BERT-Attack/results/All/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/all_og/run.sh b/BERT-Attack/scripts/all_og/run.sh index 814ca75f..98778c9a 100644 --- a/BERT-Attack/scripts/all_og/run.sh +++ b/BERT-Attack/scripts/all_og/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/all_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/all_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/all_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/all_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/all_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/all_og/tf.txt b/BERT-Attack/scripts/all_og/tf.txt index d05a0a6b..a431b210 100644 --- a/BERT-Attack/scripts/all_og/tf.txt +++ b/BERT-Attack/scripts/all_og/tf.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf0/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf1/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf2/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf4/all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/All/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf0/all --output_dir BERT-Attack/results/All/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf1/all --output_dir BERT-Attack/results/All/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf2/all --output_dir BERT-Attack/results/All/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf4/all --output_dir BERT-Attack/results/All/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf4/all --output_dir BERT-Attack/results/All/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_dnabert/emp.txt b/BERT-Attack/scripts/at_dnabert/emp.txt index e2ba653b..c7e6b24c 100644 --- a/BERT-Attack/scripts/at_dnabert/emp.txt +++ b/BERT-Attack/scripts/at_dnabert/emp.txt @@ -1 +1 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H4/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H4/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_dnabert/emp1.txt b/BERT-Attack/scripts/at_dnabert/emp1.txt index fbad2da6..1010f63d 100644 --- a/BERT-Attack/scripts/at_dnabert/emp1.txt +++ b/BERT-Attack/scripts/at_dnabert/emp1.txt @@ -1,9 +1,9 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me1/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me2/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K4me3/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K9ac/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K14ac/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K79me3/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H4ac/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/H3K36me3/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me1/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me2/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K4me3/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K9ac/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K14ac/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K79me3/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H4ac/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/H3K36me3/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_dnabert/mouse.txt b/BERT-Attack/scripts/at_dnabert/mouse.txt index c640f13a..4811f3c6 100644 --- a/BERT-Attack/scripts/at_dnabert/mouse.txt +++ b/BERT-Attack/scripts/at_dnabert/mouse.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/0/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/1/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/2/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/3/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/4/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/0/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/1/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/2/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/3/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/4/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_dnabert/prom.txt b/BERT-Attack/scripts/at_dnabert/prom.txt index 996b4693..b17c0bf5 100644 --- a/BERT-Attack/scripts/at_dnabert/prom.txt +++ b/BERT-Attack/scripts/at_dnabert/prom.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_all/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_notata/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_tata/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_all/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_notata/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_core_tata/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_all/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_notata/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_tata/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_all/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_notata/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_core_tata/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_dnabert/run.sh b/BERT-Attack/scripts/at_dnabert/run.sh index 5cec01b1..250e59cf 100644 --- a/BERT-Attack/scripts/at_dnabert/run.sh +++ b/BERT-Attack/scripts/at_dnabert/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_dnabert/emp1.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_dnabert/tf1.txt | python batch_run.py --gpus 0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/at_dnabert/emp1.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/at_dnabert/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/at_dnabert/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/at_dnabert/tf1.txt | python batch_run.py --gpus 0 +# cat BERT-Attack/scripts/at_dnabert/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_dnabert/tf.txt b/BERT-Attack/scripts/at_dnabert/tf.txt index c7b3f25f..556d7475 100644 --- a/BERT-Attack/scripts/at_dnabert/tf.txt +++ b/BERT-Attack/scripts/at_dnabert/tf.txt @@ -1,4 +1,4 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf0/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf1/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf2/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf4/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf0/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf1/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf2/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf4/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_dnabert/tf1.txt b/BERT-Attack/scripts/at_dnabert/tf1.txt index 52fadcf1..6e64626a 100644 --- a/BERT-Attack/scripts/at_dnabert/tf1.txt +++ b/BERT-Attack/scripts/at_dnabert/tf1.txt @@ -1 +1 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf4/textfooler/checkpoint-200 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf4/textfooler/checkpoint-200 --output_dir BERT-Attack/results/AT/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_hyena/emp.txt b/BERT-Attack/scripts/at_hyena/emp.txt index f3b97f04..ff3f3068 100644 --- a/BERT-Attack/scripts/at_hyena/emp.txt +++ b/BERT-Attack/scripts/at_hyena/emp.txt @@ -1,10 +1,10 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K4me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K9ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K14ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K79me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H4ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/H3K36me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3/textfooler --output_dir BERT-Attack/results/AT/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me1/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me2/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K4me3/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K9ac/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K14ac/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K79me3/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H4/textfooler --output_dir BERT-Attack/results/AT/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H4ac/textfooler --output_dir BERT-Attack/results/AT/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/H3K36me3/textfooler --output_dir BERT-Attack/results/AT/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_hyena/mouse.txt b/BERT-Attack/scripts/at_hyena/mouse.txt index 3fbf18ba..46fe2ec1 100644 --- a/BERT-Attack/scripts/at_hyena/mouse.txt +++ b/BERT-Attack/scripts/at_hyena/mouse.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/0/textfooler --output_dir BERT-Attack/results/AT/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/1/textfooler --output_dir BERT-Attack/results/AT/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/2/textfooler --output_dir BERT-Attack/results/AT/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/3/textfooler --output_dir BERT-Attack/results/AT/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/4/textfooler --output_dir BERT-Attack/results/AT/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_hyena/prom.txt b/BERT-Attack/scripts/at_hyena/prom.txt index 114708cf..b9d1f457 100644 --- a/BERT-Attack/scripts/at_hyena/prom.txt +++ b/BERT-Attack/scripts/at_hyena/prom.txt @@ -1,6 +1,6 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_300_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/prom_core_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_all/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_notata/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_300_tata/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_all/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_notata/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/prom_core_tata/textfooler --output_dir BERT-Attack/results/AT/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_hyena/run.sh b/BERT-Attack/scripts/at_hyena/run.sh index 533b5f93..da12d0aa 100644 --- a/BERT-Attack/scripts/at_hyena/run.sh +++ b/BERT-Attack/scripts/at_hyena/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_hyena/tf1.txt | python batch_run.py --gpus 0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/at_hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/at_hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/at_hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/at_hyena/tf1.txt | python batch_run.py --gpus 0 +cat BERT-Attack/scripts/at_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_hyena/tf.txt b/BERT-Attack/scripts/at_hyena/tf.txt index c3ca7636..86663d9e 100644 --- a/BERT-Attack/scripts/at_hyena/tf.txt +++ b/BERT-Attack/scripts/at_hyena/tf.txt @@ -1,4 +1,4 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf0/textfooler --output_dir BERT-Attack/results/AT/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf1/textfooler --output_dir BERT-Attack/results/AT/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf2/textfooler --output_dir BERT-Attack/results/AT/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf4/textfooler --output_dir BERT-Attack/results/AT/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_hyena/tf1.txt b/BERT-Attack/scripts/at_hyena/tf1.txt index 4c6a1f13..6106670c 100644 --- a/BERT-Attack/scripts/at_hyena/tf1.txt +++ b/BERT-Attack/scripts/at_hyena/tf1.txt @@ -1 +1 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf4/textfooler --output_dir BERT-Attack/results/AT/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_nt/emp.txt b/BERT-Attack/scripts/at_nt/emp.txt index 4051d454..4c583bd1 100644 --- a/BERT-Attack/scripts/at_nt/emp.txt +++ b/BERT-Attack/scripts/at_nt/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K4me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K9ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K14ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K79me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H4ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K36me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3/textfooler --output_dir BERT-Attack/results/AT/nt2/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me1/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me2/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K4me3/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K9ac/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K14ac/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K79me3/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H4/textfooler --output_dir BERT-Attack/results/AT/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H4ac/textfooler --output_dir BERT-Attack/results/AT/nt2/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K36me3/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt/emp1.txt b/BERT-Attack/scripts/at_nt/emp1.txt index 17f22aaa..077a6560 100644 --- a/BERT-Attack/scripts/at_nt/emp1.txt +++ b/BERT-Attack/scripts/at_nt/emp1.txt @@ -1,2 +1,2 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H3K14ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/H4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H3K14ac/textfooler --output_dir BERT-Attack/results/AT/nt2/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/H4/textfooler --output_dir BERT-Attack/results/AT/nt2/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt/mouse.txt b/BERT-Attack/scripts/at_nt/mouse.txt index ef313ef2..b264b522 100644 --- a/BERT-Attack/scripts/at_nt/mouse.txt +++ b/BERT-Attack/scripts/at_nt/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/0/textfooler --output_dir BERT-Attack/results/AT/nt2/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/1/textfooler --output_dir BERT-Attack/results/AT/nt2/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/2/textfooler --output_dir BERT-Attack/results/AT/nt2/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/3/textfooler --output_dir BERT-Attack/results/AT/nt2/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/4/textfooler --output_dir BERT-Attack/results/AT/nt2/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt/prom.txt b/BERT-Attack/scripts/at_nt/prom.txt index f54dc50b..3d98e37c 100644 --- a/BERT-Attack/scripts/at_nt/prom.txt +++ b/BERT-Attack/scripts/at_nt/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_300_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/prom_core_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_all/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_notata/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_300_tata/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_all/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_notata/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/prom_core_tata/textfooler --output_dir BERT-Attack/results/AT/nt2/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_nt/run.sh b/BERT-Attack/scripts/at_nt/run.sh index 0d7a5405..aae057bd 100644 --- a/BERT-Attack/scripts/at_nt/run.sh +++ b/BERT-Attack/scripts/at_nt/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt/emp1.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt/tf1.txt | python batch_run.py --gpus 0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/at_nt/emp1.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +#cat BERT-Attack/scripts/at_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/at_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/at_nt/tf1.txt | python batch_run.py --gpus 0 +# cat BERT-Attack/scripts/at_nt/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt/tf.txt b/BERT-Attack/scripts/at_nt/tf.txt index 69178e97..dbd32d3a 100644 --- a/BERT-Attack/scripts/at_nt/tf.txt +++ b/BERT-Attack/scripts/at_nt/tf.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt2/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/0/textfooler --output_dir BERT-Attack/results/AT/nt2/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/1/textfooler --output_dir BERT-Attack/results/AT/nt2/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/2/textfooler --output_dir BERT-Attack/results/AT/nt2/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt2/4/textfooler --output_dir BERT-Attack/results/AT/nt2/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt/tf1.txt b/BERT-Attack/scripts/at_nt/tf1.txt index db9ad569..00b93f51 100644 --- a/BERT-Attack/scripts/at_nt/tf1.txt +++ b/BERT-Attack/scripts/at_nt/tf1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/textfooler --output_dir BERT-Attack/results/AT/nt2/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_nt1/emp.txt b/BERT-Attack/scripts/at_nt1/emp.txt index 6c58a459..1a4f6895 100644 --- a/BERT-Attack/scripts/at_nt1/emp.txt +++ b/BERT-Attack/scripts/at_nt1/emp.txt @@ -1,9 +1,9 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K9ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K14ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K79me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K36me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me1/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me2/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me3/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K9ac/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K14ac/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K79me3/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4/textfooler --output_dir BERT-Attack/results/AT/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4ac/textfooler --output_dir BERT-Attack/results/AT/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K36me3/textfooler --output_dir BERT-Attack/results/AT/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt1/mouse.txt b/BERT-Attack/scripts/at_nt1/mouse.txt index c35d75c7..f7958eb3 100644 --- a/BERT-Attack/scripts/at_nt1/mouse.txt +++ b/BERT-Attack/scripts/at_nt1/mouse.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/3/textfooler --output_dir BERT-Attack/results/AT/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt1/prom.txt b/BERT-Attack/scripts/at_nt1/prom.txt index af96b408..43dec736 100644 --- a/BERT-Attack/scripts/at_nt1/prom.txt +++ b/BERT-Attack/scripts/at_nt1/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_all/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_notata/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_tata/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_all/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_notata/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_tata/textfooler --output_dir BERT-Attack/results/AT/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_nt1/run.sh b/BERT-Attack/scripts/at_nt1/run.sh index 1edf0171..587dcd7c 100644 --- a/BERT-Attack/scripts/at_nt1/run.sh +++ b/BERT-Attack/scripts/at_nt1/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt1/tf1.txt | python batch_run.py --gpus 0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/at_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/at_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/at_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/at_nt1/tf1.txt | python batch_run.py --gpus 0 +cat BERT-Attack/scripts/at_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt1/tf.txt b/BERT-Attack/scripts/at_nt1/tf.txt index 678d576b..25efbbd8 100644 --- a/BERT-Attack/scripts/at_nt1/tf.txt +++ b/BERT-Attack/scripts/at_nt1/tf.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/0/textfooler --output_dir BERT-Attack/results/AT/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/1/textfooler --output_dir BERT-Attack/results/AT/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/2/textfooler --output_dir BERT-Attack/results/AT/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/4/textfooler --output_dir BERT-Attack/results/AT/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_nt1/tf1.txt b/BERT-Attack/scripts/at_nt1/tf1.txt index ec9ea90b..e40faedb 100644 --- a/BERT-Attack/scripts/at_nt1/tf1.txt +++ b/BERT-Attack/scripts/at_nt1/tf1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/textfooler --output_dir BERT-Attack/results/AT/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_og/emp.txt b/BERT-Attack/scripts/at_og/emp.txt index 60512efe..ee820868 100644 --- a/BERT-Attack/scripts/at_og/emp.txt +++ b/BERT-Attack/scripts/at_og/emp.txt @@ -1,10 +1,10 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K4me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K9ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K14ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K79me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H4ac/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/H3K36me3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3/textfooler --output_dir BERT-Attack/results/AT/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me1/textfooler --output_dir BERT-Attack/results/AT/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me2/textfooler --output_dir BERT-Attack/results/AT/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K4me3/textfooler --output_dir BERT-Attack/results/AT/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K9ac/textfooler --output_dir BERT-Attack/results/AT/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K14ac/textfooler --output_dir BERT-Attack/results/AT/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K79me3/textfooler --output_dir BERT-Attack/results/AT/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H4/textfooler --output_dir BERT-Attack/results/AT/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H4ac/textfooler --output_dir BERT-Attack/results/AT/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/H3K36me3/textfooler --output_dir BERT-Attack/results/AT/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_og/mouse.txt b/BERT-Attack/scripts/at_og/mouse.txt index 1625f1af..7efe9779 100644 --- a/BERT-Attack/scripts/at_og/mouse.txt +++ b/BERT-Attack/scripts/at_og/mouse.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/0/textfooler --output_dir BERT-Attack/results/AT/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/1/textfooler --output_dir BERT-Attack/results/AT/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/2/textfooler --output_dir BERT-Attack/results/AT/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/3/textfooler --output_dir BERT-Attack/results/AT/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/4/textfooler --output_dir BERT-Attack/results/AT/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_og/prom.txt b/BERT-Attack/scripts/at_og/prom.txt index 748edccf..48cb5a0e 100644 --- a/BERT-Attack/scripts/at_og/prom.txt +++ b/BERT-Attack/scripts/at_og/prom.txt @@ -1,6 +1,6 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_notata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_core_tata/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_all/textfooler --output_dir BERT-Attack/results/AT/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_notata/textfooler --output_dir BERT-Attack/results/AT/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_tata/textfooler --output_dir BERT-Attack/results/AT/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_all/textfooler --output_dir BERT-Attack/results/AT/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_notata/textfooler --output_dir BERT-Attack/results/AT/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_core_tata/textfooler --output_dir BERT-Attack/results/AT/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/at_og/prom1.txt b/BERT-Attack/scripts/at_og/prom1.txt index 8a1334a9..68ddc35e 100644 --- a/BERT-Attack/scripts/at_og/prom1.txt +++ b/BERT-Attack/scripts/at_og/prom1.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/prom_300_all/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/prom_300_all/textfooler --output_dir BERT-Attack/results/AT/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_og/run.sh b/BERT-Attack/scripts/at_og/run.sh index 82cc333d..bbddeff3 100644 --- a/BERT-Attack/scripts/at_og/run.sh +++ b/BERT-Attack/scripts/at_og/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_og/prom1.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_og/tf1.txt | python batch_run.py --gpus 0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/at_og/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +#cat BERT-Attack/scripts/at_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/at_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/at_og/prom1.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/at_og/tf1.txt | python batch_run.py --gpus 0 +cat BERT-Attack/scripts/at_og/tf.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_og/tf.txt b/BERT-Attack/scripts/at_og/tf.txt index 9f4635df..902a117a 100644 --- a/BERT-Attack/scripts/at_og/tf.txt +++ b/BERT-Attack/scripts/at_og/tf.txt @@ -1,4 +1,4 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/0/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/1/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/2/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/4/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/0/textfooler --output_dir BERT-Attack/results/AT/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/1/textfooler --output_dir BERT-Attack/results/AT/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/2/textfooler --output_dir BERT-Attack/results/AT/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/4/textfooler --output_dir BERT-Attack/results/AT/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/at_og/tf1.txt b/BERT-Attack/scripts/at_og/tf1.txt index 7649ff92..75dae218 100644 --- a/BERT-Attack/scripts/at_og/tf1.txt +++ b/BERT-Attack/scripts/at_og/tf1.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf3/textfooler --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/AT/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf3/textfooler --output_dir BERT-Attack/results/AT/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/bert_quant/emp.txt b/BERT-Attack/scripts/bert_quant/emp.txt index a6ab3d4a..93494e8a 100644 --- a/BERT-Attack/scripts/bert_quant/emp.txt +++ b/BERT-Attack/scripts/bert_quant/emp.txt @@ -1,3 +1,3 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/hlv8980/data/H3/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/hlv8980/data/H3K4me1/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /scratch/hlv8980/data/H3K4me2/train.csv \ No newline at end of file +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3 --output_dir BERT-Attack/results/bert_quant/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/anonymous/data/H3/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K4me1 --output_dir BERT-Attack/results/bert_quant/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/anonymous/data/H3K4me1/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K4me2 --output_dir BERT-Attack/results/bert_quant/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /scratch/anonymous/data/H3K4me2/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant/emp2.txt b/BERT-Attack/scripts/bert_quant/emp2.txt index 46bb455b..060cd1f9 100644 --- a/BERT-Attack/scripts/bert_quant/emp2.txt +++ b/BERT-Attack/scripts/bert_quant/emp2.txt @@ -1,3 +1,3 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/hlv8980/data/H4/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /scratch/hlv8980/data/H3K9ac/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /scratch/hlv8980/data/H3K14ac/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H4 --output_dir BERT-Attack/results/bert_quant/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/anonymous/data/H4/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K9ac --output_dir BERT-Attack/results/bert_quant/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /scratch/anonymous/data/H3K9ac/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K14ac --output_dir BERT-Attack/results/bert_quant/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /scratch/anonymous/data/H3K14ac/train.csv diff --git a/BERT-Attack/scripts/bert_quant/extra.txt b/BERT-Attack/scripts/bert_quant/extra.txt index 9f5c1b02..345506a2 100644 --- a/BERT-Attack/scripts/bert_quant/extra.txt +++ b/BERT-Attack/scripts/bert_quant/extra.txt @@ -1,2 +1,2 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/prom_300_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/3/five_percent/train.csv +python bertattack4.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/prom_300_notata/origin --output_dir BERT-Attack/results/quant/bert/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file GUE/prom_300_notata/five_percent/train.csv +python bertattack4.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf3/origin --output_dir BERT-Attack/results/quant/bert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file GUE/3/five_percent/train.csv diff --git a/BERT-Attack/scripts/bert_quant/mouse.txt b/BERT-Attack/scripts/bert_quant/mouse.txt index 034e1fcf..517ced83 100644 --- a/BERT-Attack/scripts/bert_quant/mouse.txt +++ b/BERT-Attack/scripts/bert_quant/mouse.txt @@ -1,3 +1,3 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 80 --quantize --train_file /scratch/hlv8980/data/0/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file /scratch/hlv8980/data/1/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file /scratch/hlv8980/data/4/train.csv \ No newline at end of file +python bertattack4.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_0 --output_dir BERT-Attack/results/bert_quant/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 80 --quantize --train_file /scratch/anonymous/data/0/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_1 --output_dir BERT-Attack/results/bert_quant/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file /scratch/anonymous/data/1/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_4 --output_dir BERT-Attack/results/bert_quant/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file /scratch/anonymous/data/4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant/prom.txt b/BERT-Attack/scripts/bert_quant/prom.txt index 047648b1..8458fb01 100644 --- a/BERT-Attack/scripts/bert_quant/prom.txt +++ b/BERT-Attack/scripts/bert_quant/prom.txt @@ -1 +1 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /scratch/hlv8980/data/prom_core_notata/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_notata --output_dir BERT-Attack/results/bert_quant/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /scratch/anonymous/data/prom_core_notata/train.csv diff --git a/BERT-Attack/scripts/bert_quant/prom1.txt b/BERT-Attack/scripts/bert_quant/prom1.txt index 0eb4025c..527b5c3b 100644 --- a/BERT-Attack/scripts/bert_quant/prom1.txt +++ b/BERT-Attack/scripts/bert_quant/prom1.txt @@ -1,2 +1,2 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /scratch/hlv8980/data/prom_300_all/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /scratch/hlv8980/data/prom_300_notata/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_all --output_dir BERT-Attack/results/bert_quant/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /scratch/anonymous/data/prom_300_all/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_notata --output_dir BERT-Attack/results/bert_quant/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /scratch/anonymous/data/prom_300_notata/train.csv diff --git a/BERT-Attack/scripts/bert_quant/run.sh b/BERT-Attack/scripts/bert_quant/run.sh index 0d57b308..63eed0a8 100644 --- a/BERT-Attack/scripts/bert_quant/run.sh +++ b/BERT-Attack/scripts/bert_quant/run.sh @@ -1,9 +1,9 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack +cd BERT-Attack export PYTHONPATH=$PYTHONPATH:$PWD -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/emp2.txt | python batch_run.py --gpus 0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/mouse.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/prom.txt | python batch_run.py --gpus 0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/prom1.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant/extra.txt | python batch_run.py --gpus 0,0 +# cat BERT-Attack/scripts/bert_quant/emp2.txt | python batch_run.py --gpus 0,0,0,0 +# cat BERT-Attack/scripts/bert_quant/mouse.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/bert_quant/prom.txt | python batch_run.py --gpus 0,0 +# cat BERT-Attack/scripts/bert_quant/prom1.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/bert_quant/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/bert_quant/extra.txt | python batch_run.py --gpus 0,0 diff --git a/BERT-Attack/scripts/bert_quant/tf.txt b/BERT-Attack/scripts/bert_quant/tf.txt index 8e7fa5d5..e14115ca 100644 --- a/BERT-Attack/scripts/bert_quant/tf.txt +++ b/BERT-Attack/scripts/bert_quant/tf.txt @@ -1,5 +1,5 @@ -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /scratch/hlv8980/data/tf0/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file /scratch/hlv8980/data/tf1/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /scratch/hlv8980/data/tf2/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/hlv8980/data/tf3/train.csv -python bertattack4.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /scratch/hlv8980/data/tf4/train.csv \ No newline at end of file +python bertattack4.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_0 --output_dir BERT-Attack/results/bert_quant/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /scratch/anonymous/data/tf0/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_1 --output_dir BERT-Attack/results/bert_quant/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file /scratch/anonymous/data/tf1/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_2 --output_dir BERT-Attack/results/bert_quant/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /scratch/anonymous/data/tf2/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_3 --output_dir BERT-Attack/results/bert_quant/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/anonymous/data/tf3/train.csv +python bertattack4.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_4 --output_dir BERT-Attack/results/bert_quant/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /scratch/anonymous/data/tf4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/emp.txt b/BERT-Attack/scripts/bert_quant_softmax/emp.txt index be27225e..7969a1f7 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/emp.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/emp.txt @@ -1,5 +1,5 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/hlv8980/data/H3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/hlv8980/data/H3K4me1/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /scratch/hlv8980/data/H3K4me2/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /scratch/hlv8980/data/H3K4me3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /scratch/hlv8980/data/H3K9ac/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3 --output_dir BERT-Attack/results/bert_quant_softmax/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/anonymous/data/H3/train.csv +python bertattack4_softmax.py --data_path GUE/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K4me1 --output_dir BERT-Attack/results/bert_quant_softmax/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /scratch/anonymous/data/H3K4me1/train.csv +python bertattack4_softmax.py --data_path GUE/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K4me2 --output_dir BERT-Attack/results/bert_quant_softmax/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /scratch/anonymous/data/H3K4me2/train.csv +python bertattack4_softmax.py --data_path GUE/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K4me3 --output_dir BERT-Attack/results/bert_quant_softmax/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /scratch/anonymous/data/H3K4me3/train.csv +python bertattack4_softmax.py --data_path GUE/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K9ac --output_dir BERT-Attack/results/bert_quant_softmax/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /scratch/anonymous/data/H3K9ac/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/emp2.txt b/BERT-Attack/scripts/bert_quant_softmax/emp2.txt index d4b4d7c2..38a07483 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/emp2.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/emp2.txt @@ -1,5 +1,5 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file /scratch/hlv8980/data/H3K79me3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/hlv8980/data/H4/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file /scratch/hlv8980/data/H4ac/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /scratch/hlv8980/data/H3K36me3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /scratch/hlv8980/data/H3K14ac/train.csv +python bertattack4_softmax.py --data_path GUE/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K79me3 --output_dir BERT-Attack/results/bert_quant_softmax/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file /scratch/anonymous/data/H3K79me3/train.csv +python bertattack4_softmax.py --data_path GUE/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H4 --output_dir BERT-Attack/results/bert_quant_softmax/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /scratch/anonymous/data/H4/train.csv +python bertattack4_softmax.py --data_path GUE/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H4ac --output_dir BERT-Attack/results/bert_quant_softmax/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file /scratch/anonymous/data/H4ac/train.csv +python bertattack4_softmax.py --data_path GUE/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K36me3 --output_dir BERT-Attack/results/bert_quant_softmax/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /scratch/anonymous/data/H3K36me3/train.csv +python bertattack4_softmax.py --data_path GUE/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_H3K14ac --output_dir BERT-Attack/results/bert_quant_softmax/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /scratch/anonymous/data/H3K14ac/train.csv diff --git a/BERT-Attack/scripts/bert_quant_softmax/extra.txt b/BERT-Attack/scripts/bert_quant_softmax/extra.txt index 394f6310..3c316bdd 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/extra.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/extra.txt @@ -1,6 +1,6 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/3/five_percent/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/4/five_percent/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/dnabert/tf4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/bert_softmax/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/3/origin --output_dir BERT-Attack/results/quant/bert_softmax/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 --quantize --train_file GUE/3/five_percent/train.csv +python bertattack4_softmax.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/4/origin --output_dir BERT-Attack/results/quant/bert_softmax/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 --quantize --train_file GUE/4/five_percent/train.csv +python bertattack4_softmax.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf1/origin --output_dir BERT-Attack/results/quant/bert_softmax/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 --quantize --train_file GUE/tf1/five_percent/train.csv +python bertattack4_softmax.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf2/origin --output_dir BERT-Attack/results/quant/bert_softmax/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file GUE/tf2/five_percent/train.csv +python bertattack4_softmax.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf3/origin --output_dir BERT-Attack/results/quant/bert_softmax/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 --quantize --train_file GUE/tf3/five_percent/train.csv +python bertattack4_softmax.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/dnabert/tf4/origin --output_dir BERT-Attack/results/quant/bert_softmax/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file GUE/tf4/five_percent/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/mouse.txt b/BERT-Attack/scripts/bert_quant_softmax/mouse.txt index f9c9774e..c54c0808 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/mouse.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/mouse.txt @@ -1,5 +1,5 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 --quantize --train_file /scratch/hlv8980/data/0/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 --quantize --train_file /scratch/hlv8980/data/1/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 --quantize --train_file /scratch/hlv8980/data/2/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 --quantize --train_file /scratch/hlv8980/data/3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 --quantize --train_file /scratch/hlv8980/data/4/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_0 --output_dir BERT-Attack/results/bert_quant_softmax/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 --quantize --train_file /scratch/anonymous/data/0/train.csv +python bertattack4_softmax.py --data_path GUE/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_1 --output_dir BERT-Attack/results/bert_quant_softmax/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 --quantize --train_file /scratch/anonymous/data/1/train.csv +python bertattack4_softmax.py --data_path GUE/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_2 --output_dir BERT-Attack/results/bert_quant_softmax/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 --quantize --train_file /scratch/anonymous/data/2/train.csv +python bertattack4_softmax.py --data_path GUE/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_3 --output_dir BERT-Attack/results/bert_quant_softmax/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 --quantize --train_file /scratch/anonymous/data/3/train.csv +python bertattack4_softmax.py --data_path GUE/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_4 --output_dir BERT-Attack/results/bert_quant_softmax/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 --quantize --train_file /scratch/anonymous/data/4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/prom.txt b/BERT-Attack/scripts/bert_quant_softmax/prom.txt index ccde3607..41982fba 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/prom.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/prom.txt @@ -1,6 +1,6 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 --quantize --train_file /scratch/hlv8980/data/prom_core_all/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 --quantize --train_file /scratch/hlv8980/data/prom_core_notata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file /scratch/hlv8980/data/prom_core_tata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 --quantize --train_file /scratch/hlv8980/data/0/prom_300_all.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 --quantize --train_file /scratch/hlv8980/data/prom_300_notata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file /scratch/hlv8980/data/prom_300_tata/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_all --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 --quantize --train_file /scratch/anonymous/data/prom_core_all/train.csv +python bertattack4_softmax.py --data_path GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_notata --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 --quantize --train_file /scratch/anonymous/data/prom_core_notata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_tata --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file /scratch/anonymous/data/prom_core_tata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_all --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 --quantize --train_file /scratch/anonymous/data/0/prom_300_all.csv +python bertattack4_softmax.py --data_path GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_notata --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 --quantize --train_file /scratch/anonymous/data/prom_300_notata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_tata --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file /scratch/anonymous/data/prom_300_tata/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/prom1.txt b/BERT-Attack/scripts/bert_quant_softmax/prom1.txt index 594dddda..afcdf868 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/prom1.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/prom1.txt @@ -1,6 +1,6 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/hlv8980/data/prom_core_all/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/hlv8980/data/prom_core_notata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 --quantize --train_file /scratch/hlv8980/data/prom_core_tata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 --quantize --train_file /scratch/hlv8980/data/prom_300_all/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/hlv8980/data/prom_300_notata/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 --quantize --train_file /scratch/hlv8980/data/prom_300_tata/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_all --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/anonymous/data/prom_core_all/train.csv +python bertattack4_softmax.py --data_path GUE/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_notata --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/anonymous/data/prom_core_notata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_core_tata --output_dir BERT-Attack/results/bert_quant_softmax/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 --quantize --train_file /scratch/anonymous/data/prom_core_tata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_all --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 --quantize --train_file /scratch/anonymous/data/prom_300_all/train.csv +python bertattack4_softmax.py --data_path GUE/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_notata --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 --quantize --train_file /scratch/anonymous/data/prom_300_notata/train.csv +python bertattack4_softmax.py --data_path GUE/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_prom_300_tata --output_dir BERT-Attack/results/bert_quant_softmax/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 --quantize --train_file /scratch/anonymous/data/prom_300_tata/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/bert_quant_softmax/run.sh b/BERT-Attack/scripts/bert_quant_softmax/run.sh index 1c5f40ef..edef455d 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/run.sh +++ b/BERT-Attack/scripts/bert_quant_softmax/run.sh @@ -1,8 +1,8 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/emp2.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/prom1.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/emp.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/bert_quant_softmax/extra.txt | python batch_run.py --gpus 0,0,0,0,0 +cd BERT-Attack +# cat BERT-Attack/scripts/bert_quant_softmax/emp2.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant_softmax/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant_softmax/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant_softmax/prom1.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant_softmax/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/bert_quant_softmax/emp.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/bert_quant_softmax/extra.txt | python batch_run.py --gpus 0,0,0,0,0 diff --git a/BERT-Attack/scripts/bert_quant_softmax/tf.txt b/BERT-Attack/scripts/bert_quant_softmax/tf.txt index 589dcf35..1b6806b7 100644 --- a/BERT-Attack/scripts/bert_quant_softmax/tf.txt +++ b/BERT-Attack/scripts/bert_quant_softmax/tf.txt @@ -1,5 +1,5 @@ -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 --quantize --train_file /scratch/hlv8980/data/tf0/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 --quantize --train_file /scratch/hlv8980/data/tf1/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /scratch/hlv8980/data/tf2/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 --quantize --train_file /scratch/hlv8980/data/tf3/train.csv -python bertattack4_softmax.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_zhihan_softmax1_Full_double/zhihan_softmax1_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/bert_quant_softmax/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /scratch/hlv8980/data/tf4/train.csv \ No newline at end of file +python bertattack4_softmax.py --data_path GUE/tf0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_0 --output_dir BERT-Attack/results/bert_quant_softmax/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 --quantize --train_file /scratch/anonymous/data/tf0/train.csv +python bertattack4_softmax.py --data_path GUE/tf1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_1 --output_dir BERT-Attack/results/bert_quant_softmax/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 --quantize --train_file /scratch/anonymous/data/tf1/train.csv +python bertattack4_softmax.py --data_path GUE/tf2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_2 --output_dir BERT-Attack/results/bert_quant_softmax/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /scratch/anonymous/data/tf2/train.csv +python bertattack4_softmax.py --data_path GUE/tf3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_3 --output_dir BERT-Attack/results/bert_quant_softmax/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 --quantize --train_file /scratch/anonymous/data/tf3/train.csv +python bertattack4_softmax.py --data_path GUE/tf4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/dnabert2_4 --output_dir BERT-Attack/results/bert_quant_softmax/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 --quantize --train_file /scratch/anonymous/data/tf4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/covid.txt b/BERT-Attack/scripts/covid.txt index 71708cf8..5a8f6d8f 100644 --- a/BERT-Attack/scripts/covid.txt +++ b/BERT-Attack/scripts/covid.txt @@ -1,8 +1,8 @@ -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat1.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat2.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 6000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat3.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 6000 --end 9000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat4.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 9000 --end 12000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat5.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 12000 --end 15000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat6.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 15000 --end 18000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat7.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 18000 --end 21000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid-cat8.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 21000 --end 24000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat1.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat2.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 6000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat3.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 6000 --end 9000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat4.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 9000 --end 12000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat5.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 12000 --end 15000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat6.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 15000 --end 18000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat7.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 18000 --end 21000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid-cat8.json --num_label 9 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 21000 --end 24000 diff --git a/BERT-Attack/scripts/covid_target.txt b/BERT-Attack/scripts/covid_target.txt index 5e559e95..5da8f5ac 100644 --- a/BERT-Attack/scripts/covid_target.txt +++ b/BERT-Attack/scripts/covid_target.txt @@ -1,8 +1,8 @@ -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat1.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat2.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 6000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat3.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 6000 --end 9000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat4.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 9000 --end 12000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat5.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 12000 --end 15000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat6.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 15000 --end 18000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat7.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 18000 --end 21000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_covid --output_dir results/covid_target-cat8.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 21000 --end 24000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat1.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat2.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 6000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat3.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 6000 --end 9000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat4.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 9000 --end 12000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat5.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 12000 --end 15000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat6.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 15000 --end 18000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat7.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 18000 --end 21000 +python bertattack2.py --data_path BERT-Attack/GUE/virus/covid/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_covid --output_dir results/covid_target-cat8.json --num_label 9 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 21000 --end 24000 diff --git a/BERT-Attack/scripts/freelb/emp.txt b/BERT-Attack/scripts/freelb/emp.txt index 60473bf7..97930ef0 100644 --- a/BERT-Attack/scripts/freelb/emp.txt +++ b/BERT-Attack/scripts/freelb/emp.txt @@ -1,10 +1,10 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3 --output_dir BERT-Attack/results/freelb/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me1 --output_dir BERT-Attack/results/freelb/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me2 --output_dir BERT-Attack/results/freelb/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K4me3 --output_dir BERT-Attack/results/freelb/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K9ac --output_dir BERT-Attack/results/freelb/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K14ac --output_dir BERT-Attack/results/freelb/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K79me3 --output_dir BERT-Attack/results/freelb/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H4 --output_dir BERT-Attack/results/freelb/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H4ac --output_dir BERT-Attack/results/freelb/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_H3K36me3 --output_dir BERT-Attack/results/freelb/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb/mouse.txt b/BERT-Attack/scripts/freelb/mouse.txt index 45262306..f96fc377 100644 --- a/BERT-Attack/scripts/freelb/mouse.txt +++ b/BERT-Attack/scripts/freelb/mouse.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_0 --output_dir BERT-Attack/results/freelb/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_1 --output_dir BERT-Attack/results/freelb/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_2 --output_dir BERT-Attack/results/freelb/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_3 --output_dir BERT-Attack/results/freelb/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_4 --output_dir BERT-Attack/results/freelb/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb/prom.txt b/BERT-Attack/scripts/freelb/prom.txt index d1da3b43..ccd1a1a0 100644 --- a/BERT-Attack/scripts/freelb/prom.txt +++ b/BERT-Attack/scripts/freelb/prom.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_all --output_dir BERT-Attack/results/freelb/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_notata --output_dir BERT-Attack/results/freelb/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_300_tata --output_dir BERT-Attack/results/freelb/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_all --output_dir BERT-Attack/results/freelb/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_notata --output_dir BERT-Attack/results/freelb/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_prom_core_tata --output_dir BERT-Attack/results/freelb/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb/run.sh b/BERT-Attack/scripts/freelb/run.sh index 0badaf04..ffae0fff 100644 --- a/BERT-Attack/scripts/freelb/run.sh +++ b/BERT-Attack/scripts/freelb/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb/tf1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/freelb/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/freelb/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/freelb/tf1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb/tf.txt b/BERT-Attack/scripts/freelb/tf.txt index cd53f2f5..9b941d5b 100644 --- a/BERT-Attack/scripts/freelb/tf.txt +++ b/BERT-Attack/scripts/freelb/tf.txt @@ -1,5 +1,5 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers/checkpoints/dnabert_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_0 --output_dir BERT-Attack/results/freelb/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_1 --output_dir BERT-Attack/results/freelb/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_2 --output_dir BERT-Attack/results/freelb/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_3 --output_dir BERT-Attack/results/freelb/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path FreeLB/huggingface-transformers/checkpoints/dnabert_4 --output_dir BERT-Attack/results/freelb/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb/tf1.txt b/BERT-Attack/scripts/freelb/tf1.txt index 762f54d2..fbad5ef6 100644 --- a/BERT-Attack/scripts/freelb/tf1.txt +++ b/BERT-Attack/scripts/freelb/tf1.txt @@ -1 +1 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/dnabert/dnabert_tf3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python bertattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/dnabert/dnabert_tf3 --output_dir BERT-Attack/results/freelb/dnabert/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_hyena/emp.txt b/BERT-Attack/scripts/freelb_hyena/emp.txt index 81fa43f6..b5fab9e5 100644 --- a/BERT-Attack/scripts/freelb_hyena/emp.txt +++ b/BERT-Attack/scripts/freelb_hyena/emp.txt @@ -1,9 +1,9 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3 --output_dir BERT-Attack/results/freelb/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me1 --output_dir BERT-Attack/results/freelb/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me2 --output_dir BERT-Attack/results/freelb/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K4me3 --output_dir BERT-Attack/results/freelb/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K9ac --output_dir BERT-Attack/results/freelb/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K14ac --output_dir BERT-Attack/results/freelb/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K79me3 --output_dir BERT-Attack/results/freelb/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H4 --output_dir BERT-Attack/results/freelb/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H4ac --output_dir BERT-Attack/results/freelb/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_hyena/emp1.txt b/BERT-Attack/scripts/freelb_hyena/emp1.txt index d5ec22c8..9a37db6d 100644 --- a/BERT-Attack/scripts/freelb_hyena/emp1.txt +++ b/BERT-Attack/scripts/freelb_hyena/emp1.txt @@ -1 +1 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_H3K36me3 --output_dir BERT-Attack/results/freelb/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_hyena/mouse.txt b/BERT-Attack/scripts/freelb_hyena/mouse.txt index 7f29c7d2..f445a3aa 100644 --- a/BERT-Attack/scripts/freelb_hyena/mouse.txt +++ b/BERT-Attack/scripts/freelb_hyena/mouse.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_0 --output_dir BERT-Attack/results/freelb/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_1 --output_dir BERT-Attack/results/freelb/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_2 --output_dir BERT-Attack/results/freelb/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_3 --output_dir BERT-Attack/results/freelb/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_4 --output_dir BERT-Attack/results/freelb/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_hyena/prom.txt b/BERT-Attack/scripts/freelb_hyena/prom.txt index 90d99021..1d12040a 100644 --- a/BERT-Attack/scripts/freelb_hyena/prom.txt +++ b/BERT-Attack/scripts/freelb_hyena/prom.txt @@ -1,6 +1,6 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_all --output_dir BERT-Attack/results/freelb/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_notata --output_dir BERT-Attack/results/freelb/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_300_tata --output_dir BERT-Attack/results/freelb/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_all --output_dir BERT-Attack/results/freelb/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_notata --output_dir BERT-Attack/results/freelb/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_prom_core_tata --output_dir BERT-Attack/results/freelb/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_hyena/run.sh b/BERT-Attack/scripts/freelb_hyena/run.sh index 72d87acd..45d350b1 100644 --- a/BERT-Attack/scripts/freelb_hyena/run.sh +++ b/BERT-Attack/scripts/freelb_hyena/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_hyena/emp.txt | python batch_run.py --gpus 1,1,1,1,1,1,1,1,1,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_hyena/mouse.txt | python batch_run.py --gpus 1,1,1,1,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_hyena/prom.txt | python batch_run.py --gpus 1,1,1,1,1,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_hyena/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/freelb_hyena/emp.txt | python batch_run.py --gpus 1,1,1,1,1,1,1,1,1,0 +# cat BERT-Attack/scripts/freelb_hyena/mouse.txt | python batch_run.py --gpus 1,1,1,1,0 +# cat BERT-Attack/scripts/freelb_hyena/prom.txt | python batch_run.py --gpus 1,1,1,1,1,0 +cat BERT-Attack/scripts/freelb_hyena/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_hyena/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_hyena/tf.txt b/BERT-Attack/scripts/freelb_hyena/tf.txt index 05ea4676..7a21378d 100644 --- a/BERT-Attack/scripts/freelb_hyena/tf.txt +++ b/BERT-Attack/scripts/freelb_hyena/tf.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_tf0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_tf1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_tf2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_tf3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/hyena/hyena_tf4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_tf0 --output_dir BERT-Attack/results/freelb/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_tf1 --output_dir BERT-Attack/results/freelb/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_tf2 --output_dir BERT-Attack/results/freelb/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_tf3 --output_dir BERT-Attack/results/freelb/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/hyena/hyena_tf4 --output_dir BERT-Attack/results/freelb/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt/emp.txt b/BERT-Attack/scripts/freelb_nt/emp.txt index d7900b30..2d6d1321 100644 --- a/BERT-Attack/scripts/freelb_nt/emp.txt +++ b/BERT-Attack/scripts/freelb_nt/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/freelb/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3 --output_dir BERT-Attack/results/freelb/nt/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me1 --output_dir BERT-Attack/results/freelb/nt/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me2 --output_dir BERT-Attack/results/freelb/nt/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K4me3 --output_dir BERT-Attack/results/freelb/nt/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K9ac --output_dir BERT-Attack/results/freelb/nt/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K14ac --output_dir BERT-Attack/results/freelb/nt/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K79me3 --output_dir BERT-Attack/results/freelb/nt/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H4 --output_dir BERT-Attack/results/freelb/nt/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H4ac --output_dir BERT-Attack/results/freelb/nt/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_H3K36me3 --output_dir BERT-Attack/results/nt/freelb/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt/mouse.txt b/BERT-Attack/scripts/freelb_nt/mouse.txt index 1e4da31a..61e6e07f 100644 --- a/BERT-Attack/scripts/freelb_nt/mouse.txt +++ b/BERT-Attack/scripts/freelb_nt/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_0 --output_dir BERT-Attack/results/freelb/nt/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_1 --output_dir BERT-Attack/results/freelb/nt/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_2 --output_dir BERT-Attack/results/freelb/nt/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_3 --output_dir BERT-Attack/results/freelb/nt/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_4 --output_dir BERT-Attack/results/freelb/nt/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt/prom.txt b/BERT-Attack/scripts/freelb_nt/prom.txt index 6f22a9e0..4a238eb3 100644 --- a/BERT-Attack/scripts/freelb_nt/prom.txt +++ b/BERT-Attack/scripts/freelb_nt/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_all --output_dir BERT-Attack/results/freelb/nt/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_notata --output_dir BERT-Attack/results/freelb/nt/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_300_tata --output_dir BERT-Attack/results/freelb/nt/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_all --output_dir BERT-Attack/results/freelb/nt/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_notata --output_dir BERT-Attack/results/freelb/nt/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_prom_core_tata --output_dir BERT-Attack/results/freelb/nt/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_nt/run.sh b/BERT-Attack/scripts/freelb_nt/run.sh index 9d2f4961..73d88311 100644 --- a/BERT-Attack/scripts/freelb_nt/run.sh +++ b/BERT-Attack/scripts/freelb_nt/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/freelb_nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt/tf.txt b/BERT-Attack/scripts/freelb_nt/tf.txt index 95a9e997..3018a945 100644 --- a/BERT-Attack/scripts/freelb_nt/tf.txt +++ b/BERT-Attack/scripts/freelb_nt/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt2/nt2_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_0 --output_dir BERT-Attack/results/freelb/nt/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_1 --output_dir BERT-Attack/results/freelb/nt/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_2 --output_dir BERT-Attack/results/freelb/nt/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_3 --output_dir BERT-Attack/results/freelb/nt/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt2/nt2_4 --output_dir BERT-Attack/results/freelb/nt/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1/emp.txt b/BERT-Attack/scripts/freelb_nt1/emp.txt index 1491158e..1c182313 100644 --- a/BERT-Attack/scripts/freelb_nt1/emp.txt +++ b/BERT-Attack/scripts/freelb_nt1/emp.txt @@ -1,9 +1,9 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3 --output_dir BERT-Attack/results/freelb/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me1 --output_dir BERT-Attack/results/freelb/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me2 --output_dir BERT-Attack/results/freelb/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me3 --output_dir BERT-Attack/results/freelb/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K9ac --output_dir BERT-Attack/results/freelb/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K14ac --output_dir BERT-Attack/results/freelb/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K79me3 --output_dir BERT-Attack/results/freelb/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H4 --output_dir BERT-Attack/results/freelb/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H4ac --output_dir BERT-Attack/results/freelb/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1/emp1.txt b/BERT-Attack/scripts/freelb_nt1/emp1.txt index 4117a02a..cf2a7e7d 100644 --- a/BERT-Attack/scripts/freelb_nt1/emp1.txt +++ b/BERT-Attack/scripts/freelb_nt1/emp1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K36me3 --output_dir BERT-Attack/results/freelb/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1/mouse.txt b/BERT-Attack/scripts/freelb_nt1/mouse.txt index d29d6899..d65a788f 100644 --- a/BERT-Attack/scripts/freelb_nt1/mouse.txt +++ b/BERT-Attack/scripts/freelb_nt1/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir BERT-Attack/results/freelb/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir BERT-Attack/results/freelb/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir BERT-Attack/results/freelb/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir BERT-Attack/results/freelb/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir BERT-Attack/results/freelb/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1/prom.txt b/BERT-Attack/scripts/freelb_nt1/prom.txt index f42d4dee..912af0cb 100644 --- a/BERT-Attack/scripts/freelb_nt1/prom.txt +++ b/BERT-Attack/scripts/freelb_nt1/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_all --output_dir BERT-Attack/results/freelb/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_notata --output_dir BERT-Attack/results/freelb/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_tata --output_dir BERT-Attack/results/freelb/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_all --output_dir BERT-Attack/results/freelb/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_notata --output_dir BERT-Attack/results/freelb/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_tata --output_dir BERT-Attack/results/freelb/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_nt1/run.sh b/BERT-Attack/scripts/freelb_nt1/run.sh index dd8c754f..6e9317b2 100644 --- a/BERT-Attack/scripts/freelb_nt1/run.sh +++ b/BERT-Attack/scripts/freelb_nt1/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/freelb_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt1/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1/tf.txt b/BERT-Attack/scripts/freelb_nt1/tf.txt index a818e26d..b3a31d1a 100644 --- a/BERT-Attack/scripts/freelb_nt1/tf.txt +++ b/BERT-Attack/scripts/freelb_nt1/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir BERT-Attack/results/freelb/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir BERT-Attack/results/freelb/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir BERT-Attack/results/freelb/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir BERT-Attack/results/freelb/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir BERT-Attack/results/freelb/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1_old/emp.txt b/BERT-Attack/scripts/freelb_nt1_old/emp.txt index dfca15f4..3e3ae5e0 100644 --- a/BERT-Attack/scripts/freelb_nt1_old/emp.txt +++ b/BERT-Attack/scripts/freelb_nt1_old/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3 --output_dir BERT-Attack/results/freelb/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me1 --output_dir BERT-Attack/results/freelb/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me2 --output_dir BERT-Attack/results/freelb/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K4me3 --output_dir BERT-Attack/results/freelb/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K9ac --output_dir BERT-Attack/results/freelb/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K14ac --output_dir BERT-Attack/results/freelb/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K79me3 --output_dir BERT-Attack/results/freelb/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H4 --output_dir BERT-Attack/results/freelb/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H4ac --output_dir BERT-Attack/results/freelb/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_H3K36me3 --output_dir BERT-Attack/results/freelb/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1_old/mouse.txt b/BERT-Attack/scripts/freelb_nt1_old/mouse.txt index ce49edb9..80a15c35 100644 --- a/BERT-Attack/scripts/freelb_nt1_old/mouse.txt +++ b/BERT-Attack/scripts/freelb_nt1_old/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_0 --output_dir BERT-Attack/results/freelb/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_1 --output_dir BERT-Attack/results/freelb/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_2 --output_dir BERT-Attack/results/freelb/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_3 --output_dir BERT-Attack/results/freelb/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_4 --output_dir BERT-Attack/results/freelb/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_nt1_old/prom.txt b/BERT-Attack/scripts/freelb_nt1_old/prom.txt index f73fb618..1740c698 100644 --- a/BERT-Attack/scripts/freelb_nt1_old/prom.txt +++ b/BERT-Attack/scripts/freelb_nt1_old/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_all --output_dir BERT-Attack/results/freelb/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_notata --output_dir BERT-Attack/results/freelb/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_300_tata --output_dir BERT-Attack/results/freelb/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_all --output_dir BERT-Attack/results/freelb/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_notata --output_dir BERT-Attack/results/freelb/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_prom_core_tata --output_dir BERT-Attack/results/freelb/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1_old/run.sh b/BERT-Attack/scripts/freelb_nt1_old/run.sh index 22d0379d..b3f85f04 100644 --- a/BERT-Attack/scripts/freelb_nt1_old/run.sh +++ b/BERT-Attack/scripts/freelb_nt1_old/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/freelb_nt1/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt1/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt1/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/freelb_nt1/tf.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_nt1_old/tf.txt b/BERT-Attack/scripts/freelb_nt1_old/tf.txt index ca2f9065..ecd9c5ba 100644 --- a/BERT-Attack/scripts/freelb_nt1_old/tf.txt +++ b/BERT-Attack/scripts/freelb_nt1_old/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_tf0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_tf1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_tf2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_tf3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/nt1/nt1_tf4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_tf0 --output_dir BERT-Attack/results/freelb/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_tf1 --output_dir BERT-Attack/results/freelb/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_tf2 --output_dir BERT-Attack/results/freelb/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_tf3 --output_dir BERT-Attack/results/freelb/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/nt1/nt1_tf4 --output_dir BERT-Attack/results/freelb/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_og/emp.txt b/BERT-Attack/scripts/freelb_og/emp.txt index a7676654..fb8d4df5 100644 --- a/BERT-Attack/scripts/freelb_og/emp.txt +++ b/BERT-Attack/scripts/freelb_og/emp.txt @@ -1,9 +1,9 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3 --output_dir BERT-Attack/results/freelb/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K4me1 --output_dir BERT-Attack/results/freelb/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K4me2 --output_dir BERT-Attack/results/freelb/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K4me3 --output_dir BERT-Attack/results/freelb/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K9ac --output_dir BERT-Attack/results/freelb/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K14ac --output_dir BERT-Attack/results/freelb/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K79me3 --output_dir BERT-Attack/results/freelb/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H4 --output_dir BERT-Attack/results/freelb/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H4ac --output_dir BERT-Attack/results/freelb/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_og/emp1.txt b/BERT-Attack/scripts/freelb_og/emp1.txt index bc02af7a..c8187145 100644 --- a/BERT-Attack/scripts/freelb_og/emp1.txt +++ b/BERT-Attack/scripts/freelb_og/emp1.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_H3K36me3 --output_dir BERT-Attack/results/freelb/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_og/mouse.txt b/BERT-Attack/scripts/freelb_og/mouse.txt index f28de7e4..45b218f5 100644 --- a/BERT-Attack/scripts/freelb_og/mouse.txt +++ b/BERT-Attack/scripts/freelb_og/mouse.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_0 --output_dir BERT-Attack/results/freelb/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_1 --output_dir BERT-Attack/results/freelb/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_2 --output_dir BERT-Attack/results/freelb/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_3 --output_dir BERT-Attack/results/freelb/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 diff --git a/BERT-Attack/scripts/freelb_og/prom.txt b/BERT-Attack/scripts/freelb_og/prom.txt index b6e32811..b8680578 100644 --- a/BERT-Attack/scripts/freelb_og/prom.txt +++ b/BERT-Attack/scripts/freelb_og/prom.txt @@ -1,6 +1,6 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_300_all --output_dir BERT-Attack/results/freelb/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_300_notata --output_dir BERT-Attack/results/freelb/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_300_tata --output_dir BERT-Attack/results/freelb/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_core_all --output_dir BERT-Attack/results/freelb/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_core_notata --output_dir BERT-Attack/results/freelb/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_prom_core_tata --output_dir BERT-Attack/results/freelb/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_og/run.sh b/BERT-Attack/scripts/freelb_og/run.sh index 24dda59b..b2f6cb02 100644 --- a/BERT-Attack/scripts/freelb_og/run.sh +++ b/BERT-Attack/scripts/freelb_og/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/freelb_og/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/freelb_og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_og/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/freelb_og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/freelb_og/emp1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/freelb_og/tf.txt b/BERT-Attack/scripts/freelb_og/tf.txt index 116ffd14..390bf841 100644 --- a/BERT-Attack/scripts/freelb_og/tf.txt +++ b/BERT-Attack/scripts/freelb_og/tf.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/og/og_tf4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/og/og_tf4 --output_dir BERT-Attack/results/freelb/og/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/generate.txt b/BERT-Attack/scripts/generate.txt index 64b8a052..4eea114a 100644 --- a/BERT-Attack/scripts/generate.txt +++ b/BERT-Attack/scripts/generate.txt @@ -1 +1 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/test.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 10 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/test.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 10 \ No newline at end of file diff --git a/BERT-Attack/scripts/hyena/emp.txt b/BERT-Attack/scripts/hyena/emp.txt index b9bf1273..1b58ba31 100644 --- a/BERT-Attack/scripts/hyena/emp.txt +++ b/BERT-Attack/scripts/hyena/emp.txt @@ -1,10 +1,10 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K4me1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K4me2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K4me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K9ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K14ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K79me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H4ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/H3K36me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3/origin --output_dir BERT-Attack/results/hyena/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K4me1/origin --output_dir BERT-Attack/results/hyena/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K4me2/origin --output_dir BERT-Attack/results/hyena/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K4me3/origin --output_dir BERT-Attack/results/hyena/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K9ac/origin --output_dir BERT-Attack/results/hyena/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K14ac/origin --output_dir BERT-Attack/results/hyena/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K79me3/origin --output_dir BERT-Attack/results/hyena/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H4/origin --output_dir BERT-Attack/results/hyena/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H4ac/origin --output_dir BERT-Attack/results/hyena/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 +python hyenaattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/H3K36me3/origin --output_dir BERT-Attack/results/hyena/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 100 \ No newline at end of file diff --git a/BERT-Attack/scripts/hyena/mouse.txt b/BERT-Attack/scripts/hyena/mouse.txt index 00dc57de..27208cb9 100644 --- a/BERT-Attack/scripts/hyena/mouse.txt +++ b/BERT-Attack/scripts/hyena/mouse.txt @@ -1,5 +1,5 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/0/origin --output_dir BERT-Attack/results/hyena/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/1/origin --output_dir BERT-Attack/results/hyena/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/2/origin --output_dir BERT-Attack/results/hyena/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/3/origin --output_dir BERT-Attack/results/hyena/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python hyenaattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/4/origin --output_dir BERT-Attack/results/hyena/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file diff --git a/BERT-Attack/scripts/hyena/prom.txt b/BERT-Attack/scripts/hyena/prom.txt index 371f23a5..fc7aaa8d 100644 --- a/BERT-Attack/scripts/hyena/prom.txt +++ b/BERT-Attack/scripts/hyena/prom.txt @@ -1,6 +1,6 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_300_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_300_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_300_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_core_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_core_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/prom_core_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_300_all/origin --output_dir BERT-Attack/results/hyena/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_300_notata/origin --output_dir BERT-Attack/results/hyena/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_300_tata/origin --output_dir BERT-Attack/results/hyena/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_core_all/origin --output_dir BERT-Attack/results/hyena/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_core_notata/origin --output_dir BERT-Attack/results/hyena/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python hyenaattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/prom_core_tata/origin --output_dir BERT-Attack/results/hyena/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 diff --git a/BERT-Attack/scripts/hyena/run.sh b/BERT-Attack/scripts/hyena/run.sh index 031924d5..84dbac47 100644 --- a/BERT-Attack/scripts/hyena/run.sh +++ b/BERT-Attack/scripts/hyena/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/hyena/tf1.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/hyena/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/hyena/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/hyena/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/hyena/tf1.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/hyena/tf.txt b/BERT-Attack/scripts/hyena/tf.txt index 995d210b..21fb7e7a 100644 --- a/BERT-Attack/scripts/hyena/tf.txt +++ b/BERT-Attack/scripts/hyena/tf.txt @@ -1,4 +1,4 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/hyena-dna/hyena/output_pipe/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python hyenaattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/0/origin --output_dir BERT-Attack/results/hyena/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python hyenaattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/1/origin --output_dir BERT-Attack/results/hyena/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 +python hyenaattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/2/origin --output_dir BERT-Attack/results/hyena/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python hyenaattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path hyena-dna/hyena/output_pipe/4/origin --output_dir BERT-Attack/results/hyena/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 diff --git a/BERT-Attack/scripts/hyena/tf1.txt b/BERT-Attack/scripts/hyena/tf1.txt index c3e0c24a..c973de47 100644 --- a/BERT-Attack/scripts/hyena/tf1.txt +++ b/BERT-Attack/scripts/hyena/tf1.txt @@ -1 +1 @@ -python hyenaattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/hyena/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file +python hyenaattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/hyena/tf3/origin --output_dir BERT-Attack/results/hyena/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/emp.txt b/BERT-Attack/scripts/meta/emp.txt index bc26f380..7ba30768 100644 --- a/BERT-Attack/scripts/meta/emp.txt +++ b/BERT-Attack/scripts/meta/emp.txt @@ -1,5 +1,5 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 diff --git a/BERT-Attack/scripts/meta/emp2.txt b/BERT-Attack/scripts/meta/emp2.txt index f9630fe1..31909519 100644 --- a/BERT-Attack/scripts/meta/emp2.txt +++ b/BERT-Attack/scripts/meta/emp2.txt @@ -1,5 +1,5 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 +python bertattack3.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/mouse.txt b/BERT-Attack/scripts/meta/mouse.txt index bcf99ab6..f300013a 100644 --- a/BERT-Attack/scripts/meta/mouse.txt +++ b/BERT-Attack/scripts/meta/mouse.txt @@ -1,5 +1,5 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python bertattack3.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 +python bertattack3.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python bertattack3.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python bertattack3.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/prom.txt b/BERT-Attack/scripts/meta/prom.txt index e5edcda6..49255c9d 100644 --- a/BERT-Attack/scripts/meta/prom.txt +++ b/BERT-Attack/scripts/meta/prom.txt @@ -1,6 +1,6 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 diff --git a/BERT-Attack/scripts/meta/prom_300_all.txt b/BERT-Attack/scripts/meta/prom_300_all.txt index ffa5b4af..8b7c3cc2 100644 --- a/BERT-Attack/scripts/meta/prom_300_all.txt +++ b/BERT-Attack/scripts/meta/prom_300_all.txt @@ -1,6 +1,6 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_all/prom_300_all-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_all/prom_300_all-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/prom_300_notata.txt b/BERT-Attack/scripts/meta/prom_300_notata.txt index 47969948..83daa3cd 100644 --- a/BERT-Attack/scripts/meta/prom_300_notata.txt +++ b/BERT-Attack/scripts/meta/prom_300_notata.txt @@ -1,6 +1,6 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 800 --end 1600 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1600 --end 2400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2400 --end 3200 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3200 --end 4000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_notata-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 4800 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 800 --end 1600 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1600 --end 2400 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2400 --end 3200 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3200 --end 4000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_notata-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 4800 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/run.sh b/BERT-Attack/scripts/meta/run.sh index 132cebe3..d89f2bf3 100644 --- a/BERT-Attack/scripts/meta/run.sh +++ b/BERT-Attack/scripts/meta/run.sh @@ -1,6 +1,6 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/meta/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/meta/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/meta/emp.txt | python batch_run.py --gpus 0,0,0,0,0,1,1,1,1,1 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/meta/test.txt | python batch_run.py --gpus 0,0,1,1 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/meta/test2.txt | python batch_run.py --gpus 0,0,1,1 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/meta/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/meta/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/meta/emp.txt | python batch_run.py --gpus 0,0,0,0,0,1,1,1,1,1 +cat BERT-Attack/scripts/meta/test.txt | python batch_run.py --gpus 0,0,1,1 +cat BERT-Attack/scripts/meta/test2.txt | python batch_run.py --gpus 0,0,1,1 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/test.txt b/BERT-Attack/scripts/meta/test.txt index 978235ff..20cf5512 100644 --- a/BERT-Attack/scripts/meta/test.txt +++ b/BERT-Attack/scripts/meta/test.txt @@ -1,4 +1,4 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_tata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_300_tata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_core_tata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/prom_core_tata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_tata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_300_tata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_core_tata-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/prom_core_tata-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 300 --end 600 \ No newline at end of file diff --git a/BERT-Attack/scripts/meta/tf0123.txt b/BERT-Attack/scripts/meta/tf0123.txt index 3b09f523..ee4fae6e 100644 --- a/BERT-Attack/scripts/meta/tf0123.txt +++ b/BERT-Attack/scripts/meta/tf0123.txt @@ -1,4 +1,4 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python bertattack3.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python bertattack3.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 +python bertattack3.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python bertattack3.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 diff --git a/BERT-Attack/scripts/meta/tf4.txt b/BERT-Attack/scripts/meta/tf4.txt index dfa8f204..ddbd9987 100644 --- a/BERT-Attack/scripts/meta/tf4.txt +++ b/BERT-Attack/scripts/meta/tf4.txt @@ -1,4 +1,4 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf4-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf4-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf4-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/tf4-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 +python bertattack3.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf4-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 +python bertattack3.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf4-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 +python bertattack3.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf4-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 +python bertattack3.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/meta/tf4-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 diff --git a/BERT-Attack/scripts/nt/emp.txt b/BERT-Attack/scripts/nt/emp.txt index dbbebd16..f449158d 100644 --- a/BERT-Attack/scripts/nt/emp.txt +++ b/BERT-Attack/scripts/nt/emp.txt @@ -1,10 +1,10 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K4me1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K4me2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K4me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K9ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K14ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K79me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H4ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/H3K36me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3/origin --output_dir BERT-Attack/results/nt/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K4me1/origin --output_dir BERT-Attack/results/nt/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K4me2/origin --output_dir BERT-Attack/results/nt/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K4me3/origin --output_dir BERT-Attack/results/nt/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K9ac/origin --output_dir BERT-Attack/results/nt/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K14ac/origin --output_dir BERT-Attack/results/nt/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K79me3/origin --output_dir BERT-Attack/results/nt/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H4/origin --output_dir BERT-Attack/results/nt/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H4ac/origin --output_dir BERT-Attack/results/nt/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/H3K36me3/origin --output_dir BERT-Attack/results/nt/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt/mouse.txt b/BERT-Attack/scripts/nt/mouse.txt index 77342ee0..e0a31e17 100644 --- a/BERT-Attack/scripts/nt/mouse.txt +++ b/BERT-Attack/scripts/nt/mouse.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/0/origin --output_dir BERT-Attack/results/nt/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/1/origin --output_dir BERT-Attack/results/nt/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/2/origin --output_dir BERT-Attack/results/nt/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/3/origin --output_dir BERT-Attack/results/nt/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/4/origin --output_dir BERT-Attack/results/nt/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt/prom.txt b/BERT-Attack/scripts/nt/prom.txt index 792526bc..974f3bfd 100644 --- a/BERT-Attack/scripts/nt/prom.txt +++ b/BERT-Attack/scripts/nt/prom.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_300_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_300_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_300_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_core_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_core_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/prom_core_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_300_all/origin --output_dir BERT-Attack/results/nt/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_300_notata/origin --output_dir BERT-Attack/results/nt/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_300_tata/origin --output_dir BERT-Attack/results/nt/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_core_all/origin --output_dir BERT-Attack/results/nt/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_core_notata/origin --output_dir BERT-Attack/results/nt/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/prom_core_tata/origin --output_dir BERT-Attack/results/nt/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 diff --git a/BERT-Attack/scripts/nt/run.sh b/BERT-Attack/scripts/nt/run.sh index 4ebc4256..303efc23 100644 --- a/BERT-Attack/scripts/nt/run.sh +++ b/BERT-Attack/scripts/nt/run.sh @@ -1,5 +1,5 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt/tf1.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/nt/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/nt/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/nt/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/nt/tf1.txt | python batch_run.py --gpus 0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt/tf.txt b/BERT-Attack/scripts/nt/tf.txt index 7f294699..0ce86164 100644 --- a/BERT-Attack/scripts/nt/tf.txt +++ b/BERT-Attack/scripts/nt/tf.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide/output_pipe/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/0/origin --output_dir BERT-Attack/results/nt/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/1/origin --output_dir BERT-Attack/results/nt/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/2/origin --output_dir BERT-Attack/results/nt/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nucleotide-transformer/nucleotide/output_pipe/4/origin --output_dir BERT-Attack/results/nt/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt/tf1.txt b/BERT-Attack/scripts/nt/tf1.txt index b0ee8023..765f2b57 100644 --- a/BERT-Attack/scripts/nt/tf1.txt +++ b/BERT-Attack/scripts/nt/tf1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/origin --output_dir BERT-Attack/results/nt/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 diff --git a/BERT-Attack/scripts/nt1/emp.txt b/BERT-Attack/scripts/nt1/emp.txt index 51cfa85a..b51c1723 100644 --- a/BERT-Attack/scripts/nt1/emp.txt +++ b/BERT-Attack/scripts/nt1/emp.txt @@ -1,2 +1,2 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 310 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H4ac --output_dir BERT-Attack/results/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 310 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K36me3 --output_dir BERT-Attack/results/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/emp2.txt b/BERT-Attack/scripts/nt1/emp2.txt index 3ddec457..a2ae32e3 100644 --- a/BERT-Attack/scripts/nt1/emp2.txt +++ b/BERT-Attack/scripts/nt1/emp2.txt @@ -1,3 +1,3 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3 --output_dir BERT-Attack/results/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K4me1 --output_dir BERT-Attack/results/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K4me2 --output_dir BERT-Attack/results/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/emp3.txt b/BERT-Attack/scripts/nt1/emp3.txt index fb139e9e..b44393b2 100644 --- a/BERT-Attack/scripts/nt1/emp3.txt +++ b/BERT-Attack/scripts/nt1/emp3.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 340 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 250 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 260 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 140 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K4me3 --output_dir BERT-Attack/results/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 340 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K9ac --output_dir BERT-Attack/results/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 250 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K14ac --output_dir BERT-Attack/results/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 300 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H3K79me3 --output_dir BERT-Attack/results/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 260 +python ntattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_H4 --output_dir BERT-Attack/results/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 140 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/mouse.txt b/BERT-Attack/scripts/nt1/mouse.txt index 6703261a..d208dca8 100644 --- a/BERT-Attack/scripts/nt1/mouse.txt +++ b/BERT-Attack/scripts/nt1/mouse.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 650 +python ntattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_1 --output_dir BERT-Attack/results/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 650 diff --git a/BERT-Attack/scripts/nt1/mouse2.txt b/BERT-Attack/scripts/nt1/mouse2.txt index fa73a53d..2ca607e5 100644 --- a/BERT-Attack/scripts/nt1/mouse2.txt +++ b/BERT-Attack/scripts/nt1/mouse2.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 80 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_2 --output_dir BERT-Attack/results/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python ntattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_3 --output_dir BERT-Attack/results/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python ntattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_4 --output_dir BERT-Attack/results/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 +python ntattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_0 --output_dir BERT-Attack/results/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 80 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/prom.txt b/BERT-Attack/scripts/nt1/prom.txt index c5453656..62d1b3c3 100644 --- a/BERT-Attack/scripts/nt1/prom.txt +++ b/BERT-Attack/scripts/nt1/prom.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir BERT-Attack/results/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/prom1.txt b/BERT-Attack/scripts/nt1/prom1.txt index 7e64c923..9173c4fd 100644 --- a/BERT-Attack/scripts/nt1/prom1.txt +++ b/BERT-Attack/scripts/nt1/prom1.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_prom_300_all --output_dir BERT-Attack/results/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_prom_300_notata --output_dir BERT-Attack/results/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_prom_300_tata --output_dir BERT-Attack/results/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_prom_core_all --output_dir BERT-Attack/results/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python ntattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir BERT-Attack/results/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/run.sh b/BERT-Attack/scripts/nt1/run.sh index 76477bd4..6b4ca071 100644 --- a/BERT-Attack/scripts/nt1/run.sh +++ b/BERT-Attack/scripts/nt1/run.sh @@ -1,7 +1,7 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/emp3.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/mouse.txt | python batch_run.py --gpus 0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/prom.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/prom1.txt | python batch_run.py --gpus 0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/tf1.txt | python batch_run.py --gpus 0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1/prom.txt | python batch_run.py --gpus 0 +cd BERT-Attack +# cat BERT-Attack/scripts/nt1/emp3.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/nt1/mouse.txt | python batch_run.py --gpus 0 +# cat BERT-Attack/scripts/nt1/prom.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/nt1/prom1.txt | python batch_run.py --gpus 0,0,0 +#cat BERT-Attack/scripts/nt1/tf1.txt | python batch_run.py --gpus 0 +cat BERT-Attack/scripts/nt1/prom.txt | python batch_run.py --gpus 0 diff --git a/BERT-Attack/scripts/nt1/tf.txt b/BERT-Attack/scripts/nt1/tf.txt index 93544c77..abb31f73 100644 --- a/BERT-Attack/scripts/nt1/tf.txt +++ b/BERT-Attack/scripts/nt1/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 340 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 320 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 290 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_nt_Full_double/nt_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 \ No newline at end of file +python ntattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_0 --output_dir BERT-Attack/results/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 340 +python ntattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_1 --output_dir BERT-Attack/results/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 320 +python ntattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_2 --output_dir BERT-Attack/results/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_3 --output_dir BERT-Attack/results/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 290 +python ntattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path nt_4 --output_dir BERT-Attack/results/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 200 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1/tf1.txt b/BERT-Attack/scripts/nt1/tf1.txt index b23ab5c0..f5e0da1f 100644 --- a/BERT-Attack/scripts/nt1/tf1.txt +++ b/BERT-Attack/scripts/nt1/tf1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 290 +python ntattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/origin --output_dir BERT-Attack/results/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 290 diff --git a/BERT-Attack/scripts/nt1_quant/emp.txt b/BERT-Attack/scripts/nt1_quant/emp.txt index 3d55e559..232ffc9a 100644 --- a/BERT-Attack/scripts/nt1_quant/emp.txt +++ b/BERT-Attack/scripts/nt1_quant/emp.txt @@ -1,2 +1,2 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H4ac/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K36me3/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4ac/origin --output_dir BERT-Attack/results/quant/nt1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file GUE/H4ac/train.csv +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir BERT-Attack/results/quant/nt1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file GUE/H3K36me3/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant/emp2.txt b/BERT-Attack/scripts/nt1_quant/emp2.txt index 3470e9e0..c82544d8 100644 --- a/BERT-Attack/scripts/nt1_quant/emp2.txt +++ b/BERT-Attack/scripts/nt1_quant/emp2.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me1/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me2/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K14ac/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K79me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K79me3/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H4/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3/origin --output_dir BERT-Attack/results/quant/nt1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file GUE/H3/train.csv +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me1/origin --output_dir BERT-Attack/results/quant/nt1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file GUE/H3K4me1/train.csv +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me2/origin --output_dir BERT-Attack/results/quant/nt1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file GUE/H3K4me2/train.csv +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir BERT-Attack/results/quant/nt1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file GUE/H3K14ac/train.csv +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K79me3/origin --output_dir BERT-Attack/results/quant/nt1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file GUE/H3K79me3/train.csv +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4/origin --output_dir BERT-Attack/results/quant/nt1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file GUE/H4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant/emp3.txt b/BERT-Attack/scripts/nt1_quant/emp3.txt index 14f36a5f..b529c6ee 100644 --- a/BERT-Attack/scripts/nt1_quant/emp3.txt +++ b/BERT-Attack/scripts/nt1_quant/emp3.txt @@ -1,2 +1,2 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me3/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K9ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K9ac/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me3/origin --output_dir BERT-Attack/results/quant/nt1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file GUE/H3K4me3/train.csv +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K9ac/origin --output_dir BERT-Attack/results/quant/nt1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file GUE/H3K9ac/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant/mouse.txt b/BERT-Attack/scripts/nt1_quant/mouse.txt index 1ba43a98..bd66970e 100644 --- a/BERT-Attack/scripts/nt1_quant/mouse.txt +++ b/BERT-Attack/scripts/nt1_quant/mouse.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/1/train.csv +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/1/origin --output_dir BERT-Attack/results/quant/nt1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file GUE/1/train.csv diff --git a/BERT-Attack/scripts/nt1_quant/mouse2.txt b/BERT-Attack/scripts/nt1_quant/mouse2.txt index 85938cf6..71ccd983 100644 --- a/BERT-Attack/scripts/nt1_quant/mouse2.txt +++ b/BERT-Attack/scripts/nt1_quant/mouse2.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/2/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 35 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/3/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/4/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/0/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/2/origin --output_dir BERT-Attack/results/quant/nt1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file GUE/2/train.csv +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/3/origin --output_dir BERT-Attack/results/quant/nt1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 35 --quantize --train_file GUE/3/train.csv +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/4/origin --output_dir BERT-Attack/results/quant/nt1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file GUE/4/train.csv +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/0/origin --output_dir BERT-Attack/results/quant/nt1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/0/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant/prom.txt b/BERT-Attack/scripts/nt1_quant/prom.txt index 0c196ca7..d8fd28dd 100644 --- a/BERT-Attack/scripts/nt1_quant/prom.txt +++ b/BERT-Attack/scripts/nt1_quant/prom.txt @@ -1,3 +1,3 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 54 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_all/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_notata/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_tata/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_all/origin --output_dir BERT-Attack/results/quant/nt1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 54 --quantize --train_file GUE/prom_core_all/train.csv +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir BERT-Attack/results/quant/nt1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file GUE/prom_core_notata/train.csv +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir BERT-Attack/results/quant/nt1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file GUE/prom_core_tata/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant/prom1.txt b/BERT-Attack/scripts/nt1_quant/prom1.txt index c509e803..4ca1954a 100644 --- a/BERT-Attack/scripts/nt1_quant/prom1.txt +++ b/BERT-Attack/scripts/nt1_quant/prom1.txt @@ -1,3 +1,3 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_all/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_notata/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_tata/train.csv +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_all/origin --output_dir BERT-Attack/results/quant/nt1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file GUE/prom_300_all/train.csv +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_notata/origin --output_dir BERT-Attack/results/quant/nt1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file GUE/prom_300_notata/train.csv +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_tata/origin --output_dir BERT-Attack/results/quant/nt1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file GUE/prom_300_tata/train.csv diff --git a/BERT-Attack/scripts/nt1_quant/run.sh b/BERT-Attack/scripts/nt1_quant/run.sh index 7e00f93a..594091f5 100644 --- a/BERT-Attack/scripts/nt1_quant/run.sh +++ b/BERT-Attack/scripts/nt1_quant/run.sh @@ -1,7 +1,7 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/emp3.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/prom.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/prom1.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/emp2.txt | python batch_run.py --gpus 0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant/mouse2.txt | python batch_run.py --gpus 0 +cd BERT-Attack +# cat BERT-Attack/scripts/nt1_quant/emp3.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/nt1_quant/prom.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/nt1_quant/prom1.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/nt1_quant/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/nt1_quant/emp2.txt | python batch_run.py --gpus 0,0 +cat BERT-Attack/scripts/nt1_quant/mouse2.txt | python batch_run.py --gpus 0 diff --git a/BERT-Attack/scripts/nt1_quant/tf.txt b/BERT-Attack/scripts/nt1_quant/tf.txt index e69a4322..5b36f6bf 100644 --- a/BERT-Attack/scripts/nt1_quant/tf.txt +++ b/BERT-Attack/scripts/nt1_quant/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/0/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/1/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/2/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/3/train.csv -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/4/train.csv \ No newline at end of file +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf0/origin --output_dir BERT-Attack/results/quant/nt1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file GUE/0/train.csv +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf1/origin --output_dir BERT-Attack/results/quant/nt1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file GUE/1/train.csv +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf2/origin --output_dir BERT-Attack/results/quant/nt1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/2/train.csv +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/origin --output_dir BERT-Attack/results/quant/nt1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file GUE/3/train.csv +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf4/origin --output_dir BERT-Attack/results/quant/nt1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/4/train.csv \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/emp.txt b/BERT-Attack/scripts/nt1_quant_softmax/emp.txt index 843cd64b..8f260dbd 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/emp.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/emp.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H4ac/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K79me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K79me3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K36me3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K14ac/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/H4ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4ac/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 31 --quantize --train_file GUE/H4ac/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K79me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K79me3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 26 --quantize --train_file GUE/H3K79me3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file GUE/H3K36me3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file GUE/H3K14ac/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/emp2.txt b/BERT-Attack/scripts/nt1_quant_softmax/emp2.txt index c298377e..0821b097 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/emp2.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/emp2.txt @@ -1,2 +1,2 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me1/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/H3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file GUE/H3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K4me1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me1/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file GUE/H3K4me1/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/emp3.txt b/BERT-Attack/scripts/nt1_quant_softmax/emp3.txt index 037d3cad..7dcd1901 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/emp3.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/emp3.txt @@ -1,6 +1,6 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H4/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K9ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K9ac/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K36me3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K14ac/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/H3K4me2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/H3K4me2/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/H3K4me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file GUE/H3K4me3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H4/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 14 --quantize --train_file GUE/H4/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K9ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K9ac/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 25 --quantize --train_file GUE/H3K9ac/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K36me3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K36me3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file GUE/H3K36me3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K14ac/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K14ac/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 30 --quantize --train_file GUE/H3K14ac/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/H3K4me2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/H3K4me2/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 28 --quantize --train_file GUE/H3K4me2/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/mouse.txt b/BERT-Attack/scripts/nt1_quant_softmax/mouse.txt index a083e4a9..4ada2b26 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/mouse.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/mouse.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/1/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/1/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 65 --quantize --train_file GUE/1/train.csv --attn_softmax softmax1 diff --git a/BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt b/BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt index f92f5ab2..d8bbf61c 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt @@ -1,4 +1,4 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/2/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 35 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/4/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/0/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/2/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 40 --quantize --train_file GUE/2/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 35 --quantize --train_file GUE/3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/4/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 18 --quantize --train_file GUE/4/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/0/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/0/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/prom.txt b/BERT-Attack/scripts/nt1_quant_softmax/prom.txt index c9e92647..db8c6111 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/prom.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/prom.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_tata/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 54 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_all/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_core_notata/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_all/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_all/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_notata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_notata/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/prom_core_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_tata/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 --quantize --train_file GUE/prom_core_tata/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/prom_core_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_all/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 54 --quantize --train_file GUE/prom_core_all/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/prom_core_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_core_notata/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file GUE/prom_core_notata/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/prom_300_all/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_all/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file GUE/prom_300_all/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/prom_300_notata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_notata/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 48 --quantize --train_file GUE/prom_300_notata/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/prom1.txt b/BERT-Attack/scripts/nt1_quant_softmax/prom1.txt index 2e3607ad..49a6b4bc 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/prom1.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/prom1.txt @@ -1 +1 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/prom_300_tata/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/prom_300_tata/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/prom_300_tata/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/prom_300_tata/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 60 --quantize --train_file GUE/prom_300_tata/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/nt1_quant_softmax/run.sh b/BERT-Attack/scripts/nt1_quant_softmax/run.sh index c0e8325e..0ceb22a8 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/run.sh +++ b/BERT-Attack/scripts/nt1_quant_softmax/run.sh @@ -1,8 +1,8 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/emp2.txt | python batch_run.py --gpus 0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/prom.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/prom1.txt | python batch_run.py --gpus 0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/emp.txt | python batch_run.py --gpus 0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/mouse.txt | python batch_run.py --gpus 0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt | python batch_run.py --gpus 0,0,0,0 +cd BERT-Attack +# cat BERT-Attack/scripts/nt1_quant_softmax/emp2.txt | python batch_run.py --gpus 0,0,0,0,0 +# cat BERT-Attack/scripts/nt1_quant_softmax/prom.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/nt1_quant_softmax/prom1.txt | python batch_run.py --gpus 0,0,0 +# cat BERT-Attack/scripts/nt1_quant_softmax/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +cat BERT-Attack/scripts/nt1_quant_softmax/emp.txt | python batch_run.py --gpus 0,0 +# cat BERT-Attack/scripts/nt1_quant_softmax/mouse.txt | python batch_run.py --gpus 0 +# cat BERT-Attack/scripts/nt1_quant_softmax/mouse2.txt | python batch_run.py --gpus 0,0,0,0 diff --git a/BERT-Attack/scripts/nt1_quant_softmax/tf.txt b/BERT-Attack/scripts/nt1_quant_softmax/tf.txt index d367f5f5..fe92c32a 100644 --- a/BERT-Attack/scripts/nt1_quant_softmax/tf.txt +++ b/BERT-Attack/scripts/nt1_quant_softmax/tf.txt @@ -1,5 +1,5 @@ -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf0/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf0/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf1/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf1/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf2/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf2/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf3/train.csv --attn_softmax softmax1 -python ntattack.py --data_path /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/nt1/tf4/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/quant/nt1_softmax1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file /projects/p32013/DNABERT-meta/GUE/tf4/train.csv --attn_softmax softmax1 \ No newline at end of file +python ntattack.py --data_path GUE/tf0/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf0/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 34 --quantize --train_file GUE/tf0/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/tf1/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf1/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 32 --quantize --train_file GUE/tf1/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/tf2/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf2/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/tf2/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/tf3/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf3/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 29 --quantize --train_file GUE/tf3/train.csv --attn_softmax softmax1 +python ntattack.py --data_path GUE/tf4/five_percent/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/nt1/tf4/origin --output_dir BERT-Attack/results/quant/nt1_softmax1/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 20 --quantize --train_file GUE/tf4/train.csv --attn_softmax softmax1 \ No newline at end of file diff --git a/BERT-Attack/scripts/og/emp.txt b/BERT-Attack/scripts/og/emp.txt index 8ce8de2f..99618e6e 100644 --- a/BERT-Attack/scripts/og/emp.txt +++ b/BERT-Attack/scripts/og/emp.txt @@ -1,6 +1,6 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K4me1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K4me2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K4me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K9ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K14ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3 --output_dir BERT-Attack/results/og/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K4me1 --output_dir BERT-Attack/results/og/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K4me2 --output_dir BERT-Attack/results/og/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K4me3 --output_dir BERT-Attack/results/og/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K9ac --output_dir BERT-Attack/results/og/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K14ac --output_dir BERT-Attack/results/og/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 diff --git a/BERT-Attack/scripts/og/emp2.txt b/BERT-Attack/scripts/og/emp2.txt index 7e3aef10..3261dd97 100644 --- a/BERT-Attack/scripts/og/emp2.txt +++ b/BERT-Attack/scripts/og/emp2.txt @@ -1,4 +1,4 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K79me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H4ac --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_H3K36me3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K79me3 --output_dir BERT-Attack/results/og/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H4 --output_dir BERT-Attack/results/og/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H4ac --output_dir BERT-Attack/results/og/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 +python ogattack.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_H3K36me3 --output_dir BERT-Attack/results/og/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file diff --git a/BERT-Attack/scripts/og/mouse.txt b/BERT-Attack/scripts/og/mouse.txt index 551796c4..defbe772 100644 --- a/BERT-Attack/scripts/og/mouse.txt +++ b/BERT-Attack/scripts/og/mouse.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_0 --output_dir BERT-Attack/results/og/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python ogattack.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_1 --output_dir BERT-Attack/results/og/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 +python ogattack.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_2 --output_dir BERT-Attack/results/og/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python ogattack.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_3 --output_dir BERT-Attack/results/og/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python ogattack.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_4 --output_dir BERT-Attack/results/og/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file diff --git a/BERT-Attack/scripts/og/prom.txt b/BERT-Attack/scripts/og/prom.txt index 95953284..469e756a 100644 --- a/BERT-Attack/scripts/og/prom.txt +++ b/BERT-Attack/scripts/og/prom.txt @@ -1,4 +1,4 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_core_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_core_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_core_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_300_tata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_core_all --output_dir BERT-Attack/results/og/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_core_notata --output_dir BERT-Attack/results/og/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_core_tata --output_dir BERT-Attack/results/og/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_300_tata --output_dir BERT-Attack/results/og/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 diff --git a/BERT-Attack/scripts/og/prom1.txt b/BERT-Attack/scripts/og/prom1.txt index 7830153c..deea4092 100644 --- a/BERT-Attack/scripts/og/prom1.txt +++ b/BERT-Attack/scripts/og/prom1.txt @@ -1,2 +1,2 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_300_all --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_prom_300_notata --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 480 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_300_all --output_dir BERT-Attack/results/og/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python ogattack.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_prom_300_notata --output_dir BERT-Attack/results/og/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 480 diff --git a/BERT-Attack/scripts/og/run.sh b/BERT-Attack/scripts/og/run.sh index e7e727c1..9f973163 100644 --- a/BERT-Attack/scripts/og/run.sh +++ b/BERT-Attack/scripts/og/run.sh @@ -1,8 +1,8 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/emp2.txt | python batch_run.py --gpus 0,0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/prom.txt | python batch_run.py --gpus 0,0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/prom1.txt | python batch_run.py --gpus 0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 -#cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/og/tf1.txt | python batch_run.py --gpus 0 \ No newline at end of file +cd BERT-Attack +#cat BERT-Attack/scripts/og/emp2.txt | python batch_run.py --gpus 0,0,0,0 +#cat BERT-Attack/scripts/og/mouse.txt | python batch_run.py --gpus 0,0,0,0,0 +#cat BERT-Attack/scripts/og/prom.txt | python batch_run.py --gpus 0,0,0,0 +#cat BERT-Attack/scripts/og/prom1.txt | python batch_run.py --gpus 0,0 +#cat BERT-Attack/scripts/og/tf.txt | python batch_run.py --gpus 0,0,0,0,0 +#cat BERT-Attack/scripts/og/emp.txt | python batch_run.py --gpus 0,0,0,0,0,0 +cat BERT-Attack/scripts/og/tf1.txt | python batch_run.py --gpus 0 \ No newline at end of file diff --git a/BERT-Attack/scripts/og/tf.txt b/BERT-Attack/scripts/og/tf.txt index 206a88d9..2dc2faf8 100644 --- a/BERT-Attack/scripts/og/tf.txt +++ b/BERT-Attack/scripts/og/tf.txt @@ -1,5 +1,5 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_0 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_1 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_2 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_3 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/GERM_ICML/output_og_Full_double/og_dnabert2_Full_double_4 --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_0 --output_dir BERT-Attack/results/og/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python ogattack.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_1 --output_dir BERT-Attack/results/og/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 +python ogattack.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_2 --output_dir BERT-Attack/results/og/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python ogattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_3 --output_dir BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python ogattack.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/og_4 --output_dir BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file diff --git a/BERT-Attack/scripts/og/tf1.txt b/BERT-Attack/scripts/og/tf1.txt index 206ac534..7318c135 100644 --- a/BERT-Attack/scripts/og/tf1.txt +++ b/BERT-Attack/scripts/og/tf1.txt @@ -1 +1 @@ -python ogattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/hlv8980/Attack_Benchmark/models/og/tf3/origin --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file +python ogattack.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /scratch/anonymous/Attack_Benchmark/models/og/tf3/origin --output_dir BERT-Attack/results/og/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 \ No newline at end of file diff --git a/BERT-Attack/scripts/prom_300_all.txt b/BERT-Attack/scripts/prom_300_all.txt index 80147ef4..cc5d2233 100644 --- a/BERT-Attack/scripts/prom_300_all.txt +++ b/BERT-Attack/scripts/prom_300_all.txt @@ -1,6 +1,6 @@ -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 -python bertattack.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_dnabert2_Full_double_prom_300_all --output_dir results/prom_300_all-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat5.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 +python bertattack.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_prom_300_all --output_dir results/prom_300_all-cat6.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file diff --git a/BERT-Attack/scripts/prom_300_explain.txt b/BERT-Attack/scripts/prom_300_explain.txt index b0494e69..e6fadd8b 100644 --- a/BERT-Attack/scripts/prom_300_explain.txt +++ b/BERT-Attack/scripts/prom_300_explain.txt @@ -1,6 +1,6 @@ -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat1-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat2-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat3-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat4-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat5-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 -python bertattack3.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path /projects/p32013/DNABERT-meta/meta-100M --output_dir results/prom_300_all-cat6-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat1-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat2-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 2000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat3-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 3000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat4-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 4000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat5-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 4000 --end 5000 +python bertattack3.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --clm_path meta-100M --output_dir results/prom_300_all-cat6-1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5000 --end 6000 \ No newline at end of file diff --git a/BERT-Attack/scripts/reconstructed.txt b/BERT-Attack/scripts/reconstructed.txt index 3d3b8d3f..3e615e79 100644 --- a/BERT-Attack/scripts/reconstructed.txt +++ b/BERT-Attack/scripts/reconstructed.txt @@ -1,8 +1,8 @@ -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat1.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat2.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat3.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat4.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat5.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 2500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat6.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2500 --end 3000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat7.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 3500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed-cat8.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3500 --end 4000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat1.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat2.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat3.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat4.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat5.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 2500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat6.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2500 --end 3000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat7.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 3500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed-cat8.json --num_label 3 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3500 --end 4000 diff --git a/BERT-Attack/scripts/reconstructed_target.txt b/BERT-Attack/scripts/reconstructed_target.txt index fbcdb944..b25d60b7 100644 --- a/BERT-Attack/scripts/reconstructed_target.txt +++ b/BERT-Attack/scripts/reconstructed_target.txt @@ -1,8 +1,8 @@ -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat1.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat2.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat3.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat4.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat5.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 2500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat6.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2500 --end 3000 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat7.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 3500 -python bertattack2.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path /projects/p32013/DNA/FT/DNABERT-2-FT/finetune/output_zhihan_Full_double/zhihan_vanilla_dnabert2_Full_double_reconstructed --output_dir results/reconstructed_target-cat8.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3500 --end 4000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat1.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat2.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 500 --end 1000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat3.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1000 --end 1500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat4.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 1500 --end 2000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat5.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2000 --end 2500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat6.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 2500 --end 3000 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat7.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3000 --end 3500 +python bertattack2.py --data_path BERT-Attack/GUE/splice/reconstructed/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --tgt_path dnabert2_reconstructed --output_dir results/reconstructed_target-cat8.json --num_label 3 --target 1 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 3500 --end 4000 diff --git a/BERT-Attack/scripts/run.sh b/BERT-Attack/scripts/run.sh index f7755aee..e0e32e8e 100644 --- a/BERT-Attack/scripts/run.sh +++ b/BERT-Attack/scripts/run.sh @@ -1,3 +1,3 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/prom_300_explain.txt | python batch_run.py --gpus 0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/0.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/prom_300_explain.txt | python batch_run.py --gpus 0,0,0,0,0,0 +# cat BERT-Attack/scripts/0.txt | python batch_run.py --gpus 0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/run2.sh b/BERT-Attack/scripts/run2.sh index 0a34c370..73039280 100644 --- a/BERT-Attack/scripts/run2.sh +++ b/BERT-Attack/scripts/run2.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/covid_target.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/reconstructed.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 -# cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/reconstructed_target.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +# cat BERT-Attack/scripts/covid_target.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 +cat BERT-Attack/scripts/reconstructed.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 +# cat BERT-Attack/scripts/reconstructed_target.txt | python batch_run.py --gpus 0,0,0,0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/single/emp.txt b/BERT-Attack/scripts/single/emp.txt index ac902f83..99fc7406 100644 --- a/BERT-Attack/scripts/single/emp.txt +++ b/BERT-Attack/scripts/single/emp.txt @@ -1,10 +1,10 @@ -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K4me1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K4me1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K4me2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K4me2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2800 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K4me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K4me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K9ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K9ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2500 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K14ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K14ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3000 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K79me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K79me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2600 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1400 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H4ac/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H4ac.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3100 +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3K36me3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3K36me3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4000 \ No newline at end of file diff --git a/BERT-Attack/scripts/single/mouse.txt b/BERT-Attack/scripts/single/mouse.txt index c7e8055c..15a79e43 100644 --- a/BERT-Attack/scripts/single/mouse.txt +++ b/BERT-Attack/scripts/single/mouse.txt @@ -1,5 +1,5 @@ -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file +python bertattack3_single.py --data_path BERT-Attack/GUE/mouse/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 800 +python bertattack3_single.py --data_path BERT-Attack/GUE/mouse/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6500 +python bertattack3_single.py --data_path BERT-Attack/GUE/mouse/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 400 +python bertattack3_single.py --data_path BERT-Attack/GUE/mouse/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 350 +python bertattack3_single.py --data_path BERT-Attack/GUE/mouse/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 1800 \ No newline at end of file diff --git a/BERT-Attack/scripts/single/prom.txt b/BERT-Attack/scripts/single/prom.txt index e100ddf7..9bc29ef3 100644 --- a/BERT-Attack/scripts/single/prom.txt +++ b/BERT-Attack/scripts/single/prom.txt @@ -1,6 +1,6 @@ -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_300_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_300_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 6000 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_300_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_300_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_300_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_300_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_core_all/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_core_all.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 5400 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_core_notata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_core_notata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 4800 +python bertattack3_single.py --data_path BERT-Attack/GUE/prom/prom_core_tata/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/prom_core_tata.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 600 diff --git a/BERT-Attack/scripts/single/run.sh b/BERT-Attack/scripts/single/run.sh index 2f2f28cc..4701e51b 100644 --- a/BERT-Attack/scripts/single/run.sh +++ b/BERT-Attack/scripts/single/run.sh @@ -1,2 +1,2 @@ -cd /projects/p32013/DNABERT-meta/BERT-Attack -cat /projects/p32013/DNABERT-meta/BERT-Attack/scripts/single/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 \ No newline at end of file +cd BERT-Attack +cat BERT-Attack/scripts/single/prom.txt | python batch_run.py --gpus 0,0,0,0,0,0 \ No newline at end of file diff --git a/BERT-Attack/scripts/single/test.txt b/BERT-Attack/scripts/single/test.txt index 182c77eb..6b660e97 100644 --- a/BERT-Attack/scripts/single/test.txt +++ b/BERT-Attack/scripts/single/test.txt @@ -1 +1 @@ -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5 --end 10 \ No newline at end of file +python bertattack3_single.py --data_path BERT-Attack/GUE/EMP/H3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/H3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 5 --end 10 \ No newline at end of file diff --git a/BERT-Attack/scripts/single/tf.txt b/BERT-Attack/scripts/single/tf.txt index 62138421..696ae9c9 100644 --- a/BERT-Attack/scripts/single/tf.txt +++ b/BERT-Attack/scripts/single/tf.txt @@ -1,5 +1,5 @@ -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 -python bertattack3_single.py --data_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir /projects/p32013/DNABERT-meta/BERT-Attack/results/single/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python bertattack3_single.py --data_path BERT-Attack/GUE/tf/0/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/tf0.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3400 +python bertattack3_single.py --data_path BERT-Attack/GUE/tf/1/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/tf1.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 3200 +python bertattack3_single.py --data_path BERT-Attack/GUE/tf/2/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/tf2.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 +python bertattack3_single.py --data_path BERT-Attack/GUE/tf/3/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/tf3.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2900 +python bertattack3_single.py --data_path BERT-Attack/GUE/tf/4/cat.csv --mlm_path zhihan1996/DNABERT-2-117M --output_dir BERT-Attack/results/single/tf4.json --num_label 2 --use_bpe 0 --k 48 --threshold_pred_score 0 --start 0 --end 2000 diff --git a/BERT-Attack/test.py b/BERT-Attack/test.py index 283a3735..c662dacd 100644 --- a/BERT-Attack/test.py +++ b/BERT-Attack/test.py @@ -1,6 +1,6 @@ # Install necessary libraries # !pip install torch transformers textattack datasets -# export HF_HOME="/projects/p32013/.cache/" +# export HF_HOME="/.cache/" import torch from transformers import BertTokenizer, BertForSequenceClassification diff --git a/FreeLB/huggingface-transformers/launch/run.sh b/FreeLB/huggingface-transformers/launch/run.sh index 4c387608..90cb6ba5 100644 --- a/FreeLB/huggingface-transformers/launch/run.sh +++ b/FreeLB/huggingface-transformers/launch/run.sh @@ -4,7 +4,7 @@ tasks=( "H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9 model="hyena" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -14,10 +14,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/FreeLB/huggingface-transformers/launch/run_0.sh b/FreeLB/huggingface-transformers/launch/run_0.sh index 616f3116..69865147 100644 --- a/FreeLB/huggingface-transformers/launch/run_0.sh +++ b/FreeLB/huggingface-transformers/launch/run_0.sh @@ -2,7 +2,7 @@ function runexp { -export GLUE_DIR='/projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse' +export GLUE_DIR='BERT-Attack/GUE/mouse' export TASK_NAME=${1} gpu=${2} # The GPU you want to use @@ -52,7 +52,7 @@ python examples/run_glue_freelb2.py \ # runexp TASK_NAME gpu model_name adv_lr adv_mag anorm asteps lr bsize grad_accu hdp adp ts ws seed wd model_type -runexp 0 0 /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 1e-1 6e-1 0 2 1e-5 32 1 0.1 0 20935 1256 42 1e-2 dnabert +runexp 0 0 /scratch/anonymous/dnabert2_0 1e-1 6e-1 0 2 1e-5 32 1 0.1 0 20935 1256 42 1e-2 dnabert # runexp MRPC 0 albert-xxlarge-v2 3e-2 0 0 4 2e-5 16 1 0.1 0 800 200 42 1e-2 diff --git a/FreeLB/huggingface-transformers/launch/run_dnabert.sh b/FreeLB/huggingface-transformers/launch/run_dnabert.sh index ca440c20..403486e1 100644 --- a/FreeLB/huggingface-transformers/launch/run_dnabert.sh +++ b/FreeLB/huggingface-transformers/launch/run_dnabert.sh @@ -5,7 +5,7 @@ tasks=( "H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9 model="dnabert" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -15,10 +15,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/FreeLB/huggingface-transformers/launch/run_hyena.sh b/FreeLB/huggingface-transformers/launch/run_hyena.sh index 0ed8245a..bb38935f 100644 --- a/FreeLB/huggingface-transformers/launch/run_hyena.sh +++ b/FreeLB/huggingface-transformers/launch/run_hyena.sh @@ -4,7 +4,7 @@ tasks=( "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" model="hyena" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -14,10 +14,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/FreeLB/huggingface-transformers/launch/run_nt1.sh b/FreeLB/huggingface-transformers/launch/run_nt1.sh index 577b2d2b..55573725 100644 --- a/FreeLB/huggingface-transformers/launch/run_nt1.sh +++ b/FreeLB/huggingface-transformers/launch/run_nt1.sh @@ -4,7 +4,7 @@ tasks=( "H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9 model="nt1" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -14,10 +14,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/FreeLB/huggingface-transformers/launch/run_nt2.sh b/FreeLB/huggingface-transformers/launch/run_nt2.sh index b346cb31..9bb4a485 100644 --- a/FreeLB/huggingface-transformers/launch/run_nt2.sh +++ b/FreeLB/huggingface-transformers/launch/run_nt2.sh @@ -4,7 +4,7 @@ tasks=( "tf2" "tf3" "tf4" "0" "1" "2" "3" "4" ) model="nt2" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -14,10 +14,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/FreeLB/huggingface-transformers/launch/run_og.sh b/FreeLB/huggingface-transformers/launch/run_og.sh index 84d2c0be..1c346683 100644 --- a/FreeLB/huggingface-transformers/launch/run_og.sh +++ b/FreeLB/huggingface-transformers/launch/run_og.sh @@ -4,7 +4,7 @@ tasks=( "H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9 model="og" -project_root="/projects/p32013/DNABERT-meta/FreeLB/huggingface-transformers" +project_root="FreeLB/huggingface-transformers" log_dir="${project_root}/logs" ckpt_dir="${project_root}/checkpoints" @@ -14,10 +14,10 @@ mkdir -p "${ckpt_dir}" function runexp { local task=$1 - export GUE_DIR='/projects/p32013/DNABERT-meta/GUE' + export GUE_DIR='GUE' gpu=0 - mname="/scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin" + mname="/scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin" alr=1e-1 amag=6e-1 anorm=0 diff --git a/GenoArmory.py b/GenoArmory.py index 7e55d148..fe3a5a28 100644 --- a/GenoArmory.py +++ b/GenoArmory.py @@ -1115,7 +1115,7 @@ def run_textfooler_attack_script( counter_fitting_embeddings_path=f"./TextFooler/embeddings/subword_{target_model}_embeddings.txt" counter_fitting_cos_sim_path=f"./TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{target_model}.npy" USE_cache_path="./TextFooler/tf_cache" - tokenizer_path=f"/scratch/hlv8980/Attack_Benchmark/models/{target_model}/{dataset_dir}/origin" + tokenizer_path=f"/scratch/anonymous/Attack_Benchmark/models/{target_model}/{dataset_dir}/origin" command_template = ( f'python {attack_script_path} --dataset_path {dataset_path} ' diff --git a/LICENSE b/LICENSE index e7c1a5a3..0384832f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2024 MAGICS-LAB +Copyright (c) 2024 Anonymous Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/PGD/run.sh b/PGD/run.sh index a0d1bb90..5fc5ddc2 100644 --- a/PGD/run.sh +++ b/PGD/run.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='nt1' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/${model}/${task} \ + --output_dir PGD/results/${model}/${task} \ --model_type nt --overwrite_cache echo "${task} finished" diff --git a/PGD/run2.sh b/PGD/run2.sh index a398089d..8163466c 100644 --- a/PGD/run2.sh +++ b/PGD/run2.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") # tasks=("H3") @@ -6,11 +6,11 @@ tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9a model='hyena' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/${model}/${task} \ + --output_dir PGD/results/${model}/${task} \ --model_type hyena --overwrite_cache echo "${task} finished" diff --git a/PGD/run_adfar_dnabert.sh b/PGD/run_adfar_dnabert.sh index e7cad441..3639566b 100644 --- a/PGD/run_adfar_dnabert.sh +++ b/PGD/run_adfar_dnabert.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD #tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("2") model='dnabert' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/ADFAR/${model}/${task} \ + --output_dir PGD/results/ADFAR/${model}/${task} \ --model_type bert --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_adfar_hyena.sh b/PGD/run_adfar_hyena.sh index f4781dfd..110a79fe 100644 --- a/PGD/run_adfar_hyena.sh +++ b/PGD/run_adfar_hyena.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='hyena' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/hyena/4times_adv_double_0-7 \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/hyena/4times_adv_double_0-7 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/ADFAR/${model}/${task} \ + --output_dir PGD/results/ADFAR/${model}/${task} \ --model_type hyena --overwrite_cache echo "${task} finished" diff --git a/PGD/run_adfar_nt1.sh b/PGD/run_adfar_nt1.sh index d6061122..9021627f 100644 --- a/PGD/run_adfar_nt1.sh +++ b/PGD/run_adfar_nt1.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD #tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("H3K9ac") model='nt1' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/ADFAR/${model}/${task} \ + --output_dir PGD/results/ADFAR/${model}/${task} \ --model_type nt --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_adfar_nt2.sh b/PGD/run_adfar_nt2.sh index c3668edf..68048111 100644 --- a/PGD/run_adfar_nt2.sh +++ b/PGD/run_adfar_nt2.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='nt2' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/ADFAR/${model}/${task} \ + --output_dir PGD/results/ADFAR/${model}/${task} \ --model_type nt --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_adfar_og.sh b/PGD/run_adfar_og.sh index 93febd10..748170c7 100644 --- a/PGD/run_adfar_og.sh +++ b/PGD/run_adfar_og.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") @@ -6,13 +6,13 @@ tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9a model='og' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/${model}/${task}/4times_adv_double_0-7 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/ADFAR/${model}/${task} \ + --output_dir PGD/results/ADFAR/${model}/${task} \ --model_type og --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_all.sh b/PGD/run_all.sh index 7c01d100..9a4480e3 100644 --- a/PGD/run_all.sh +++ b/PGD/run_all.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3K14ac" "H3" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") #tasks=( "H3" "H3K9ac" "prom_core_notata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") @@ -6,13 +6,13 @@ tasks=("H3K14ac" "H3" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9a model='nt2' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/all \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/all \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/All/${model}/${task} \ + --output_dir PGD/results/All/${model}/${task} \ --model_type nt --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_at_dnabert.sh b/PGD/run_at_dnabert.sh index 3ee0d857..e2c29315 100644 --- a/PGD/run_at_dnabert.sh +++ b/PGD/run_at_dnabert.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD #tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("H3K14ac" "H3K36me3" ) model='dnabert' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/textfooler/checkpoint-200 \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/textfooler/checkpoint-200 \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/AT/${model}/${task} \ + --output_dir PGD/results/AT/${model}/${task} \ --model_type bert --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_at_hyena.sh b/PGD/run_at_hyena.sh index cf2cfbab..9a644a9e 100644 --- a/PGD/run_at_hyena.sh +++ b/PGD/run_at_hyena.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='hyena' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/textfooler \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/textfooler \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/AT/${model}/${task} \ + --output_dir PGD/results/AT/${model}/${task} \ --model_type hyena --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_at_nt1.sh b/PGD/run_at_nt1.sh index cc0422ad..39fa682a 100644 --- a/PGD/run_at_nt1.sh +++ b/PGD/run_at_nt1.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD # tasks=("H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=( "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") @@ -6,13 +6,13 @@ tasks=( "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom model='nt1' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/textfooler \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/textfooler \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/AT/${model}/${task} \ + --output_dir PGD/results/AT/${model}/${task} \ --model_type nt --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_at_nt2.sh b/PGD/run_at_nt2.sh index b56b170b..309d48a5 100644 --- a/PGD/run_at_nt2.sh +++ b/PGD/run_at_nt2.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD # tasks=( "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=( "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") @@ -6,13 +6,13 @@ tasks=( "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "pr model='nt2' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/textfooler \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/textfooler \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/AT/${model}/${task} \ + --output_dir PGD/results/AT/${model}/${task} \ --model_type nt --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_at_og.sh b/PGD/run_at_og.sh index 2773b4ad..7826d2e5 100644 --- a/PGD/run_at_og.sh +++ b/PGD/run_at_og.sh @@ -1,17 +1,17 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='og' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/textfooler \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/textfooler \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/AT/${model}/${task} \ + --output_dir PGD/results/AT/${model}/${task} \ --model_type og --overwrite_cache \ - --tokenizer_name /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin + --tokenizer_name /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin echo "${task} finished" done diff --git a/PGD/run_freelb_dnabert.sh b/PGD/run_freelb_dnabert.sh index 39bc4456..1586a42e 100644 --- a/PGD/run_freelb_dnabert.sh +++ b/PGD/run_freelb_dnabert.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='dnabert' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/FreeLB/${model}/${task} \ + --output_dir PGD/results/FreeLB/${model}/${task} \ --model_type bert --overwrite_cache echo "${task} finished" diff --git a/PGD/run_freelb_hyena.sh b/PGD/run_freelb_hyena.sh index bbbd4476..7619ef3e 100644 --- a/PGD/run_freelb_hyena.sh +++ b/PGD/run_freelb_hyena.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='hyena' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/five_percent \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ + python test.py --data_dir GUE/${task}/five_percent \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/FreeLB/${model}/${task} \ + --output_dir PGD/results/FreeLB/${model}/${task} \ --model_type hyena --overwrite_cache echo "${task} finished" diff --git a/PGD/run_freelb_nt.sh b/PGD/run_freelb_nt.sh index a886100c..ae02f460 100644 --- a/PGD/run_freelb_nt.sh +++ b/PGD/run_freelb_nt.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='nt1' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/FreeLB/${model}/${task} \ + --output_dir PGD/results/FreeLB/${model}/${task} \ --model_type nt --overwrite_cache echo "${task} finished" diff --git a/PGD/run_freelb_nt2.sh b/PGD/run_freelb_nt2.sh index 314d8678..a0e1c304 100644 --- a/PGD/run_freelb_nt2.sh +++ b/PGD/run_freelb_nt2.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='nt2' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/FreeLB/${model}/${task} \ + --output_dir PGD/results/FreeLB/${model}/${task} \ --model_type nt --overwrite_cache echo "${task} finished" diff --git a/PGD/run_freelb_og.sh b/PGD/run_freelb_og.sh index d6f7e490..4df1e7bb 100644 --- a/PGD/run_freelb_og.sh +++ b/PGD/run_freelb_og.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD #tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=( "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='og' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/FreeLB/${model}/${model}_${task} \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/FreeLB/${model}/${task} \ + --output_dir PGD/results/FreeLB/${model}/${task} \ --model_type og --overwrite_cache echo "${task} finished" diff --git a/PGD/run_nt2.sh b/PGD/run_nt2.sh index 83d9136f..e83472c1 100644 --- a/PGD/run_nt2.sh +++ b/PGD/run_nt2.sh @@ -1,15 +1,15 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") model='nt2' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/${model}/${task} \ + --output_dir PGD/results/${model}/${task} \ --model_type nt --overwrite_cache echo "${task} finished" diff --git a/PGD/run_og.sh b/PGD/run_og.sh index ace56f0e..0e280d4a 100644 --- a/PGD/run_og.sh +++ b/PGD/run_og.sh @@ -1,4 +1,4 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD #tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("tf4") @@ -6,11 +6,11 @@ tasks=("tf4") model='og' for task in "${tasks[@]}"; do - python test.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + python test.py --data_dir GUE/${task} \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 16 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/${model}/${task} \ + --output_dir PGD/results/${model}/${task} \ --model_type og --overwrite_cache echo "${task} finished" diff --git a/PGD/test.sh b/PGD/test.sh index 6e1025a4..8974d526 100644 --- a/PGD/test.sh +++ b/PGD/test.sh @@ -1,10 +1,10 @@ -cd /projects/p32013/DNABERT-meta/PGD +cd PGD -python test.py --data_dir /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0 \ - --model_name_or_path /projects/p32013/DNABERT-meta/nucleotide-transformer/nucleotide1/output_pipe/0/origin \ +python test.py --data_dir BERT-Attack/GUE/mouse/0 \ + --model_name_or_path nucleotide-transformer/nucleotide1/output_pipe/0/origin \ --task_name 0 --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 32 \ - --output_dir /projects/p32013/DNABERT-meta/PGD/results/0 \ + --output_dir PGD/results/0 \ --model_type nt --overwrite_cache diff --git a/README.md b/README.md index 6fd54432..6215c13a 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,6 @@

- -[![arXiv](https://img.shields.io/badge/arXiv-GenoArmory-ff0000.svg?style=for-the-badge)](https://arxiv.org/abs/2505.10983) [![Github](https://img.shields.io/badge/GenoArmory-000000?style=for-the-badge&logo=github&logoColor=white)](https://github.com/MAGICS-LAB/GenoArmory) [![Hugging Face Pretrained](https://huggingface.co/datasets/huggingface/badges/resolve/main/model-on-hf-md-dark.svg)](https://huggingface.co/collections/magicslabnu/gfm-67f4d4a9327ee4acdcb3806b) [![Hugging Face Dataset](https://huggingface.co/datasets/huggingface/badges/resolve/main/dataset-on-hf-md.svg)](https://huggingface.co/datasets/magicslabnu/GenoAdv) ## Installation @@ -21,7 +19,7 @@ pip install genoarmory ``` You can also install package from our source code: ```bash -git clone https://github.com/MAGICS-LAB/GenoArmory.git +git clone https://anonymous.git conda create -n genoarmory pip=3.9 pip install . ``` @@ -35,12 +33,12 @@ import json # You need to initialize GenoArmory with a model and tokenizer. # For visualization, you don't need a real model/tokenizer, so you can use None if the method doesn't use them. gen = GenoArmory(model=None, tokenizer=None) -params_file = '/projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json' +params_file = 'scripts/PGD/pgd_dnabert.json' # Visulization gen.visualization( - folder_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test', - output_pdf_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test' + folder_path='BERT-Attack/results/meta/test', + output_pdf_path='BERT-Attack/results/meta/test' ) # Attack @@ -55,7 +53,7 @@ if params_file: gen.attack( attack_method='pgd', - model_path='magicslabnu/GERM', + model_path='anonymous_model', **kwargs ) ``` @@ -66,17 +64,17 @@ GenoArmory can also be used from the command line: ```bash # Attack -python GenoArmory.py --model_path magicslabnu/GERM attack --method pgd --params_file /projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json +python GenoArmory.py --model_path anonymous_model attack --method pgd --params_file scripts/PGD/pgd_dnabert.json # Defense -python GenoArmory.py --model_path magicslabnu/GERM defense --method at --params_file /projects/p32013/DNABERT-meta/scripts/AT/at_pgd_dnabert.json +python GenoArmory.py --model_path anonymous_model defense --method at --params_file scripts/AT/at_pgd_dnabert.json # Visualization -python GenoArmory.py --model_path magicslabnu/GERM visualize --folder_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test --save_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test/frequency.pdf +python GenoArmory.py --model_path anonymous_model visualize --folder_path BERT-Attack/results/meta/test --save_path BERT-Attack/results/meta/test/frequency.pdf # Read MetaData -python GenoArmory.py --model_path magicslabnu/GERM read --type attack --method TextFooler --model_name dnabert +python GenoArmory.py --model_path anonymous_model read --type attack --method TextFooler --model_name dnabert ``` @@ -108,20 +106,3 @@ For detailed documentation, visit [docs](We will release soon). This project is licensed under the MIT License. -## Citation - -If you have any question regarding our paper or codes, please feel free to start an issue. - -If you use GenoArmory in your work, please kindly cite our paper: - -``` -@misc{luo2025genoarmoryunifiedevaluationframework, - title={GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models}, - author={Haozheng Luo and Chenghao Qiu and Yimin Wang and Shang Wu and Jiahao Yu and Han Liu and Binghui Wang and Yan Chen}, - year={2025}, - eprint={2505.10983}, - archivePrefix={arXiv}, - primaryClass={cs.LG}, - url={https://arxiv.org/abs/2505.10983}, -} -``` diff --git a/TNF/generate_data.py b/TNF/generate_data.py index 63521ff2..1d72589c 100644 --- a/TNF/generate_data.py +++ b/TNF/generate_data.py @@ -2,8 +2,8 @@ import pandas as pd # Define directories -source_root = "/projects/p32013/DNABERT-meta/TNF/results" -dest_root = "/projects/p32013/DNABERT-meta/GUE" +source_root = "TNF/results" +dest_root = "GUE" # Iterate through all subdirectories in the source root directory for subdir in os.listdir(source_root): diff --git a/TNF/results/0/result.json b/TNF/results/0/result.json deleted file mode 100644 index f71b201f..00000000 --- a/TNF/results/0/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.6155066079295154, - "lgb": 0.7330396475770925 -} \ No newline at end of file diff --git a/TNF/results/1/result.json b/TNF/results/1/result.json deleted file mode 100644 index 813827f4..00000000 --- a/TNF/results/1/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.4301533219761499, - "lgb": 0.469335604770017 -} \ No newline at end of file diff --git a/TNF/results/2/result.json b/TNF/results/2/result.json deleted file mode 100644 index 1c117fcc..00000000 --- a/TNF/results/2/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5734463276836158, - "lgb": 0.7288135593220338 -} \ No newline at end of file diff --git a/TNF/results/3/result.json b/TNF/results/3/result.json deleted file mode 100644 index 38f969bc..00000000 --- a/TNF/results/3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.62, - "lgb": 0.6 -} \ No newline at end of file diff --git a/TNF/results/4/result.json b/TNF/results/4/result.json deleted file mode 100644 index b82a2379..00000000 --- a/TNF/results/4/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5381498987170831, - "lgb": 0.48548278190411887 -} \ No newline at end of file diff --git a/TNF/results/H3/result.json b/TNF/results/H3/result.json deleted file mode 100644 index cf3677c3..00000000 --- a/TNF/results/H3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.6558951965065503, - "lgb": 0.6262008733624455 -} \ No newline at end of file diff --git a/TNF/results/H3K14ac/result.json b/TNF/results/H3K14ac/result.json deleted file mode 100644 index fbca87b5..00000000 --- a/TNF/results/H3K14ac/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7423544197737746, - "lgb": 0.7892752408881442 -} \ No newline at end of file diff --git a/TNF/results/H3K36me3/result.json b/TNF/results/H3K36me3/result.json deleted file mode 100644 index 746be940..00000000 --- a/TNF/results/H3K36me3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7466872110939907, - "lgb": 0.8234206471494607 -} \ No newline at end of file diff --git a/TNF/results/H3K4me1/result.json b/TNF/results/H3K4me1/result.json deleted file mode 100644 index e88e639b..00000000 --- a/TNF/results/H3K4me1/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7653958944281525, - "lgb": 0.8785085881860075 -} \ No newline at end of file diff --git a/TNF/results/H3K4me2/result.json b/TNF/results/H3K4me2/result.json deleted file mode 100644 index d5331a35..00000000 --- a/TNF/results/H3K4me2/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7030456852791879, - "lgb": 0.6934010152284263 -} \ No newline at end of file diff --git a/TNF/results/H3K4me3/result.json b/TNF/results/H3K4me3/result.json deleted file mode 100644 index 49710fdb..00000000 --- a/TNF/results/H3K4me3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.635118807893677, - "lgb": 0.78372935964559 -} \ No newline at end of file diff --git a/TNF/results/H3K79me3/result.json b/TNF/results/H3K79me3/result.json deleted file mode 100644 index b0ab42f3..00000000 --- a/TNF/results/H3K79me3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5841446453407511, - "lgb": 0.541029207232267 -} \ No newline at end of file diff --git a/TNF/results/H3K9ac/result.json b/TNF/results/H3K9ac/result.json deleted file mode 100644 index 507d8f0c..00000000 --- a/TNF/results/H3K9ac/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7100183823529411, - "lgb": 0.7339154411764706 -} \ No newline at end of file diff --git a/TNF/results/H4/result.json b/TNF/results/H4/result.json deleted file mode 100644 index 6da75857..00000000 --- a/TNF/results/H4/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.6655896607431341, - "lgb": 0.574313408723748 -} \ No newline at end of file diff --git a/TNF/results/H4ac/result.json b/TNF/results/H4ac/result.json deleted file mode 100644 index 35424333..00000000 --- a/TNF/results/H4ac/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.6669288242233582, - "lgb": 0.7778214707038931 -} \ No newline at end of file diff --git a/TNF/results/prom_300_all/result.json b/TNF/results/prom_300_all/result.json deleted file mode 100644 index 3eda35e0..00000000 --- a/TNF/results/prom_300_all/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5712814173877214, - "lgb": 0.6510094767202307 -} \ No newline at end of file diff --git a/TNF/results/prom_300_notata/result.json b/TNF/results/prom_300_notata/result.json deleted file mode 100644 index a9880966..00000000 --- a/TNF/results/prom_300_notata/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5062324085243265, - "lgb": 0.41857659831121835 -} \ No newline at end of file diff --git a/TNF/results/prom_300_tata/result.json b/TNF/results/prom_300_tata/result.json deleted file mode 100644 index 177209f8..00000000 --- a/TNF/results/prom_300_tata/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.667296786389414, - "lgb": 0.7580340264650284 -} \ No newline at end of file diff --git a/TNF/results/prom_core_all/result.json b/TNF/results/prom_core_all/result.json deleted file mode 100644 index 1759ca8c..00000000 --- a/TNF/results/prom_core_all/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5054575986565911, - "lgb": 0.464735516372796 -} \ No newline at end of file diff --git a/TNF/results/prom_core_notata/result.json b/TNF/results/prom_core_notata/result.json deleted file mode 100644 index f02dfc4a..00000000 --- a/TNF/results/prom_core_notata/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.45548450565666504, - "lgb": 0.4537629119527791 -} \ No newline at end of file diff --git a/TNF/results/prom_core_tata/result.json b/TNF/results/prom_core_tata/result.json deleted file mode 100644 index 48425440..00000000 --- a/TNF/results/prom_core_tata/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.7794970986460348, - "lgb": 0.746615087040619 -} \ No newline at end of file diff --git a/TNF/results/tf0/result.json b/TNF/results/tf0/result.json deleted file mode 100644 index 75d8c45d..00000000 --- a/TNF/results/tf0/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.46070931849791374, - "lgb": 0.47079276773296247 -} \ No newline at end of file diff --git a/TNF/results/tf1/result.json b/TNF/results/tf1/result.json deleted file mode 100644 index 1d0317ad..00000000 --- a/TNF/results/tf1/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.45780757097791797, - "lgb": 0.5035488958990536 -} \ No newline at end of file diff --git a/TNF/results/tf2/result.json b/TNF/results/tf2/result.json deleted file mode 100644 index e212226c..00000000 --- a/TNF/results/tf2/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.4923453766074709, - "lgb": 0.5052051439069197 -} \ No newline at end of file diff --git a/TNF/results/tf3/result.json b/TNF/results/tf3/result.json deleted file mode 100644 index ac578519..00000000 --- a/TNF/results/tf3/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.5070904645476773, - "lgb": 0.5012224938875306 -} \ No newline at end of file diff --git a/TNF/results/tf4/result.json b/TNF/results/tf4/result.json deleted file mode 100644 index d8cb06ea..00000000 --- a/TNF/results/tf4/result.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "xgb": 0.45124593716143013, - "lgb": 0.46208017334777896 -} \ No newline at end of file diff --git a/TextFooler/output/ADFAR/dnabert/0/results_log b/TextFooler/output/ADFAR/dnabert/0/results_log index c16fa077..1873128d 100644 --- a/TextFooler/output/ADFAR/dnabert/0/results_log +++ b/TextFooler/output/ADFAR/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 65.200%, avg changed rate: 4.408%, num of queries: 292.9 +For target model GUE/0/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 65.200%, avg changed rate: 4.408%, num of queries: 292.9 diff --git a/TextFooler/output/ADFAR/dnabert/1/results_log b/TextFooler/output/ADFAR/dnabert/1/results_log index 899c370b..fc02d529 100644 --- a/TextFooler/output/ADFAR/dnabert/1/results_log +++ b/TextFooler/output/ADFAR/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 49.600%, adv accuracy: 8.700%, avg changed rate: 9.056%, num of queries: 571.3 +For target model GUE/1/five_percent/cat.csv: original accuracy: 49.600%, adv accuracy: 8.700%, avg changed rate: 9.056%, num of queries: 571.3 diff --git a/TextFooler/output/ADFAR/dnabert/2/results_log b/TextFooler/output/ADFAR/dnabert/2/results_log index 596c67da..2bfbf5af 100644 --- a/TextFooler/output/ADFAR/dnabert/2/results_log +++ b/TextFooler/output/ADFAR/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 85.300%, avg changed rate: 3.195%, num of queries: 186.3 +For target model GUE/2/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 85.300%, avg changed rate: 3.195%, num of queries: 186.3 diff --git a/TextFooler/output/ADFAR/dnabert/3/results_log b/TextFooler/output/ADFAR/dnabert/3/results_log index 33cc8ea1..0cb23018 100644 --- a/TextFooler/output/ADFAR/dnabert/3/results_log +++ b/TextFooler/output/ADFAR/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 89.300%, avg changed rate: 1.330%, num of queries: 89.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 89.300%, avg changed rate: 1.330%, num of queries: 89.5 diff --git a/TextFooler/output/ADFAR/dnabert/4/results_log b/TextFooler/output/ADFAR/dnabert/4/results_log index 75e681c5..07d6b078 100644 --- a/TextFooler/output/ADFAR/dnabert/4/results_log +++ b/TextFooler/output/ADFAR/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 58.500%, adv accuracy: 15.300%, avg changed rate: 1.781%, num of queries: 133.9 +For target model GUE/4/five_percent/cat.csv: original accuracy: 58.500%, adv accuracy: 15.300%, avg changed rate: 1.781%, num of queries: 133.9 diff --git a/TextFooler/output/ADFAR/dnabert/H3/results_log b/TextFooler/output/ADFAR/dnabert/H3/results_log index 9fe07542..13a8834b 100644 --- a/TextFooler/output/ADFAR/dnabert/H3/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 77.100%, adv accuracy: 32.600%, avg changed rate: 0.243%, num of queries: 167.0 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 77.100%, adv accuracy: 32.600%, avg changed rate: 0.243%, num of queries: 167.0 diff --git a/TextFooler/output/ADFAR/dnabert/H3K14ac/results_log b/TextFooler/output/ADFAR/dnabert/H3K14ac/results_log index f0f8884d..6079dc3f 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K14ac/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 74.100%, adv accuracy: 0.000%, avg changed rate: 0.782%, num of queries: 301.7 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 74.100%, adv accuracy: 0.000%, avg changed rate: 0.782%, num of queries: 301.7 diff --git a/TextFooler/output/ADFAR/dnabert/H3K36me3/results_log b/TextFooler/output/ADFAR/dnabert/H3K36me3/results_log index 25a5d25c..9f835bbd 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K36me3/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 55.900%, adv accuracy: 0.000%, avg changed rate: 0.234%, num of queries: 161.0 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 55.900%, adv accuracy: 0.000%, avg changed rate: 0.234%, num of queries: 161.0 diff --git a/TextFooler/output/ADFAR/dnabert/H3K4me1/results_log b/TextFooler/output/ADFAR/dnabert/H3K4me1/results_log index e4623609..cd702f76 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K4me1/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 96.500%, adv accuracy: 0.000%, avg changed rate: 1.397%, num of queries: 451.4 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 96.500%, adv accuracy: 0.000%, avg changed rate: 1.397%, num of queries: 451.4 diff --git a/TextFooler/output/ADFAR/dnabert/H3K4me2/results_log b/TextFooler/output/ADFAR/dnabert/H3K4me2/results_log index 4571bf4b..f60328fa 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K4me2/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 42.200%, adv accuracy: 0.000%, avg changed rate: 0.325%, num of queries: 185.0 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 42.200%, adv accuracy: 0.000%, avg changed rate: 0.325%, num of queries: 185.0 diff --git a/TextFooler/output/ADFAR/dnabert/H3K4me3/results_log b/TextFooler/output/ADFAR/dnabert/H3K4me3/results_log index 736b2560..0a874bfd 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K4me3/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 46.000%, adv accuracy: 0.100%, avg changed rate: 0.905%, num of queries: 343.3 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 46.000%, adv accuracy: 0.100%, avg changed rate: 0.905%, num of queries: 343.3 diff --git a/TextFooler/output/ADFAR/dnabert/H3K79me3/results_log b/TextFooler/output/ADFAR/dnabert/H3K79me3/results_log index 1e0b4caf..a55abf3f 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K79me3/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 55.200%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 164.2 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 55.200%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 164.2 diff --git a/TextFooler/output/ADFAR/dnabert/H3K9ac/results_log b/TextFooler/output/ADFAR/dnabert/H3K9ac/results_log index d38585e7..deb2379d 100644 --- a/TextFooler/output/ADFAR/dnabert/H3K9ac/results_log +++ b/TextFooler/output/ADFAR/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 0.200%, adv accuracy: 0.000%, avg changed rate: 1.800%, num of queries: 580.0 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 0.200%, adv accuracy: 0.000%, avg changed rate: 1.800%, num of queries: 580.0 diff --git a/TextFooler/output/ADFAR/dnabert/H4/results_log b/TextFooler/output/ADFAR/dnabert/H4/results_log index 294bccc1..8a137f54 100644 --- a/TextFooler/output/ADFAR/dnabert/H4/results_log +++ b/TextFooler/output/ADFAR/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 44.900%, adv accuracy: 34.300%, avg changed rate: 0.238%, num of queries: 161.3 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 44.900%, adv accuracy: 34.300%, avg changed rate: 0.238%, num of queries: 161.3 diff --git a/TextFooler/output/ADFAR/dnabert/H4ac/results_log b/TextFooler/output/ADFAR/dnabert/H4ac/results_log index eb61f3df..e90f7aa4 100644 --- a/TextFooler/output/ADFAR/dnabert/H4ac/results_log +++ b/TextFooler/output/ADFAR/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 2.200%, avg changed rate: 0.306%, num of queries: 409.1 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 2.200%, avg changed rate: 0.306%, num of queries: 409.1 diff --git a/TextFooler/output/ADFAR/dnabert/prom_300_all/results_log b/TextFooler/output/ADFAR/dnabert/prom_300_all/results_log index 50a0b781..a5791bd3 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_300_all/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 49.900%, adv accuracy: 4.200%, avg changed rate: 3.168%, num of queries: 823.0 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 49.900%, adv accuracy: 4.200%, avg changed rate: 3.168%, num of queries: 823.0 diff --git a/TextFooler/output/ADFAR/dnabert/prom_300_notata/results_log b/TextFooler/output/ADFAR/dnabert/prom_300_notata/results_log index f0e1ea32..c559800a 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 49.300%, adv accuracy: 49.300%, avg changed rate: nan%, num of queries: 3274.2 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 49.300%, adv accuracy: 49.300%, avg changed rate: nan%, num of queries: 3274.2 diff --git a/TextFooler/output/ADFAR/dnabert/prom_300_tata/results_log b/TextFooler/output/ADFAR/dnabert/prom_300_tata/results_log index cc7a3346..00163c17 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 81.500%, adv accuracy: 72.400%, avg changed rate: 0.542%, num of queries: 157.3 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 81.500%, adv accuracy: 72.400%, avg changed rate: 0.542%, num of queries: 157.3 diff --git a/TextFooler/output/ADFAR/dnabert/prom_core_all/results_log b/TextFooler/output/ADFAR/dnabert/prom_core_all/results_log index 56ef3af7..464d2ba9 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_core_all/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 26.000%, avg changed rate: 2.344%, num of queries: 293.5 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 26.000%, avg changed rate: 2.344%, num of queries: 293.5 diff --git a/TextFooler/output/ADFAR/dnabert/prom_core_notata/results_log b/TextFooler/output/ADFAR/dnabert/prom_core_notata/results_log index 1a2b3d60..f0954480 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 1.600%, avg changed rate: 3.921%, num of queries: 172.3 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 1.600%, avg changed rate: 3.921%, num of queries: 172.3 diff --git a/TextFooler/output/ADFAR/dnabert/prom_core_tata/results_log b/TextFooler/output/ADFAR/dnabert/prom_core_tata/results_log index 5ab16533..f0575c40 100644 --- a/TextFooler/output/ADFAR/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/ADFAR/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 73.900%, adv accuracy: 72.400%, avg changed rate: 1.619%, num of queries: 72.1 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 73.900%, adv accuracy: 72.400%, avg changed rate: 1.619%, num of queries: 72.1 diff --git a/TextFooler/output/ADFAR/dnabert/tf0/results_log b/TextFooler/output/ADFAR/dnabert/tf0/results_log index 91842b42..952c95d8 100644 --- a/TextFooler/output/ADFAR/dnabert/tf0/results_log +++ b/TextFooler/output/ADFAR/dnabert/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 0.000%, avg changed rate: 1.897%, num of queries: 131.1 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 0.000%, avg changed rate: 1.897%, num of queries: 131.1 diff --git a/TextFooler/output/ADFAR/dnabert/tf1/results_log b/TextFooler/output/ADFAR/dnabert/tf1/results_log index 7c29f198..91a91755 100644 --- a/TextFooler/output/ADFAR/dnabert/tf1/results_log +++ b/TextFooler/output/ADFAR/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.000%, avg changed rate: 2.086%, num of queries: 128.9 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.000%, avg changed rate: 2.086%, num of queries: 128.9 diff --git a/TextFooler/output/ADFAR/dnabert/tf2/results_log b/TextFooler/output/ADFAR/dnabert/tf2/results_log index 588c98fe..be8d2e62 100644 --- a/TextFooler/output/ADFAR/dnabert/tf2/results_log +++ b/TextFooler/output/ADFAR/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 6.200%, avg changed rate: 3.620%, num of queries: 269.2 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 6.200%, avg changed rate: 3.620%, num of queries: 269.2 diff --git a/TextFooler/output/ADFAR/dnabert/tf3/results_log b/TextFooler/output/ADFAR/dnabert/tf3/results_log index 58516487..0d1bf3ad 100644 --- a/TextFooler/output/ADFAR/dnabert/tf3/results_log +++ b/TextFooler/output/ADFAR/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 52.300%, adv accuracy: 52.300%, avg changed rate: nan%, num of queries: 1066.9 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 52.300%, adv accuracy: 52.300%, avg changed rate: nan%, num of queries: 1066.9 diff --git a/TextFooler/output/ADFAR/dnabert/tf4/results_log b/TextFooler/output/ADFAR/dnabert/tf4/results_log index 507729f5..1888bfed 100644 --- a/TextFooler/output/ADFAR/dnabert/tf4/results_log +++ b/TextFooler/output/ADFAR/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 1.200%, avg changed rate: 2.877%, num of queries: 197.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 1.200%, avg changed rate: 2.877%, num of queries: 197.9 diff --git a/TextFooler/output/ADFAR/hyena/0/results_log b/TextFooler/output/ADFAR/hyena/0/results_log index ef2a12de..67be6d76 100644 --- a/TextFooler/output/ADFAR/hyena/0/results_log +++ b/TextFooler/output/ADFAR/hyena/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/ADFAR/hyena/1/results_log b/TextFooler/output/ADFAR/hyena/1/results_log index ad0e58c6..46b959af 100644 --- a/TextFooler/output/ADFAR/hyena/1/results_log +++ b/TextFooler/output/ADFAR/hyena/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 50.200%, adv accuracy: 45.000%, avg changed rate: 36.729%, num of queries: 149.7 +For target model GUE/1/five_percent/cat.csv: original accuracy: 50.200%, adv accuracy: 45.000%, avg changed rate: 36.729%, num of queries: 149.7 diff --git a/TextFooler/output/ADFAR/hyena/2/results_log b/TextFooler/output/ADFAR/hyena/2/results_log index cc71552b..7c40de0d 100644 --- a/TextFooler/output/ADFAR/hyena/2/results_log +++ b/TextFooler/output/ADFAR/hyena/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 diff --git a/TextFooler/output/ADFAR/hyena/3/results_log b/TextFooler/output/ADFAR/hyena/3/results_log index 4474ca86..2a76ba7f 100644 --- a/TextFooler/output/ADFAR/hyena/3/results_log +++ b/TextFooler/output/ADFAR/hyena/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 153.3 +For target model GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 153.3 diff --git a/TextFooler/output/ADFAR/hyena/4/results_log b/TextFooler/output/ADFAR/hyena/4/results_log index 5b9dacf4..3a937be5 100644 --- a/TextFooler/output/ADFAR/hyena/4/results_log +++ b/TextFooler/output/ADFAR/hyena/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 58.000%, adv accuracy: 20.500%, avg changed rate: 11.519%, num of queries: 118.9 +For target model GUE/4/five_percent/cat.csv: original accuracy: 58.000%, adv accuracy: 20.500%, avg changed rate: 11.519%, num of queries: 118.9 diff --git a/TextFooler/output/ADFAR/hyena/H3/results_log b/TextFooler/output/ADFAR/hyena/H3/results_log index 7db0417f..a1138ffc 100644 --- a/TextFooler/output/ADFAR/hyena/H3/results_log +++ b/TextFooler/output/ADFAR/hyena/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 69.200%, adv accuracy: 69.200%, avg changed rate: nan%, num of queries: 753.2 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 69.200%, adv accuracy: 69.200%, avg changed rate: nan%, num of queries: 753.2 diff --git a/TextFooler/output/ADFAR/hyena/H3K14ac/results_log b/TextFooler/output/ADFAR/hyena/H3K14ac/results_log index 0a4e2f90..f699194f 100644 --- a/TextFooler/output/ADFAR/hyena/H3K14ac/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 42.700%, adv accuracy: 42.600%, avg changed rate: 1.600%, num of queries: 749.9 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 42.700%, adv accuracy: 42.600%, avg changed rate: 1.600%, num of queries: 749.9 diff --git a/TextFooler/output/ADFAR/hyena/H3K36me3/results_log b/TextFooler/output/ADFAR/hyena/H3K36me3/results_log index 97bec271..1ad9ea9b 100644 --- a/TextFooler/output/ADFAR/hyena/H3K36me3/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 16.300%, avg changed rate: 7.577%, num of queries: 623.1 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 16.300%, avg changed rate: 7.577%, num of queries: 623.1 diff --git a/TextFooler/output/ADFAR/hyena/H3K4me1/results_log b/TextFooler/output/ADFAR/hyena/H3K4me1/results_log index 77556ce2..9407a140 100644 --- a/TextFooler/output/ADFAR/hyena/H3K4me1/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 48.600%, adv accuracy: 24.600%, avg changed rate: 6.393%, num of queries: 651.7 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 48.600%, adv accuracy: 24.600%, avg changed rate: 6.393%, num of queries: 651.7 diff --git a/TextFooler/output/ADFAR/hyena/H3K4me2/results_log b/TextFooler/output/ADFAR/hyena/H3K4me2/results_log index 5692efae..1ae7755d 100644 --- a/TextFooler/output/ADFAR/hyena/H3K4me2/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 52.400%, adv accuracy: 15.200%, avg changed rate: 12.678%, num of queries: 646.3 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 52.400%, adv accuracy: 15.200%, avg changed rate: 12.678%, num of queries: 646.3 diff --git a/TextFooler/output/ADFAR/hyena/H3K4me3/results_log b/TextFooler/output/ADFAR/hyena/H3K4me3/results_log index 8af9111b..58bc483a 100644 --- a/TextFooler/output/ADFAR/hyena/H3K4me3/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 53.400%, adv accuracy: 52.200%, avg changed rate: 22.033%, num of queries: 749.1 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 53.400%, adv accuracy: 52.200%, avg changed rate: 22.033%, num of queries: 749.1 diff --git a/TextFooler/output/ADFAR/hyena/H3K79me3/results_log b/TextFooler/output/ADFAR/hyena/H3K79me3/results_log index 2f25dc5f..432bd713 100644 --- a/TextFooler/output/ADFAR/hyena/H3K79me3/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 54.400%, adv accuracy: 34.400%, avg changed rate: 6.995%, num of queries: 681.2 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 54.400%, adv accuracy: 34.400%, avg changed rate: 6.995%, num of queries: 681.2 diff --git a/TextFooler/output/ADFAR/hyena/H3K9ac/results_log b/TextFooler/output/ADFAR/hyena/H3K9ac/results_log index 1bf7781f..d4c973d4 100644 --- a/TextFooler/output/ADFAR/hyena/H3K9ac/results_log +++ b/TextFooler/output/ADFAR/hyena/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 8.100%, avg changed rate: 6.888%, num of queries: 604.2 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 8.100%, avg changed rate: 6.888%, num of queries: 604.2 diff --git a/TextFooler/output/ADFAR/hyena/H4/results_log b/TextFooler/output/ADFAR/hyena/H4/results_log index 18914de6..c7632cfc 100644 --- a/TextFooler/output/ADFAR/hyena/H4/results_log +++ b/TextFooler/output/ADFAR/hyena/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 69.900%, adv accuracy: 62.200%, avg changed rate: 7.774%, num of queries: 713.0 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 69.900%, adv accuracy: 62.200%, avg changed rate: 7.774%, num of queries: 713.0 diff --git a/TextFooler/output/ADFAR/hyena/H4ac/results_log b/TextFooler/output/ADFAR/hyena/H4ac/results_log index 4661eedc..5d9c3d9a 100644 --- a/TextFooler/output/ADFAR/hyena/H4ac/results_log +++ b/TextFooler/output/ADFAR/hyena/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 37.900%, avg changed rate: 18.193%, num of queries: 730.8 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 37.900%, avg changed rate: 18.193%, num of queries: 730.8 diff --git a/TextFooler/output/ADFAR/hyena/prom_300_all/results_log b/TextFooler/output/ADFAR/hyena/prom_300_all/results_log index a19dbb1a..91c7b696 100644 --- a/TextFooler/output/ADFAR/hyena/prom_300_all/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 33.000%, avg changed rate: 10.483%, num of queries: 412.9 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 33.000%, avg changed rate: 10.483%, num of queries: 412.9 diff --git a/TextFooler/output/ADFAR/hyena/prom_300_notata/results_log b/TextFooler/output/ADFAR/hyena/prom_300_notata/results_log index 3421e06d..c3eed312 100644 --- a/TextFooler/output/ADFAR/hyena/prom_300_notata/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 46.800%, avg changed rate: 12.704%, num of queries: 448.5 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 46.800%, avg changed rate: 12.704%, num of queries: 448.5 diff --git a/TextFooler/output/ADFAR/hyena/prom_300_tata/results_log b/TextFooler/output/ADFAR/hyena/prom_300_tata/results_log index 328c9d4a..84e90d92 100644 --- a/TextFooler/output/ADFAR/hyena/prom_300_tata/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 84.400%, adv accuracy: 75.900%, avg changed rate: 9.702%, num of queries: 375.9 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 84.400%, adv accuracy: 75.900%, avg changed rate: 9.702%, num of queries: 375.9 diff --git a/TextFooler/output/ADFAR/hyena/prom_core_all/results_log b/TextFooler/output/ADFAR/hyena/prom_core_all/results_log index 2c1238e8..ad419819 100644 --- a/TextFooler/output/ADFAR/hyena/prom_core_all/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.500%, adv accuracy: 44.600%, avg changed rate: 23.251%, num of queries: 104.1 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.500%, adv accuracy: 44.600%, avg changed rate: 23.251%, num of queries: 104.1 diff --git a/TextFooler/output/ADFAR/hyena/prom_core_notata/results_log b/TextFooler/output/ADFAR/hyena/prom_core_notata/results_log index c1bc2a25..da8ce4d7 100644 --- a/TextFooler/output/ADFAR/hyena/prom_core_notata/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 105.6 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 105.6 diff --git a/TextFooler/output/ADFAR/hyena/prom_core_tata/results_log b/TextFooler/output/ADFAR/hyena/prom_core_tata/results_log index ac1662ee..5d1054af 100644 --- a/TextFooler/output/ADFAR/hyena/prom_core_tata/results_log +++ b/TextFooler/output/ADFAR/hyena/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 104.3 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 104.3 diff --git a/TextFooler/output/ADFAR/hyena/tf0/results_log b/TextFooler/output/ADFAR/hyena/tf0/results_log index 4758141e..8505e98c 100644 --- a/TextFooler/output/ADFAR/hyena/tf0/results_log +++ b/TextFooler/output/ADFAR/hyena/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 diff --git a/TextFooler/output/ADFAR/hyena/tf1/results_log b/TextFooler/output/ADFAR/hyena/tf1/results_log index f5bd2b85..fcabb127 100644 --- a/TextFooler/output/ADFAR/hyena/tf1/results_log +++ b/TextFooler/output/ADFAR/hyena/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/ADFAR/hyena/tf2/results_log b/TextFooler/output/ADFAR/hyena/tf2/results_log index 25df8bac..4d707333 100644 --- a/TextFooler/output/ADFAR/hyena/tf2/results_log +++ b/TextFooler/output/ADFAR/hyena/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 45.200%, avg changed rate: 24.638%, num of queries: 149.7 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 45.200%, avg changed rate: 24.638%, num of queries: 149.7 diff --git a/TextFooler/output/ADFAR/hyena/tf3/results_log b/TextFooler/output/ADFAR/hyena/tf3/results_log index 4fb7baf1..c4f8f168 100644 --- a/TextFooler/output/ADFAR/hyena/tf3/results_log +++ b/TextFooler/output/ADFAR/hyena/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 41.500%, avg changed rate: 21.734%, num of queries: 148.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 41.500%, avg changed rate: 21.734%, num of queries: 148.2 diff --git a/TextFooler/output/ADFAR/hyena/tf4/results_log b/TextFooler/output/ADFAR/hyena/tf4/results_log index 1097bdb5..7ffd0e93 100644 --- a/TextFooler/output/ADFAR/hyena/tf4/results_log +++ b/TextFooler/output/ADFAR/hyena/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 50.200%, adv accuracy: 50.200%, avg changed rate: nan%, num of queries: 152.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 50.200%, adv accuracy: 50.200%, avg changed rate: nan%, num of queries: 152.9 diff --git a/TextFooler/output/ADFAR/nt1/0/results_log b/TextFooler/output/ADFAR/nt1/0/results_log index 0b5ab830..725668d7 100644 --- a/TextFooler/output/ADFAR/nt1/0/results_log +++ b/TextFooler/output/ADFAR/nt1/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 80.600%, adv accuracy: 68.700%, avg changed rate: 3.461%, num of queries: 31.1 -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 69.700%, adv accuracy: 64.100%, avg changed rate: 1.998%, num of queries: 26.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 80.600%, adv accuracy: 68.700%, avg changed rate: 3.461%, num of queries: 31.1 +For target model GUE/0/five_percent/cat.csv: original accuracy: 69.700%, adv accuracy: 64.100%, avg changed rate: 1.998%, num of queries: 26.3 diff --git a/TextFooler/output/ADFAR/nt1/1/results_log b/TextFooler/output/ADFAR/nt1/1/results_log index e4385dee..5698e4ac 100644 --- a/TextFooler/output/ADFAR/nt1/1/results_log +++ b/TextFooler/output/ADFAR/nt1/1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 51.300%, adv accuracy: 43.000%, avg changed rate: 4.557%, num of queries: 35.3 -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 41.700%, avg changed rate: 10.106%, num of queries: 37.1 +For target model GUE/1/five_percent/cat.csv: original accuracy: 51.300%, adv accuracy: 43.000%, avg changed rate: 4.557%, num of queries: 35.3 +For target model GUE/1/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 41.700%, avg changed rate: 10.106%, num of queries: 37.1 diff --git a/TextFooler/output/ADFAR/nt1/2/results_log b/TextFooler/output/ADFAR/nt1/2/results_log index d1dc396a..f2b5b906 100644 --- a/TextFooler/output/ADFAR/nt1/2/results_log +++ b/TextFooler/output/ADFAR/nt1/2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 87.600%, adv accuracy: 85.500%, avg changed rate: 2.169%, num of queries: 26.5 -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.200%, avg changed rate: 5.972%, num of queries: 34.8 +For target model GUE/2/five_percent/cat.csv: original accuracy: 87.600%, adv accuracy: 85.500%, avg changed rate: 2.169%, num of queries: 26.5 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.200%, avg changed rate: 5.972%, num of queries: 34.8 diff --git a/TextFooler/output/ADFAR/nt1/3/results_log b/TextFooler/output/ADFAR/nt1/3/results_log index 54bee583..6d3d8e80 100644 --- a/TextFooler/output/ADFAR/nt1/3/results_log +++ b/TextFooler/output/ADFAR/nt1/3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 95.100%, avg changed rate: nan%, num of queries: 38.4 -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 38.8 +For target model GUE/3/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 95.100%, avg changed rate: nan%, num of queries: 38.4 +For target model GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 38.8 diff --git a/TextFooler/output/ADFAR/nt1/4/results_log b/TextFooler/output/ADFAR/nt1/4/results_log index ba8d3cf8..85e58282 100644 --- a/TextFooler/output/ADFAR/nt1/4/results_log +++ b/TextFooler/output/ADFAR/nt1/4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 25.200%, adv accuracy: 17.400%, avg changed rate: 1.802%, num of queries: 28.1 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 57.800%, adv accuracy: 57.800%, avg changed rate: nan%, num of queries: 38.1 +For target model GUE/4/five_percent/cat.csv: original accuracy: 25.200%, adv accuracy: 17.400%, avg changed rate: 1.802%, num of queries: 28.1 +For target model GUE/4/five_percent/cat.csv: original accuracy: 57.800%, adv accuracy: 57.800%, avg changed rate: nan%, num of queries: 38.1 diff --git a/TextFooler/output/ADFAR/nt1/H3/results_log b/TextFooler/output/ADFAR/nt1/H3/results_log index eff82c2c..36775e2e 100644 --- a/TextFooler/output/ADFAR/nt1/H3/results_log +++ b/TextFooler/output/ADFAR/nt1/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 9.700%, adv accuracy: 0.000%, avg changed rate: 0.654%, num of queries: 90.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 69.200%, adv accuracy: 67.600%, avg changed rate: 3.425%, num of queries: 147.2 +For target model GUE/H3/cat.csv: original accuracy: 9.700%, adv accuracy: 0.000%, avg changed rate: 0.654%, num of queries: 90.5 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 69.200%, adv accuracy: 67.600%, avg changed rate: 3.425%, num of queries: 147.2 diff --git a/TextFooler/output/ADFAR/nt1/H3K14ac/results_log b/TextFooler/output/ADFAR/nt1/H3K14ac/results_log index aabf57b8..04e4c419 100644 --- a/TextFooler/output/ADFAR/nt1/H3K14ac/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 148.4 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 58.700%, adv accuracy: 33.200%, avg changed rate: 2.238%, num of queries: 128.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 148.4 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 58.700%, adv accuracy: 33.200%, avg changed rate: 2.238%, num of queries: 128.4 diff --git a/TextFooler/output/ADFAR/nt1/H3K36me3/results_log b/TextFooler/output/ADFAR/nt1/H3K36me3/results_log index e3d61d2f..d42eabef 100644 --- a/TextFooler/output/ADFAR/nt1/H3K36me3/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 69.700%, adv accuracy: 43.700%, avg changed rate: 2.340%, num of queries: 131.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 96.500%, adv accuracy: 37.400%, avg changed rate: 2.093%, num of queries: 119.6 +For target model GUE/H3K36me3/cat.csv: original accuracy: 69.700%, adv accuracy: 43.700%, avg changed rate: 2.340%, num of queries: 131.8 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 96.500%, adv accuracy: 37.400%, avg changed rate: 2.093%, num of queries: 119.6 diff --git a/TextFooler/output/ADFAR/nt1/H3K4me1/results_log b/TextFooler/output/ADFAR/nt1/H3K4me1/results_log index ea39c239..8a1d92d6 100644 --- a/TextFooler/output/ADFAR/nt1/H3K4me1/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 100.000%, adv accuracy: 12.900%, avg changed rate: 2.591%, num of queries: 110.0 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 100.000%, adv accuracy: 12.900%, avg changed rate: 2.591%, num of queries: 110.0 diff --git a/TextFooler/output/ADFAR/nt1/H3K4me2/results_log b/TextFooler/output/ADFAR/nt1/H3K4me2/results_log index 5099a624..854c6e4f 100644 --- a/TextFooler/output/ADFAR/nt1/H3K4me2/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 10.700%, adv accuracy: 1.000%, avg changed rate: 0.588%, num of queries: 95.8 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 10.700%, adv accuracy: 1.000%, avg changed rate: 0.588%, num of queries: 95.8 diff --git a/TextFooler/output/ADFAR/nt1/H3K4me3/results_log b/TextFooler/output/ADFAR/nt1/H3K4me3/results_log index def5c5d9..f379852d 100644 --- a/TextFooler/output/ADFAR/nt1/H3K4me3/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 15.000%, adv accuracy: 1.100%, avg changed rate: 0.839%, num of queries: 96.3 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 15.000%, adv accuracy: 1.100%, avg changed rate: 0.839%, num of queries: 96.3 diff --git a/TextFooler/output/ADFAR/nt1/H3K79me3/results_log b/TextFooler/output/ADFAR/nt1/H3K79me3/results_log index e552bfbe..04465746 100644 --- a/TextFooler/output/ADFAR/nt1/H3K79me3/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 15.700%, adv accuracy: 0.400%, avg changed rate: 0.956%, num of queries: 95.2 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 15.700%, adv accuracy: 0.400%, avg changed rate: 0.956%, num of queries: 95.2 diff --git a/TextFooler/output/ADFAR/nt1/H3K9ac/results_log b/TextFooler/output/ADFAR/nt1/H3K9ac/results_log index 1b3b0930..36ee51eb 100644 --- a/TextFooler/output/ADFAR/nt1/H3K9ac/results_log +++ b/TextFooler/output/ADFAR/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 44.100%, adv accuracy: 44.100%, avg changed rate: nan%, num of queries: 148.0 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 44.100%, adv accuracy: 44.100%, avg changed rate: nan%, num of queries: 148.0 diff --git a/TextFooler/output/ADFAR/nt1/H4/results_log b/TextFooler/output/ADFAR/nt1/H4/results_log index 42ec29eb..1dbca90f 100644 --- a/TextFooler/output/ADFAR/nt1/H4/results_log +++ b/TextFooler/output/ADFAR/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 65.400%, adv accuracy: 47.400%, avg changed rate: 3.957%, num of queries: 128.8 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 65.400%, adv accuracy: 47.400%, avg changed rate: 3.957%, num of queries: 128.8 diff --git a/TextFooler/output/ADFAR/nt1/H4ac/results_log b/TextFooler/output/ADFAR/nt1/H4ac/results_log index 82a17653..4d3c80b3 100644 --- a/TextFooler/output/ADFAR/nt1/H4ac/results_log +++ b/TextFooler/output/ADFAR/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 41.400%, avg changed rate: 1.527%, num of queries: 119.0 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 41.400%, avg changed rate: 1.527%, num of queries: 119.0 diff --git a/TextFooler/output/ADFAR/nt1/prom_300_all/results_log b/TextFooler/output/ADFAR/nt1/prom_300_all/results_log index 451f01ab..2fe6dc4a 100644 --- a/TextFooler/output/ADFAR/nt1/prom_300_all/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 43.700%, adv accuracy: 21.500%, avg changed rate: 2.281%, num of queries: 75.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 0.000%, adv accuracy: 0.000%, avg changed rate: nan%, num of queries: nan +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 43.700%, adv accuracy: 21.500%, avg changed rate: 2.281%, num of queries: 75.3 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 0.000%, adv accuracy: 0.000%, avg changed rate: nan%, num of queries: nan diff --git a/TextFooler/output/ADFAR/nt1/prom_300_notata/results_log b/TextFooler/output/ADFAR/nt1/prom_300_notata/results_log index 4328296a..79f4ee29 100644 --- a/TextFooler/output/ADFAR/nt1/prom_300_notata/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 48.600%, adv accuracy: 33.600%, avg changed rate: 3.358%, num of queries: 82.4 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 3.000%, adv accuracy: 0.000%, avg changed rate: 0.533%, num of queries: 53.8 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 48.600%, adv accuracy: 33.600%, avg changed rate: 3.358%, num of queries: 82.4 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 3.000%, adv accuracy: 0.000%, avg changed rate: 0.533%, num of queries: 53.8 diff --git a/TextFooler/output/ADFAR/nt1/prom_300_tata/results_log b/TextFooler/output/ADFAR/nt1/prom_300_tata/results_log index b40f2664..83b0771f 100644 --- a/TextFooler/output/ADFAR/nt1/prom_300_tata/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 79.500%, adv accuracy: 72.600%, avg changed rate: 1.208%, num of queries: 57.8 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 77.500%, adv accuracy: 72.900%, avg changed rate: 1.797%, num of queries: 62.8 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 79.500%, adv accuracy: 72.600%, avg changed rate: 1.208%, num of queries: 57.8 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 77.500%, adv accuracy: 72.900%, avg changed rate: 1.797%, num of queries: 62.8 diff --git a/TextFooler/output/ADFAR/nt1/prom_core_all/results_log b/TextFooler/output/ADFAR/nt1/prom_core_all/results_log index bc44ea09..23093130 100644 --- a/TextFooler/output/ADFAR/nt1/prom_core_all/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 96.100%, adv accuracy: 61.600%, avg changed rate: 4.874%, num of queries: 25.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 52.800%, adv accuracy: 45.800%, avg changed rate: 5.612%, num of queries: 26.5 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 96.100%, adv accuracy: 61.600%, avg changed rate: 4.874%, num of queries: 25.0 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 52.800%, adv accuracy: 45.800%, avg changed rate: 5.612%, num of queries: 26.5 diff --git a/TextFooler/output/ADFAR/nt1/prom_core_notata/results_log b/TextFooler/output/ADFAR/nt1/prom_core_notata/results_log index 2f6fda72..1cfccfd1 100644 --- a/TextFooler/output/ADFAR/nt1/prom_core_notata/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 27.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 27.3 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 27.3 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 27.3 diff --git a/TextFooler/output/ADFAR/nt1/prom_core_tata/results_log b/TextFooler/output/ADFAR/nt1/prom_core_tata/results_log index e34d50b5..2b5aa64c 100644 --- a/TextFooler/output/ADFAR/nt1/prom_core_tata/results_log +++ b/TextFooler/output/ADFAR/nt1/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 86.400%, avg changed rate: nan%, num of queries: 27.9 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 26.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 86.400%, avg changed rate: nan%, num of queries: 27.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 26.9 diff --git a/TextFooler/output/ADFAR/nt1/tf0/results_log b/TextFooler/output/ADFAR/nt1/tf0/results_log index b8daedec..e1eb35a4 100644 --- a/TextFooler/output/ADFAR/nt1/tf0/results_log +++ b/TextFooler/output/ADFAR/nt1/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 0.000%, adv accuracy: 0.000%, avg changed rate: nan%, num of queries: nan -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 38.4 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 0.000%, adv accuracy: 0.000%, avg changed rate: nan%, num of queries: nan +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 38.4 diff --git a/TextFooler/output/ADFAR/nt1/tf1/results_log b/TextFooler/output/ADFAR/nt1/tf1/results_log index 6d69da42..c01d2fa9 100644 --- a/TextFooler/output/ADFAR/nt1/tf1/results_log +++ b/TextFooler/output/ADFAR/nt1/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 59.900%, avg changed rate: 5.360%, num of queries: 35.1 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 51.100%, avg changed rate: nan%, num of queries: 38.3 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 59.900%, avg changed rate: 5.360%, num of queries: 35.1 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 51.100%, avg changed rate: nan%, num of queries: 38.3 diff --git a/TextFooler/output/ADFAR/nt1/tf2/results_log b/TextFooler/output/ADFAR/nt1/tf2/results_log index 3fb04aa2..f3ac67f9 100644 --- a/TextFooler/output/ADFAR/nt1/tf2/results_log +++ b/TextFooler/output/ADFAR/nt1/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 67.200%, adv accuracy: 50.400%, avg changed rate: 1.603%, num of queries: 34.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 38.3 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 67.200%, adv accuracy: 50.400%, avg changed rate: 1.603%, num of queries: 34.9 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 38.3 diff --git a/TextFooler/output/ADFAR/nt1/tf3/results_log b/TextFooler/output/ADFAR/nt1/tf3/results_log index addca925..f9fe1bdb 100644 --- a/TextFooler/output/ADFAR/nt1/tf3/results_log +++ b/TextFooler/output/ADFAR/nt1/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.500%, avg changed rate: 3.465%, num of queries: 37.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 3.700%, adv accuracy: 0.000%, avg changed rate: 1.231%, num of queries: 23.8 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.500%, avg changed rate: 3.465%, num of queries: 37.7 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 3.700%, adv accuracy: 0.000%, avg changed rate: 1.231%, num of queries: 23.8 diff --git a/TextFooler/output/ADFAR/nt1/tf4/results_log b/TextFooler/output/ADFAR/nt1/tf4/results_log index 9efa945d..f2a67a39 100644 --- a/TextFooler/output/ADFAR/nt1/tf4/results_log +++ b/TextFooler/output/ADFAR/nt1/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 44.600%, avg changed rate: 4.873%, num of queries: 36.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 54.500%, adv accuracy: 36.100%, avg changed rate: 3.820%, num of queries: 34.3 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 44.600%, avg changed rate: 4.873%, num of queries: 36.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 54.500%, adv accuracy: 36.100%, avg changed rate: 3.820%, num of queries: 34.3 diff --git a/TextFooler/output/ADFAR/nt2/0/results_log b/TextFooler/output/ADFAR/nt2/0/results_log index 59ac5a90..c8a12ead 100644 --- a/TextFooler/output/ADFAR/nt2/0/results_log +++ b/TextFooler/output/ADFAR/nt2/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 63.600%, avg changed rate: 2.699%, num of queries: 149.8 -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 79.100%, adv accuracy: 63.600%, avg changed rate: 2.191%, num of queries: 124.9 +For target model GUE/0/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 63.600%, avg changed rate: 2.699%, num of queries: 149.8 +For target model GUE/0/five_percent/cat.csv: original accuracy: 79.100%, adv accuracy: 63.600%, avg changed rate: 2.191%, num of queries: 124.9 diff --git a/TextFooler/output/ADFAR/nt2/1/results_log b/TextFooler/output/ADFAR/nt2/1/results_log index b806ec95..e0dd153c 100644 --- a/TextFooler/output/ADFAR/nt2/1/results_log +++ b/TextFooler/output/ADFAR/nt2/1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 7.600%, adv accuracy: 0.000%, avg changed rate: 1.003%, num of queries: 88.2 -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 49.600%, adv accuracy: 0.300%, avg changed rate: 3.878%, num of queries: 276.4 +For target model GUE/1/five_percent/cat.csv: original accuracy: 7.600%, adv accuracy: 0.000%, avg changed rate: 1.003%, num of queries: 88.2 +For target model GUE/1/five_percent/cat.csv: original accuracy: 49.600%, adv accuracy: 0.300%, avg changed rate: 3.878%, num of queries: 276.4 diff --git a/TextFooler/output/ADFAR/nt2/2/results_log b/TextFooler/output/ADFAR/nt2/2/results_log index 6b18aa92..1d78a8f9 100644 --- a/TextFooler/output/ADFAR/nt2/2/results_log +++ b/TextFooler/output/ADFAR/nt2/2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 85.300%, avg changed rate: 3.161%, num of queries: 186.3 -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 85.300%, avg changed rate: 2.819%, num of queries: 174.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 85.300%, avg changed rate: 3.161%, num of queries: 186.3 +For target model GUE/2/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 85.300%, avg changed rate: 2.819%, num of queries: 174.9 diff --git a/TextFooler/output/ADFAR/nt2/3/results_log b/TextFooler/output/ADFAR/nt2/3/results_log index 1d0a1ff1..25dcdbf0 100644 --- a/TextFooler/output/ADFAR/nt2/3/results_log +++ b/TextFooler/output/ADFAR/nt2/3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 89.300%, avg changed rate: 1.134%, num of queries: 85.6 -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 92.700%, adv accuracy: 89.300%, avg changed rate: 1.077%, num of queries: 72.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 89.300%, avg changed rate: 1.134%, num of queries: 85.6 +For target model GUE/3/five_percent/cat.csv: original accuracy: 92.700%, adv accuracy: 89.300%, avg changed rate: 1.077%, num of queries: 72.5 diff --git a/TextFooler/output/ADFAR/nt2/4/results_log b/TextFooler/output/ADFAR/nt2/4/results_log index 005ec785..24681349 100644 --- a/TextFooler/output/ADFAR/nt2/4/results_log +++ b/TextFooler/output/ADFAR/nt2/4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 57.800%, adv accuracy: 16.800%, avg changed rate: 4.658%, num of queries: 334.9 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 22.300%, adv accuracy: 15.300%, avg changed rate: 1.344%, num of queries: 100.8 +For target model GUE/4/five_percent/cat.csv: original accuracy: 57.800%, adv accuracy: 16.800%, avg changed rate: 4.658%, num of queries: 334.9 +For target model GUE/4/five_percent/cat.csv: original accuracy: 22.300%, adv accuracy: 15.300%, avg changed rate: 1.344%, num of queries: 100.8 diff --git a/TextFooler/output/ADFAR/nt2/H3/results_log b/TextFooler/output/ADFAR/nt2/H3/results_log index c709e320..6669ebed 100644 --- a/TextFooler/output/ADFAR/nt2/H3/results_log +++ b/TextFooler/output/ADFAR/nt2/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 69.000%, adv accuracy: 34.200%, avg changed rate: 3.231%, num of queries: 1054.4 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 69.000%, adv accuracy: 34.200%, avg changed rate: 3.231%, num of queries: 1054.4 diff --git a/TextFooler/output/ADFAR/nt2/H3K14ac/results_log b/TextFooler/output/ADFAR/nt2/H3K14ac/results_log index 144ff4b7..be35a7a1 100644 --- a/TextFooler/output/ADFAR/nt2/H3K14ac/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 26.500%, adv accuracy: 0.000%, avg changed rate: 0.206%, num of queries: 134.7 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 26.500%, adv accuracy: 0.000%, avg changed rate: 0.206%, num of queries: 134.7 diff --git a/TextFooler/output/ADFAR/nt2/H3K36me3/results_log b/TextFooler/output/ADFAR/nt2/H3K36me3/results_log index fa87c903..c9babb81 100644 --- a/TextFooler/output/ADFAR/nt2/H3K36me3/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 89.800%, adv accuracy: 0.000%, avg changed rate: 0.318%, num of queries: 163.5 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 89.800%, adv accuracy: 0.000%, avg changed rate: 0.318%, num of queries: 163.5 diff --git a/TextFooler/output/ADFAR/nt2/H3K4me1/results_log b/TextFooler/output/ADFAR/nt2/H3K4me1/results_log index 4ba3da41..b8baba50 100644 --- a/TextFooler/output/ADFAR/nt2/H3K4me1/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 55.800%, adv accuracy: 0.000%, avg changed rate: 0.216%, num of queries: 136.7 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 55.800%, adv accuracy: 0.000%, avg changed rate: 0.216%, num of queries: 136.7 diff --git a/TextFooler/output/ADFAR/nt2/H3K4me2/results_log b/TextFooler/output/ADFAR/nt2/H3K4me2/results_log index d5b2209f..657ea4c5 100644 --- a/TextFooler/output/ADFAR/nt2/H3K4me2/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 35.600%, adv accuracy: 0.000%, avg changed rate: 0.375%, num of queries: 173.2 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 35.600%, adv accuracy: 0.000%, avg changed rate: 0.375%, num of queries: 173.2 diff --git a/TextFooler/output/ADFAR/nt2/H3K4me3/results_log b/TextFooler/output/ADFAR/nt2/H3K4me3/results_log index eacc5f66..79bf2941 100644 --- a/TextFooler/output/ADFAR/nt2/H3K4me3/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 6.000%, adv accuracy: 0.000%, avg changed rate: 0.210%, num of queries: 135.8 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 6.000%, adv accuracy: 0.000%, avg changed rate: 0.210%, num of queries: 135.8 diff --git a/TextFooler/output/ADFAR/nt2/H3K79me3/results_log b/TextFooler/output/ADFAR/nt2/H3K79me3/results_log index 6eaf1e5c..19cbd22d 100644 --- a/TextFooler/output/ADFAR/nt2/H3K79me3/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 91.900%, adv accuracy: 0.000%, avg changed rate: 0.385%, num of queries: 198.2 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 91.900%, adv accuracy: 0.000%, avg changed rate: 0.385%, num of queries: 198.2 diff --git a/TextFooler/output/ADFAR/nt2/H3K9ac/results_log b/TextFooler/output/ADFAR/nt2/H3K9ac/results_log index 5e152d86..828a3628 100644 --- a/TextFooler/output/ADFAR/nt2/H3K9ac/results_log +++ b/TextFooler/output/ADFAR/nt2/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 44.300%, adv accuracy: 0.000%, avg changed rate: 0.356%, num of queries: 170.9 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 44.300%, adv accuracy: 0.000%, avg changed rate: 0.356%, num of queries: 170.9 diff --git a/TextFooler/output/ADFAR/nt2/H4/results_log b/TextFooler/output/ADFAR/nt2/H4/results_log index 8135af03..b3d58977 100644 --- a/TextFooler/output/ADFAR/nt2/H4/results_log +++ b/TextFooler/output/ADFAR/nt2/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 47.100%, adv accuracy: 34.300%, avg changed rate: 0.231%, num of queries: 162.3 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 47.100%, adv accuracy: 34.300%, avg changed rate: 0.231%, num of queries: 162.3 diff --git a/TextFooler/output/ADFAR/nt2/H4ac/results_log b/TextFooler/output/ADFAR/nt2/H4ac/results_log index aa46a951..40be7aba 100644 --- a/TextFooler/output/ADFAR/nt2/H4ac/results_log +++ b/TextFooler/output/ADFAR/nt2/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 52.300%, adv accuracy: 0.000%, avg changed rate: 0.676%, num of queries: 244.9 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 63.900%, adv accuracy: 0.000%, avg changed rate: 0.399%, num of queries: 179.5 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 52.300%, adv accuracy: 0.000%, avg changed rate: 0.676%, num of queries: 244.9 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 63.900%, adv accuracy: 0.000%, avg changed rate: 0.399%, num of queries: 179.5 diff --git a/TextFooler/output/ADFAR/nt2/prom_300_all/results_log b/TextFooler/output/ADFAR/nt2/prom_300_all/results_log index 801fd8a0..7496f0d5 100644 --- a/TextFooler/output/ADFAR/nt2/prom_300_all/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 29.900%, adv accuracy: 0.000%, avg changed rate: 0.415%, num of queries: 113.1 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 51.900%, adv accuracy: 0.000%, avg changed rate: 1.213%, num of queries: 239.7 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 29.900%, adv accuracy: 0.000%, avg changed rate: 0.415%, num of queries: 113.1 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 51.900%, adv accuracy: 0.000%, avg changed rate: 1.213%, num of queries: 239.7 diff --git a/TextFooler/output/ADFAR/nt2/prom_300_notata/results_log b/TextFooler/output/ADFAR/nt2/prom_300_notata/results_log index 827ec0b3..f286c0a1 100644 --- a/TextFooler/output/ADFAR/nt2/prom_300_notata/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 56.500%, adv accuracy: 0.400%, avg changed rate: 1.686%, num of queries: 319.8 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 32.400%, adv accuracy: 0.000%, avg changed rate: 0.433%, num of queries: 121.2 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 56.500%, adv accuracy: 0.400%, avg changed rate: 1.686%, num of queries: 319.8 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 32.400%, adv accuracy: 0.000%, avg changed rate: 0.433%, num of queries: 121.2 diff --git a/TextFooler/output/ADFAR/nt2/prom_300_tata/results_log b/TextFooler/output/ADFAR/nt2/prom_300_tata/results_log index 454a1dac..dda93e95 100644 --- a/TextFooler/output/ADFAR/nt2/prom_300_tata/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.200%, adv accuracy: 72.400%, avg changed rate: 0.728%, num of queries: 155.5 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 90.100%, adv accuracy: 72.400%, avg changed rate: 0.512%, num of queries: 132.2 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.200%, adv accuracy: 72.400%, avg changed rate: 0.728%, num of queries: 155.5 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 90.100%, adv accuracy: 72.400%, avg changed rate: 0.512%, num of queries: 132.2 diff --git a/TextFooler/output/ADFAR/nt2/prom_core_all/results_log b/TextFooler/output/ADFAR/nt2/prom_core_all/results_log index 436239cb..e47fd304 100644 --- a/TextFooler/output/ADFAR/nt2/prom_core_all/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 65.200%, adv accuracy: 0.000%, avg changed rate: 1.510%, num of queries: 66.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 54.900%, adv accuracy: 0.000%, avg changed rate: 2.157%, num of queries: 88.1 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 65.200%, adv accuracy: 0.000%, avg changed rate: 1.510%, num of queries: 66.6 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 54.900%, adv accuracy: 0.000%, avg changed rate: 2.157%, num of queries: 88.1 diff --git a/TextFooler/output/ADFAR/nt2/prom_core_notata/results_log b/TextFooler/output/ADFAR/nt2/prom_core_notata/results_log index 4d0bce60..f34f6de8 100644 --- a/TextFooler/output/ADFAR/nt2/prom_core_notata/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 39.200%, adv accuracy: 0.000%, avg changed rate: 1.480%, num of queries: 64.4 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 20.600%, adv accuracy: 0.000%, avg changed rate: 1.442%, num of queries: 63.0 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 39.200%, adv accuracy: 0.000%, avg changed rate: 1.480%, num of queries: 64.4 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 20.600%, adv accuracy: 0.000%, avg changed rate: 1.442%, num of queries: 63.0 diff --git a/TextFooler/output/ADFAR/nt2/prom_core_tata/results_log b/TextFooler/output/ADFAR/nt2/prom_core_tata/results_log index 66b98b6e..187b3608 100644 --- a/TextFooler/output/ADFAR/nt2/prom_core_tata/results_log +++ b/TextFooler/output/ADFAR/nt2/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 84.700%, adv accuracy: 72.400%, avg changed rate: 1.452%, num of queries: 62.7 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 80.100%, adv accuracy: 72.400%, avg changed rate: 1.466%, num of queries: 63.8 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 84.700%, adv accuracy: 72.400%, avg changed rate: 1.452%, num of queries: 62.7 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 80.100%, adv accuracy: 72.400%, avg changed rate: 1.466%, num of queries: 63.8 diff --git a/TextFooler/output/ADFAR/nt2/tf0/results_log b/TextFooler/output/ADFAR/nt2/tf0/results_log index 84fa0d9e..84c7bb7d 100644 --- a/TextFooler/output/ADFAR/nt2/tf0/results_log +++ b/TextFooler/output/ADFAR/nt2/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 15.200%, adv accuracy: 0.000%, avg changed rate: 0.990%, num of queries: 75.2 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 48.700%, adv accuracy: 0.000%, avg changed rate: 2.360%, num of queries: 146.6 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 15.200%, adv accuracy: 0.000%, avg changed rate: 0.990%, num of queries: 75.2 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 48.700%, adv accuracy: 0.000%, avg changed rate: 2.360%, num of queries: 146.6 diff --git a/TextFooler/output/ADFAR/nt2/tf1/results_log b/TextFooler/output/ADFAR/nt2/tf1/results_log index d93182b2..dec6245a 100644 --- a/TextFooler/output/ADFAR/nt2/tf1/results_log +++ b/TextFooler/output/ADFAR/nt2/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 1.423%, num of queries: 94.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 44.800%, adv accuracy: 0.000%, avg changed rate: 1.242%, num of queries: 82.4 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 1.423%, num of queries: 94.7 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 44.800%, adv accuracy: 0.000%, avg changed rate: 1.242%, num of queries: 82.4 diff --git a/TextFooler/output/ADFAR/nt2/tf2/results_log b/TextFooler/output/ADFAR/nt2/tf2/results_log index 91bc582c..67feffef 100644 --- a/TextFooler/output/ADFAR/nt2/tf2/results_log +++ b/TextFooler/output/ADFAR/nt2/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 15.900%, adv accuracy: 0.000%, avg changed rate: 1.115%, num of queries: 84.1 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 0.000%, avg changed rate: 1.746%, num of queries: 114.4 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 15.900%, adv accuracy: 0.000%, avg changed rate: 1.115%, num of queries: 84.1 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 0.000%, avg changed rate: 1.746%, num of queries: 114.4 diff --git a/TextFooler/output/ADFAR/nt2/tf3/results_log b/TextFooler/output/ADFAR/nt2/tf3/results_log index 951acd62..d16eaf99 100644 --- a/TextFooler/output/ADFAR/nt2/tf3/results_log +++ b/TextFooler/output/ADFAR/nt2/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 52.900%, adv accuracy: 0.000%, avg changed rate: 1.142%, num of queries: 80.2 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 55.000%, adv accuracy: 0.000%, avg changed rate: 1.113%, num of queries: 82.5 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 52.900%, adv accuracy: 0.000%, avg changed rate: 1.142%, num of queries: 80.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 55.000%, adv accuracy: 0.000%, avg changed rate: 1.113%, num of queries: 82.5 diff --git a/TextFooler/output/ADFAR/nt2/tf4/results_log b/TextFooler/output/ADFAR/nt2/tf4/results_log index 307237c6..a62d71bc 100644 --- a/TextFooler/output/ADFAR/nt2/tf4/results_log +++ b/TextFooler/output/ADFAR/nt2/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 63.000%, adv accuracy: 0.000%, avg changed rate: 1.278%, num of queries: 102.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 58.200%, adv accuracy: 0.000%, avg changed rate: 1.436%, num of queries: 111.6 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 63.000%, adv accuracy: 0.000%, avg changed rate: 1.278%, num of queries: 102.7 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 58.200%, adv accuracy: 0.000%, avg changed rate: 1.436%, num of queries: 111.6 diff --git a/TextFooler/output/ADFAR/og/0/results_log b/TextFooler/output/ADFAR/og/0/results_log index 62582450..9996c563 100644 --- a/TextFooler/output/ADFAR/og/0/results_log +++ b/TextFooler/output/ADFAR/og/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 54.100%, avg changed rate: nan%, num of queries: 22.2 -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 95.600%, adv accuracy: 0.000%, avg changed rate: 2.760%, num of queries: 161.6 +For target model GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 54.100%, avg changed rate: nan%, num of queries: 22.2 +For target model GUE/0/cat.csv: original accuracy: 95.600%, adv accuracy: 0.000%, avg changed rate: 2.760%, num of queries: 161.6 diff --git a/TextFooler/output/ADFAR/og/1/results_log b/TextFooler/output/ADFAR/og/1/results_log index d7322aea..fa725028 100644 --- a/TextFooler/output/ADFAR/og/1/results_log +++ b/TextFooler/output/ADFAR/og/1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 53.000%, adv accuracy: 53.000%, avg changed rate: nan%, num of queries: 22.1 -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 2.268%, num of queries: 136.5 +For target model GUE/1/cat.csv: original accuracy: 53.000%, adv accuracy: 53.000%, avg changed rate: nan%, num of queries: 22.1 +For target model GUE/1/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 2.268%, num of queries: 136.5 diff --git a/TextFooler/output/ADFAR/og/2/results_log b/TextFooler/output/ADFAR/og/2/results_log index bb94f600..118314a7 100644 --- a/TextFooler/output/ADFAR/og/2/results_log +++ b/TextFooler/output/ADFAR/og/2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 22.6 -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 3.737%, num of queries: 213.9 +For target model GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 22.6 +For target model GUE/2/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 3.737%, num of queries: 213.9 diff --git a/TextFooler/output/ADFAR/og/3/results_log b/TextFooler/output/ADFAR/og/3/results_log index 2002e59c..efd779ba 100644 --- a/TextFooler/output/ADFAR/og/3/results_log +++ b/TextFooler/output/ADFAR/og/3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 22.7 -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 99.000%, adv accuracy: 0.100%, avg changed rate: 3.413%, num of queries: 199.9 +For target model GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 22.7 +For target model GUE/3/cat.csv: original accuracy: 99.000%, adv accuracy: 0.100%, avg changed rate: 3.413%, num of queries: 199.9 diff --git a/TextFooler/output/ADFAR/og/4/results_log b/TextFooler/output/ADFAR/og/4/results_log index f071f7ef..64e1f146 100644 --- a/TextFooler/output/ADFAR/og/4/results_log +++ b/TextFooler/output/ADFAR/og/4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 22.0 -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 44.300%, adv accuracy: 0.000%, avg changed rate: 2.689%, num of queries: 157.7 +For target model GUE/4/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 22.0 +For target model GUE/4/cat.csv: original accuracy: 44.300%, adv accuracy: 0.000%, avg changed rate: 2.689%, num of queries: 157.7 diff --git a/TextFooler/output/ADFAR/og/H3/results_log b/TextFooler/output/ADFAR/og/H3/results_log index 0af89844..01c06217 100644 --- a/TextFooler/output/ADFAR/og/H3/results_log +++ b/TextFooler/output/ADFAR/og/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 95.900%, adv accuracy: 0.000%, avg changed rate: 2.155%, num of queries: 642.3 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 103.8 +For target model GUE/H3/cat.csv: original accuracy: 95.900%, adv accuracy: 0.000%, avg changed rate: 2.155%, num of queries: 642.3 +For target model GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 103.8 diff --git a/TextFooler/output/ADFAR/og/H3K14ac/results_log b/TextFooler/output/ADFAR/og/H3K14ac/results_log index 97fdb601..1e084826 100644 --- a/TextFooler/output/ADFAR/og/H3K14ac/results_log +++ b/TextFooler/output/ADFAR/og/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.284%, num of queries: 425.4 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 39.800%, adv accuracy: 39.800%, avg changed rate: nan%, num of queries: 104.3 +For target model GUE/H3K14ac/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.284%, num of queries: 425.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 39.800%, adv accuracy: 39.800%, avg changed rate: nan%, num of queries: 104.3 diff --git a/TextFooler/output/ADFAR/og/H3K36me3/results_log b/TextFooler/output/ADFAR/og/H3K36me3/results_log index 45b21375..9f168da8 100644 --- a/TextFooler/output/ADFAR/og/H3K36me3/results_log +++ b/TextFooler/output/ADFAR/og/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 95.100%, adv accuracy: 0.000%, avg changed rate: 0.865%, num of queries: 320.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 44.600%, adv accuracy: 44.600%, avg changed rate: nan%, num of queries: 104.3 +For target model GUE/H3K36me3/cat.csv: original accuracy: 95.100%, adv accuracy: 0.000%, avg changed rate: 0.865%, num of queries: 320.2 +For target model GUE/H3K36me3/cat.csv: original accuracy: 44.600%, adv accuracy: 44.600%, avg changed rate: nan%, num of queries: 104.3 diff --git a/TextFooler/output/ADFAR/og/H3K4me1/results_log b/TextFooler/output/ADFAR/og/H3K4me1/results_log index bc4aa318..b1cda705 100644 --- a/TextFooler/output/ADFAR/og/H3K4me1/results_log +++ b/TextFooler/output/ADFAR/og/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 85.700%, adv accuracy: 0.000%, avg changed rate: 0.909%, num of queries: 331.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 44.400%, adv accuracy: 44.400%, avg changed rate: nan%, num of queries: 104.3 +For target model GUE/H3K4me1/cat.csv: original accuracy: 85.700%, adv accuracy: 0.000%, avg changed rate: 0.909%, num of queries: 331.7 +For target model GUE/H3K4me1/cat.csv: original accuracy: 44.400%, adv accuracy: 44.400%, avg changed rate: nan%, num of queries: 104.3 diff --git a/TextFooler/output/ADFAR/og/H3K4me2/results_log b/TextFooler/output/ADFAR/og/H3K4me2/results_log index cfce582e..a0b337b8 100644 --- a/TextFooler/output/ADFAR/og/H3K4me2/results_log +++ b/TextFooler/output/ADFAR/og/H3K4me2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 40.800%, adv accuracy: 0.000%, avg changed rate: 0.496%, num of queries: 227.9 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 40.300%, adv accuracy: 40.300%, avg changed rate: nan%, num of queries: 103.9 +For target model GUE/H3K4me2/cat.csv: original accuracy: 40.800%, adv accuracy: 0.000%, avg changed rate: 0.496%, num of queries: 227.9 +For target model GUE/H3K4me2/cat.csv: original accuracy: 40.300%, adv accuracy: 40.300%, avg changed rate: nan%, num of queries: 103.9 diff --git a/TextFooler/output/ADFAR/og/H3K4me3/results_log b/TextFooler/output/ADFAR/og/H3K4me3/results_log index d9251561..e76c067a 100644 --- a/TextFooler/output/ADFAR/og/H3K4me3/results_log +++ b/TextFooler/output/ADFAR/og/H3K4me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 1.176%, num of queries: 399.1 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 47.200%, adv accuracy: 47.200%, avg changed rate: nan%, num of queries: 104.1 +For target model GUE/H3K4me3/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 1.176%, num of queries: 399.1 +For target model GUE/H3K4me3/cat.csv: original accuracy: 47.200%, adv accuracy: 47.200%, avg changed rate: nan%, num of queries: 104.1 diff --git a/TextFooler/output/ADFAR/og/H3K79me3/results_log b/TextFooler/output/ADFAR/og/H3K79me3/results_log index c75b4750..3cfadfac 100644 --- a/TextFooler/output/ADFAR/og/H3K79me3/results_log +++ b/TextFooler/output/ADFAR/og/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.926%, num of queries: 585.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 47.100%, adv accuracy: 47.100%, avg changed rate: nan%, num of queries: 104.1 +For target model GUE/H3K79me3/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.926%, num of queries: 585.7 +For target model GUE/H3K79me3/cat.csv: original accuracy: 47.100%, adv accuracy: 47.100%, avg changed rate: nan%, num of queries: 104.1 diff --git a/TextFooler/output/ADFAR/og/H3K9ac/results_log b/TextFooler/output/ADFAR/og/H3K9ac/results_log index 22c8c01f..5962302b 100644 --- a/TextFooler/output/ADFAR/og/H3K9ac/results_log +++ b/TextFooler/output/ADFAR/og/H3K9ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 82.600%, adv accuracy: 0.000%, avg changed rate: 1.024%, num of queries: 360.1 -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 45.400%, adv accuracy: 45.400%, avg changed rate: nan%, num of queries: 104.2 +For target model GUE/H3K9ac/cat.csv: original accuracy: 82.600%, adv accuracy: 0.000%, avg changed rate: 1.024%, num of queries: 360.1 +For target model GUE/H3K9ac/cat.csv: original accuracy: 45.400%, adv accuracy: 45.400%, avg changed rate: nan%, num of queries: 104.2 diff --git a/TextFooler/output/ADFAR/og/H4/results_log b/TextFooler/output/ADFAR/og/H4/results_log index 1ead18fb..6ff99823 100644 --- a/TextFooler/output/ADFAR/og/H4/results_log +++ b/TextFooler/output/ADFAR/og/H4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 97.900%, adv accuracy: 0.500%, avg changed rate: 3.402%, num of queries: 975.9 -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 55.000%, adv accuracy: 55.000%, avg changed rate: nan%, num of queries: 103.9 +For target model GUE/H4/cat.csv: original accuracy: 97.900%, adv accuracy: 0.500%, avg changed rate: 3.402%, num of queries: 975.9 +For target model GUE/H4/cat.csv: original accuracy: 55.000%, adv accuracy: 55.000%, avg changed rate: nan%, num of queries: 103.9 diff --git a/TextFooler/output/ADFAR/og/H4ac/results_log b/TextFooler/output/ADFAR/og/H4ac/results_log index 259cbf92..9e73910f 100644 --- a/TextFooler/output/ADFAR/og/H4ac/results_log +++ b/TextFooler/output/ADFAR/og/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 89.800%, adv accuracy: 0.000%, avg changed rate: 0.900%, num of queries: 329.2 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 46.000%, adv accuracy: 46.000%, avg changed rate: nan%, num of queries: 104.2 +For target model GUE/H4ac/cat.csv: original accuracy: 89.800%, adv accuracy: 0.000%, avg changed rate: 0.900%, num of queries: 329.2 +For target model GUE/H4ac/cat.csv: original accuracy: 46.000%, adv accuracy: 46.000%, avg changed rate: nan%, num of queries: 104.2 diff --git a/TextFooler/output/ADFAR/og/prom_300_all/results_log b/TextFooler/output/ADFAR/og/prom_300_all/results_log index f223c15e..77f1aaf3 100644 --- a/TextFooler/output/ADFAR/og/prom_300_all/results_log +++ b/TextFooler/output/ADFAR/og/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 96.600%, adv accuracy: 0.000%, avg changed rate: 2.189%, num of queries: 390.7 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 47.400%, adv accuracy: 47.400%, avg changed rate: nan%, num of queries: 63.0 +For target model GUE/prom_300_all/cat.csv: original accuracy: 96.600%, adv accuracy: 0.000%, avg changed rate: 2.189%, num of queries: 390.7 +For target model GUE/prom_300_all/cat.csv: original accuracy: 47.400%, adv accuracy: 47.400%, avg changed rate: nan%, num of queries: 63.0 diff --git a/TextFooler/output/ADFAR/og/prom_300_notata/results_log b/TextFooler/output/ADFAR/og/prom_300_notata/results_log index 59031b08..f350d2cd 100644 --- a/TextFooler/output/ADFAR/og/prom_300_notata/results_log +++ b/TextFooler/output/ADFAR/og/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 63.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 97.300%, adv accuracy: 0.000%, avg changed rate: 1.981%, num of queries: 359.8 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 48.300%, adv accuracy: 48.300%, avg changed rate: nan%, num of queries: 63.0 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 97.300%, adv accuracy: 0.000%, avg changed rate: 1.981%, num of queries: 359.8 diff --git a/TextFooler/output/ADFAR/og/prom_300_tata/results_log b/TextFooler/output/ADFAR/og/prom_300_tata/results_log index c206bfd9..da172a3a 100644 --- a/TextFooler/output/ADFAR/og/prom_300_tata/results_log +++ b/TextFooler/output/ADFAR/og/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 62.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 94.400%, adv accuracy: 0.000%, avg changed rate: 1.318%, num of queries: 260.1 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 62.6 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 94.400%, adv accuracy: 0.000%, avg changed rate: 1.318%, num of queries: 260.1 diff --git a/TextFooler/output/ADFAR/og/prom_core_all/results_log b/TextFooler/output/ADFAR/og/prom_core_all/results_log index 96897656..2b5d2c0e 100644 --- a/TextFooler/output/ADFAR/og/prom_core_all/results_log +++ b/TextFooler/output/ADFAR/og/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 90.100%, adv accuracy: 0.000%, avg changed rate: 3.217%, num of queries: 128.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 52.000%, adv accuracy: 52.000%, avg changed rate: nan%, num of queries: 16.1 +For target model GUE/prom_core_all/cat.csv: original accuracy: 90.100%, adv accuracy: 0.000%, avg changed rate: 3.217%, num of queries: 128.6 +For target model GUE/prom_core_all/cat.csv: original accuracy: 52.000%, adv accuracy: 52.000%, avg changed rate: nan%, num of queries: 16.1 diff --git a/TextFooler/output/ADFAR/og/prom_core_notata/results_log b/TextFooler/output/ADFAR/og/prom_core_notata/results_log index b08929a1..b64a79e3 100644 --- a/TextFooler/output/ADFAR/og/prom_core_notata/results_log +++ b/TextFooler/output/ADFAR/og/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 94.500%, adv accuracy: 0.000%, avg changed rate: 4.115%, num of queries: 159.8 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 50.900%, adv accuracy: 50.900%, avg changed rate: nan%, num of queries: 16.1 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 94.500%, adv accuracy: 0.000%, avg changed rate: 4.115%, num of queries: 159.8 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 50.900%, adv accuracy: 50.900%, avg changed rate: nan%, num of queries: 16.1 diff --git a/TextFooler/output/ADFAR/og/prom_core_tata/results_log b/TextFooler/output/ADFAR/og/prom_core_tata/results_log index 25e18f39..495d1ac6 100644 --- a/TextFooler/output/ADFAR/og/prom_core_tata/results_log +++ b/TextFooler/output/ADFAR/og/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 97.600%, adv accuracy: 0.100%, avg changed rate: 3.881%, num of queries: 154.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 48.600%, adv accuracy: 48.600%, avg changed rate: nan%, num of queries: 16.1 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 97.600%, adv accuracy: 0.100%, avg changed rate: 3.881%, num of queries: 154.3 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 48.600%, adv accuracy: 48.600%, avg changed rate: nan%, num of queries: 16.1 diff --git a/TextFooler/output/ADFAR/og/tf0/results_log b/TextFooler/output/ADFAR/og/tf0/results_log index 9879181f..f7a5e2b9 100644 --- a/TextFooler/output/ADFAR/og/tf0/results_log +++ b/TextFooler/output/ADFAR/og/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 21.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 3.548%, num of queries: 201.3 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 21.9 +For target model GUE/tf0/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 3.548%, num of queries: 201.3 diff --git a/TextFooler/output/ADFAR/og/tf1/results_log b/TextFooler/output/ADFAR/og/tf1/results_log index 4081e7f4..b153acd6 100644 --- a/TextFooler/output/ADFAR/og/tf1/results_log +++ b/TextFooler/output/ADFAR/og/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 21.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.600%, adv accuracy: 0.000%, avg changed rate: 2.100%, num of queries: 127.9 +For target model GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 21.9 +For target model GUE/tf1/cat.csv: original accuracy: 48.600%, adv accuracy: 0.000%, avg changed rate: 2.100%, num of queries: 127.9 diff --git a/TextFooler/output/ADFAR/og/tf2/results_log b/TextFooler/output/ADFAR/og/tf2/results_log index 4e555ec8..56be8cb9 100644 --- a/TextFooler/output/ADFAR/og/tf2/results_log +++ b/TextFooler/output/ADFAR/og/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 21.8 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 96.200%, adv accuracy: 0.000%, avg changed rate: 3.203%, num of queries: 183.7 +For target model GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 21.8 +For target model GUE/tf2/cat.csv: original accuracy: 96.200%, adv accuracy: 0.000%, avg changed rate: 3.203%, num of queries: 183.7 diff --git a/TextFooler/output/ADFAR/og/tf3/results_log b/TextFooler/output/ADFAR/og/tf3/results_log index a7cef1e1..e364c4d5 100644 --- a/TextFooler/output/ADFAR/og/tf3/results_log +++ b/TextFooler/output/ADFAR/og/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 22.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 62.800%, adv accuracy: 0.000%, avg changed rate: 2.518%, num of queries: 150.2 +For target model GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 22.5 +For target model GUE/tf3/cat.csv: original accuracy: 62.800%, adv accuracy: 0.000%, avg changed rate: 2.518%, num of queries: 150.2 diff --git a/TextFooler/output/ADFAR/og/tf4/results_log b/TextFooler/output/ADFAR/og/tf4/results_log index 4e2da611..c6e6c345 100644 --- a/TextFooler/output/ADFAR/og/tf4/results_log +++ b/TextFooler/output/ADFAR/og/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 22.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 3.987%, num of queries: 224.1 +For target model GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 22.0 +For target model GUE/tf4/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 3.987%, num of queries: 224.1 diff --git a/TextFooler/output/AT/dnabert/0/results_log b/TextFooler/output/AT/dnabert/0/results_log index 44405f47..435bb729 100644 --- a/TextFooler/output/AT/dnabert/0/results_log +++ b/TextFooler/output/AT/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 65.400%, avg changed rate: 2.259%, num of queries: 201.2 +For target model GUE/0/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 65.400%, avg changed rate: 2.259%, num of queries: 201.2 diff --git a/TextFooler/output/AT/dnabert/1/results_log b/TextFooler/output/AT/dnabert/1/results_log index da56885d..db7a5847 100644 --- a/TextFooler/output/AT/dnabert/1/results_log +++ b/TextFooler/output/AT/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 95.400%, adv accuracy: 5.900%, avg changed rate: 3.040%, num of queries: 223.9 +For target model GUE/1/five_percent/cat.csv: original accuracy: 95.400%, adv accuracy: 5.900%, avg changed rate: 3.040%, num of queries: 223.9 diff --git a/TextFooler/output/AT/dnabert/2/results_log b/TextFooler/output/AT/dnabert/2/results_log index 7ed7adf4..dbf4544a 100644 --- a/TextFooler/output/AT/dnabert/2/results_log +++ b/TextFooler/output/AT/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 85.700%, avg changed rate: 3.767%, num of queries: 227.1 +For target model GUE/2/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 85.700%, avg changed rate: 3.767%, num of queries: 227.1 diff --git a/TextFooler/output/AT/dnabert/3/results_log b/TextFooler/output/AT/dnabert/3/results_log index 8196b582..811ebb9f 100644 --- a/TextFooler/output/AT/dnabert/3/results_log +++ b/TextFooler/output/AT/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 89.400%, avg changed rate: 2.645%, num of queries: 166.6 +For target model GUE/3/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 89.400%, avg changed rate: 2.645%, num of queries: 166.6 diff --git a/TextFooler/output/AT/dnabert/4/results_log b/TextFooler/output/AT/dnabert/4/results_log index 73556d2e..04f300bf 100644 --- a/TextFooler/output/AT/dnabert/4/results_log +++ b/TextFooler/output/AT/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 87.800%, adv accuracy: 15.400%, avg changed rate: 2.114%, num of queries: 132.5 +For target model GUE/4/five_percent/cat.csv: original accuracy: 87.800%, adv accuracy: 15.400%, avg changed rate: 2.114%, num of queries: 132.5 diff --git a/TextFooler/output/AT/dnabert/H3/results_log b/TextFooler/output/AT/dnabert/H3/results_log index feaaf263..e9aebcfa 100644 --- a/TextFooler/output/AT/dnabert/H3/results_log +++ b/TextFooler/output/AT/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 37.500%, avg changed rate: 2.087%, num of queries: 998.2 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 37.500%, avg changed rate: 2.087%, num of queries: 998.2 diff --git a/TextFooler/output/AT/dnabert/H3K14ac/results_log b/TextFooler/output/AT/dnabert/H3K14ac/results_log index 90711ac1..b8bd7c3c 100644 --- a/TextFooler/output/AT/dnabert/H3K14ac/results_log +++ b/TextFooler/output/AT/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 84.900%, adv accuracy: 0.100%, avg changed rate: 1.241%, num of queries: 417.9 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 84.900%, adv accuracy: 0.100%, avg changed rate: 1.241%, num of queries: 417.9 diff --git a/TextFooler/output/AT/dnabert/H3K36me3/results_log b/TextFooler/output/AT/dnabert/H3K36me3/results_log index bfa5ba2e..e558ac81 100644 --- a/TextFooler/output/AT/dnabert/H3K36me3/results_log +++ b/TextFooler/output/AT/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 83.800%, adv accuracy: 0.100%, avg changed rate: 1.413%, num of queries: 460.9 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 83.800%, adv accuracy: 0.100%, avg changed rate: 1.413%, num of queries: 460.9 diff --git a/TextFooler/output/AT/dnabert/H3K4me1/results_log b/TextFooler/output/AT/dnabert/H3K4me1/results_log index fae9c450..6d0b6df9 100644 --- a/TextFooler/output/AT/dnabert/H3K4me1/results_log +++ b/TextFooler/output/AT/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 80.900%, adv accuracy: 0.000%, avg changed rate: 1.302%, num of queries: 428.0 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 80.900%, adv accuracy: 0.000%, avg changed rate: 1.302%, num of queries: 428.0 diff --git a/TextFooler/output/AT/dnabert/H3K4me2/results_log b/TextFooler/output/AT/dnabert/H3K4me2/results_log index 77d769b2..84f67361 100644 --- a/TextFooler/output/AT/dnabert/H3K4me2/results_log +++ b/TextFooler/output/AT/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 69.100%, adv accuracy: 1.300%, avg changed rate: 1.527%, num of queries: 594.7 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 69.100%, adv accuracy: 1.300%, avg changed rate: 1.527%, num of queries: 594.7 diff --git a/TextFooler/output/AT/dnabert/H3K4me3/results_log b/TextFooler/output/AT/dnabert/H3K4me3/results_log index 0d1506a0..c6b601dd 100644 --- a/TextFooler/output/AT/dnabert/H3K4me3/results_log +++ b/TextFooler/output/AT/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.900%, adv accuracy: 0.000%, avg changed rate: 1.160%, num of queries: 391.8 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.900%, adv accuracy: 0.000%, avg changed rate: 1.160%, num of queries: 391.8 diff --git a/TextFooler/output/AT/dnabert/H3K79me3/results_log b/TextFooler/output/AT/dnabert/H3K79me3/results_log index 36da9a80..de23675e 100644 --- a/TextFooler/output/AT/dnabert/H3K79me3/results_log +++ b/TextFooler/output/AT/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 1.100%, avg changed rate: 2.708%, num of queries: 835.4 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 1.100%, avg changed rate: 2.708%, num of queries: 835.4 diff --git a/TextFooler/output/AT/dnabert/H3K9ac/results_log b/TextFooler/output/AT/dnabert/H3K9ac/results_log index 6b520c06..c4984571 100644 --- a/TextFooler/output/AT/dnabert/H3K9ac/results_log +++ b/TextFooler/output/AT/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 75.400%, adv accuracy: 4.200%, avg changed rate: 2.411%, num of queries: 958.5 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 75.400%, adv accuracy: 4.200%, avg changed rate: 2.411%, num of queries: 958.5 diff --git a/TextFooler/output/AT/dnabert/H4/results_log b/TextFooler/output/AT/dnabert/H4/results_log index 4510eaa0..f68d742c 100644 --- a/TextFooler/output/AT/dnabert/H4/results_log +++ b/TextFooler/output/AT/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 36.600%, avg changed rate: 4.007%, num of queries: 1252.3 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 36.600%, avg changed rate: 4.007%, num of queries: 1252.3 diff --git a/TextFooler/output/AT/dnabert/H4ac/results_log b/TextFooler/output/AT/dnabert/H4ac/results_log index ac26268f..211595ea 100644 --- a/TextFooler/output/AT/dnabert/H4ac/results_log +++ b/TextFooler/output/AT/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 87.200%, adv accuracy: 0.000%, avg changed rate: 0.990%, num of queries: 349.5 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 87.200%, adv accuracy: 0.000%, avg changed rate: 0.990%, num of queries: 349.5 diff --git a/TextFooler/output/AT/dnabert/prom_300_all/results_log b/TextFooler/output/AT/dnabert/prom_300_all/results_log index abd133ea..42c1648f 100644 --- a/TextFooler/output/AT/dnabert/prom_300_all/results_log +++ b/TextFooler/output/AT/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 2.504%, num of queries: 440.4 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 2.504%, num of queries: 440.4 diff --git a/TextFooler/output/AT/dnabert/prom_300_notata/results_log b/TextFooler/output/AT/dnabert/prom_300_notata/results_log index 3f423cf3..df849b74 100644 --- a/TextFooler/output/AT/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/AT/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 28.300%, avg changed rate: 2.047%, num of queries: 1223.6 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 28.300%, avg changed rate: 2.047%, num of queries: 1223.6 diff --git a/TextFooler/output/AT/dnabert/prom_300_tata/results_log b/TextFooler/output/AT/dnabert/prom_300_tata/results_log index 4977563f..e3812c36 100644 --- a/TextFooler/output/AT/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/AT/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 72.600%, avg changed rate: 3.152%, num of queries: 557.7 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 72.600%, avg changed rate: 3.152%, num of queries: 557.7 diff --git a/TextFooler/output/AT/dnabert/prom_core_all/results_log b/TextFooler/output/AT/dnabert/prom_core_all/results_log index f3a52007..b29fa316 100644 --- a/TextFooler/output/AT/dnabert/prom_core_all/results_log +++ b/TextFooler/output/AT/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 84.500%, adv accuracy: 0.000%, avg changed rate: 3.087%, num of queries: 124.5 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 84.500%, adv accuracy: 0.000%, avg changed rate: 3.087%, num of queries: 124.5 diff --git a/TextFooler/output/AT/dnabert/prom_core_notata/results_log b/TextFooler/output/AT/dnabert/prom_core_notata/results_log index 903cc8c9..14dab932 100644 --- a/TextFooler/output/AT/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/AT/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 90.600%, adv accuracy: 0.600%, avg changed rate: 3.100%, num of queries: 130.2 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 90.600%, adv accuracy: 0.600%, avg changed rate: 3.100%, num of queries: 130.2 diff --git a/TextFooler/output/AT/dnabert/prom_core_tata/results_log b/TextFooler/output/AT/dnabert/prom_core_tata/results_log index d4a35880..7f23afd4 100644 --- a/TextFooler/output/AT/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/AT/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 96.300%, adv accuracy: 72.400%, avg changed rate: 2.606%, num of queries: 107.0 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 96.300%, adv accuracy: 72.400%, avg changed rate: 2.606%, num of queries: 107.0 diff --git a/TextFooler/output/AT/dnabert/tf0/results_log b/TextFooler/output/AT/dnabert/tf0/results_log index efb86059..3c0d404d 100644 --- a/TextFooler/output/AT/dnabert/tf0/results_log +++ b/TextFooler/output/AT/dnabert/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 81.900%, adv accuracy: 0.800%, avg changed rate: 4.080%, num of queries: 235.3 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 81.900%, adv accuracy: 0.800%, avg changed rate: 4.080%, num of queries: 235.3 diff --git a/TextFooler/output/AT/dnabert/tf1/results_log b/TextFooler/output/AT/dnabert/tf1/results_log index b93397be..adb93423 100644 --- a/TextFooler/output/AT/dnabert/tf1/results_log +++ b/TextFooler/output/AT/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 78.400%, adv accuracy: 0.000%, avg changed rate: 3.491%, num of queries: 198.9 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 78.400%, adv accuracy: 0.000%, avg changed rate: 3.491%, num of queries: 198.9 diff --git a/TextFooler/output/AT/dnabert/tf2/results_log b/TextFooler/output/AT/dnabert/tf2/results_log index d71dbcc1..5521f914 100644 --- a/TextFooler/output/AT/dnabert/tf2/results_log +++ b/TextFooler/output/AT/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 0.200%, avg changed rate: 2.956%, num of queries: 175.4 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 0.200%, avg changed rate: 2.956%, num of queries: 175.4 diff --git a/TextFooler/output/AT/dnabert/tf3/results_log b/TextFooler/output/AT/dnabert/tf3/results_log index 312e5c5e..a22bd5b5 100644 --- a/TextFooler/output/AT/dnabert/tf3/results_log +++ b/TextFooler/output/AT/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 77.400%, adv accuracy: 0.100%, avg changed rate: 3.608%, num of queries: 205.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 77.400%, adv accuracy: 0.100%, avg changed rate: 3.608%, num of queries: 205.2 diff --git a/TextFooler/output/AT/dnabert/tf4/results_log b/TextFooler/output/AT/dnabert/tf4/results_log index f38a53cf..90c54b5b 100644 --- a/TextFooler/output/AT/dnabert/tf4/results_log +++ b/TextFooler/output/AT/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 3.000%, avg changed rate: 3.722%, num of queries: 240.3 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 3.000%, avg changed rate: 3.722%, num of queries: 240.3 diff --git a/TextFooler/output/AT/hyena/0/results_log b/TextFooler/output/AT/hyena/0/results_log index ef2a12de..67be6d76 100644 --- a/TextFooler/output/AT/hyena/0/results_log +++ b/TextFooler/output/AT/hyena/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/AT/hyena/1/results_log b/TextFooler/output/AT/hyena/1/results_log index 7dc8b763..c602ddd6 100644 --- a/TextFooler/output/AT/hyena/1/results_log +++ b/TextFooler/output/AT/hyena/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 50.100%, adv accuracy: 18.600%, avg changed rate: 7.144%, num of queries: 120.9 +For target model GUE/1/five_percent/cat.csv: original accuracy: 50.100%, adv accuracy: 18.600%, avg changed rate: 7.144%, num of queries: 120.9 diff --git a/TextFooler/output/AT/hyena/2/results_log b/TextFooler/output/AT/hyena/2/results_log index cc71552b..7c40de0d 100644 --- a/TextFooler/output/AT/hyena/2/results_log +++ b/TextFooler/output/AT/hyena/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 diff --git a/TextFooler/output/AT/hyena/3/results_log b/TextFooler/output/AT/hyena/3/results_log index 4474ca86..2a76ba7f 100644 --- a/TextFooler/output/AT/hyena/3/results_log +++ b/TextFooler/output/AT/hyena/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 153.3 +For target model GUE/3/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 94.200%, avg changed rate: nan%, num of queries: 153.3 diff --git a/TextFooler/output/AT/hyena/4/results_log b/TextFooler/output/AT/hyena/4/results_log index 1b181fa4..e47ed970 100644 --- a/TextFooler/output/AT/hyena/4/results_log +++ b/TextFooler/output/AT/hyena/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 57.700%, adv accuracy: 17.900%, avg changed rate: 10.117%, num of queries: 114.1 +For target model GUE/4/five_percent/cat.csv: original accuracy: 57.700%, adv accuracy: 17.900%, avg changed rate: 10.117%, num of queries: 114.1 diff --git a/TextFooler/output/AT/hyena/H3/results_log b/TextFooler/output/AT/hyena/H3/results_log index 4d03a0fd..23f0d3d4 100644 --- a/TextFooler/output/AT/hyena/H3/results_log +++ b/TextFooler/output/AT/hyena/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 63.400%, adv accuracy: 63.400%, avg changed rate: nan%, num of queries: 749.7 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 63.400%, adv accuracy: 63.400%, avg changed rate: nan%, num of queries: 749.7 diff --git a/TextFooler/output/AT/hyena/H3K14ac/results_log b/TextFooler/output/AT/hyena/H3K14ac/results_log index 83759dee..62f21f50 100644 --- a/TextFooler/output/AT/hyena/H3K14ac/results_log +++ b/TextFooler/output/AT/hyena/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 56.900%, adv accuracy: 47.900%, avg changed rate: 6.991%, num of queries: 722.3 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 56.900%, adv accuracy: 47.900%, avg changed rate: 6.991%, num of queries: 722.3 diff --git a/TextFooler/output/AT/hyena/H3K36me3/results_log b/TextFooler/output/AT/hyena/H3K36me3/results_log index 5a24b3d6..280be9cd 100644 --- a/TextFooler/output/AT/hyena/H3K36me3/results_log +++ b/TextFooler/output/AT/hyena/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 55.700%, adv accuracy: 53.400%, avg changed rate: 10.539%, num of queries: 746.7 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 55.700%, adv accuracy: 53.400%, avg changed rate: 10.539%, num of queries: 746.7 diff --git a/TextFooler/output/AT/hyena/H3K4me1/results_log b/TextFooler/output/AT/hyena/H3K4me1/results_log index 7797ca7a..6e5d41da 100644 --- a/TextFooler/output/AT/hyena/H3K4me1/results_log +++ b/TextFooler/output/AT/hyena/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 25.900%, avg changed rate: 14.549%, num of queries: 678.5 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 51.100%, adv accuracy: 25.900%, avg changed rate: 14.549%, num of queries: 678.5 diff --git a/TextFooler/output/AT/hyena/H3K4me2/results_log b/TextFooler/output/AT/hyena/H3K4me2/results_log index c608ce6b..0299ca6e 100644 --- a/TextFooler/output/AT/hyena/H3K4me2/results_log +++ b/TextFooler/output/AT/hyena/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 30.100%, avg changed rate: 14.061%, num of queries: 721.7 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 46.400%, adv accuracy: 30.100%, avg changed rate: 14.061%, num of queries: 721.7 diff --git a/TextFooler/output/AT/hyena/H3K4me3/results_log b/TextFooler/output/AT/hyena/H3K4me3/results_log index 31af8462..69c02e83 100644 --- a/TextFooler/output/AT/hyena/H3K4me3/results_log +++ b/TextFooler/output/AT/hyena/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 52.100%, adv accuracy: 42.100%, avg changed rate: 12.590%, num of queries: 731.2 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 52.100%, adv accuracy: 42.100%, avg changed rate: 12.590%, num of queries: 731.2 diff --git a/TextFooler/output/AT/hyena/H3K79me3/results_log b/TextFooler/output/AT/hyena/H3K79me3/results_log index e10c019c..848ef09b 100644 --- a/TextFooler/output/AT/hyena/H3K79me3/results_log +++ b/TextFooler/output/AT/hyena/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 55.200%, adv accuracy: 55.000%, avg changed rate: 15.700%, num of queries: 749.1 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 55.200%, adv accuracy: 55.000%, avg changed rate: 15.700%, num of queries: 749.1 diff --git a/TextFooler/output/AT/hyena/H3K9ac/results_log b/TextFooler/output/AT/hyena/H3K9ac/results_log index 44620f77..e951f743 100644 --- a/TextFooler/output/AT/hyena/H3K9ac/results_log +++ b/TextFooler/output/AT/hyena/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 23.900%, avg changed rate: 5.670%, num of queries: 643.8 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 23.900%, avg changed rate: 5.670%, num of queries: 643.8 diff --git a/TextFooler/output/AT/hyena/H4/results_log b/TextFooler/output/AT/hyena/H4/results_log index eb458e0a..2a52ef57 100644 --- a/TextFooler/output/AT/hyena/H4/results_log +++ b/TextFooler/output/AT/hyena/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 63.900%, adv accuracy: 59.300%, avg changed rate: 18.791%, num of queries: 731.6 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 63.900%, adv accuracy: 59.300%, avg changed rate: 18.791%, num of queries: 731.6 diff --git a/TextFooler/output/AT/hyena/H4ac/results_log b/TextFooler/output/AT/hyena/H4ac/results_log index 69786b00..0543e0d0 100644 --- a/TextFooler/output/AT/hyena/H4ac/results_log +++ b/TextFooler/output/AT/hyena/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 46.500%, adv accuracy: 39.800%, avg changed rate: 16.137%, num of queries: 735.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 46.500%, adv accuracy: 39.800%, avg changed rate: 16.137%, num of queries: 735.7 diff --git a/TextFooler/output/AT/hyena/prom_300_all/results_log b/TextFooler/output/AT/hyena/prom_300_all/results_log index 8313bdb2..121ca117 100644 --- a/TextFooler/output/AT/hyena/prom_300_all/results_log +++ b/TextFooler/output/AT/hyena/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 450.9 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 450.9 diff --git a/TextFooler/output/AT/hyena/prom_300_notata/results_log b/TextFooler/output/AT/hyena/prom_300_notata/results_log index e1a205c2..2d9aaa48 100644 --- a/TextFooler/output/AT/hyena/prom_300_notata/results_log +++ b/TextFooler/output/AT/hyena/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 54.300%, adv accuracy: 14.900%, avg changed rate: 8.239%, num of queries: 369.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 54.300%, adv accuracy: 14.900%, avg changed rate: 8.239%, num of queries: 369.9 diff --git a/TextFooler/output/AT/hyena/prom_300_tata/results_log b/TextFooler/output/AT/hyena/prom_300_tata/results_log index 1ec4d690..a27790ea 100644 --- a/TextFooler/output/AT/hyena/prom_300_tata/results_log +++ b/TextFooler/output/AT/hyena/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 81.000%, avg changed rate: 8.314%, num of queries: 403.7 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 81.000%, avg changed rate: 8.314%, num of queries: 403.7 diff --git a/TextFooler/output/AT/hyena/prom_core_all/results_log b/TextFooler/output/AT/hyena/prom_core_all/results_log index 189d16ca..9af3642f 100644 --- a/TextFooler/output/AT/hyena/prom_core_all/results_log +++ b/TextFooler/output/AT/hyena/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.300%, adv accuracy: 47.300%, avg changed rate: nan%, num of queries: 105.6 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.300%, adv accuracy: 47.300%, avg changed rate: nan%, num of queries: 105.6 diff --git a/TextFooler/output/AT/hyena/prom_core_notata/results_log b/TextFooler/output/AT/hyena/prom_core_notata/results_log index c7675b27..5bfcc03b 100644 --- a/TextFooler/output/AT/hyena/prom_core_notata/results_log +++ b/TextFooler/output/AT/hyena/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 105.4 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 105.4 diff --git a/TextFooler/output/AT/hyena/prom_core_tata/results_log b/TextFooler/output/AT/hyena/prom_core_tata/results_log index bb2eb41f..969215f0 100644 --- a/TextFooler/output/AT/hyena/prom_core_tata/results_log +++ b/TextFooler/output/AT/hyena/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 86.400%, avg changed rate: nan%, num of queries: 104.7 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 86.400%, avg changed rate: nan%, num of queries: 104.7 diff --git a/TextFooler/output/AT/hyena/tf0/results_log b/TextFooler/output/AT/hyena/tf0/results_log index 4758141e..8505e98c 100644 --- a/TextFooler/output/AT/hyena/tf0/results_log +++ b/TextFooler/output/AT/hyena/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 diff --git a/TextFooler/output/AT/hyena/tf1/results_log b/TextFooler/output/AT/hyena/tf1/results_log index f5bd2b85..fcabb127 100644 --- a/TextFooler/output/AT/hyena/tf1/results_log +++ b/TextFooler/output/AT/hyena/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/AT/hyena/tf2/results_log b/TextFooler/output/AT/hyena/tf2/results_log index 59362ce3..5f04e6d2 100644 --- a/TextFooler/output/AT/hyena/tf2/results_log +++ b/TextFooler/output/AT/hyena/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/AT/hyena/tf3/results_log b/TextFooler/output/AT/hyena/tf3/results_log index 133bdd3b..8eaa47ca 100644 --- a/TextFooler/output/AT/hyena/tf3/results_log +++ b/TextFooler/output/AT/hyena/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/AT/hyena/tf4/results_log b/TextFooler/output/AT/hyena/tf4/results_log index b3b54b6f..1d5afa63 100644 --- a/TextFooler/output/AT/hyena/tf4/results_log +++ b/TextFooler/output/AT/hyena/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 49.800%, avg changed rate: nan%, num of queries: 152.4 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 49.800%, avg changed rate: nan%, num of queries: 152.4 diff --git a/TextFooler/output/AT/nt1/0/results_log b/TextFooler/output/AT/nt1/0/results_log index f0a53b6b..279e6d43 100644 --- a/TextFooler/output/AT/nt1/0/results_log +++ b/TextFooler/output/AT/nt1/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 97.600%, adv accuracy: 70.600%, avg changed rate: 3.641%, num of queries: 29.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 97.600%, adv accuracy: 70.600%, avg changed rate: 3.641%, num of queries: 29.3 diff --git a/TextFooler/output/AT/nt1/1/results_log b/TextFooler/output/AT/nt1/1/results_log index a626c269..a72d057a 100644 --- a/TextFooler/output/AT/nt1/1/results_log +++ b/TextFooler/output/AT/nt1/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 95.400%, adv accuracy: 53.500%, avg changed rate: 4.414%, num of queries: 32.6 +For target model GUE/1/five_percent/cat.csv: original accuracy: 95.400%, adv accuracy: 53.500%, avg changed rate: 4.414%, num of queries: 32.6 diff --git a/TextFooler/output/AT/nt1/2/results_log b/TextFooler/output/AT/nt1/2/results_log index b377b483..361db1cb 100644 --- a/TextFooler/output/AT/nt1/2/results_log +++ b/TextFooler/output/AT/nt1/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 88.900%, avg changed rate: 5.225%, num of queries: 31.0 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 88.900%, avg changed rate: 5.225%, num of queries: 31.0 diff --git a/TextFooler/output/AT/nt1/3/results_log b/TextFooler/output/AT/nt1/3/results_log index b40c78ea..8b897238 100644 --- a/TextFooler/output/AT/nt1/3/results_log +++ b/TextFooler/output/AT/nt1/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 91.700%, avg changed rate: 2.805%, num of queries: 29.8 +For target model GUE/3/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 91.700%, avg changed rate: 2.805%, num of queries: 29.8 diff --git a/TextFooler/output/AT/nt1/4/results_log b/TextFooler/output/AT/nt1/4/results_log index 63be6106..9c9d22bf 100644 --- a/TextFooler/output/AT/nt1/4/results_log +++ b/TextFooler/output/AT/nt1/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 29.800%, avg changed rate: 3.481%, num of queries: 28.9 +For target model GUE/4/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 29.800%, avg changed rate: 3.481%, num of queries: 28.9 diff --git a/TextFooler/output/AT/nt1/H3/results_log b/TextFooler/output/AT/nt1/H3/results_log index 9ec41583..f256870a 100644 --- a/TextFooler/output/AT/nt1/H3/results_log +++ b/TextFooler/output/AT/nt1/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 46.300%, avg changed rate: 2.319%, num of queries: 112.2 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 46.300%, avg changed rate: 2.319%, num of queries: 112.2 diff --git a/TextFooler/output/AT/nt1/H3K14ac/results_log b/TextFooler/output/AT/nt1/H3K14ac/results_log index 08d9048d..ba010735 100644 --- a/TextFooler/output/AT/nt1/H3K14ac/results_log +++ b/TextFooler/output/AT/nt1/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 81.700%, adv accuracy: 20.400%, avg changed rate: 1.558%, num of queries: 109.3 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 81.700%, adv accuracy: 20.400%, avg changed rate: 1.558%, num of queries: 109.3 diff --git a/TextFooler/output/AT/nt1/H3K36me3/results_log b/TextFooler/output/AT/nt1/H3K36me3/results_log index 75c04080..8b3257d2 100644 --- a/TextFooler/output/AT/nt1/H3K36me3/results_log +++ b/TextFooler/output/AT/nt1/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 10.800%, avg changed rate: 1.919%, num of queries: 105.4 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 10.800%, avg changed rate: 1.919%, num of queries: 105.4 diff --git a/TextFooler/output/AT/nt1/H3K4me1/results_log b/TextFooler/output/AT/nt1/H3K4me1/results_log index 28e58515..ff71cae5 100644 --- a/TextFooler/output/AT/nt1/H3K4me1/results_log +++ b/TextFooler/output/AT/nt1/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 84.100%, adv accuracy: 7.900%, avg changed rate: 2.043%, num of queries: 104.7 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 84.100%, adv accuracy: 7.900%, avg changed rate: 2.043%, num of queries: 104.7 diff --git a/TextFooler/output/AT/nt1/H3K4me2/results_log b/TextFooler/output/AT/nt1/H3K4me2/results_log index 66b293ec..d00403a6 100644 --- a/TextFooler/output/AT/nt1/H3K4me2/results_log +++ b/TextFooler/output/AT/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 76.500%, adv accuracy: 36.700%, avg changed rate: 1.261%, num of queries: 120.4 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 76.500%, adv accuracy: 36.700%, avg changed rate: 1.261%, num of queries: 120.4 diff --git a/TextFooler/output/AT/nt1/H3K4me3/results_log b/TextFooler/output/AT/nt1/H3K4me3/results_log index 447a4b37..359d5d31 100644 --- a/TextFooler/output/AT/nt1/H3K4me3/results_log +++ b/TextFooler/output/AT/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.100%, adv accuracy: 6.000%, avg changed rate: 1.620%, num of queries: 101.2 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.100%, adv accuracy: 6.000%, avg changed rate: 1.620%, num of queries: 101.2 diff --git a/TextFooler/output/AT/nt1/H3K79me3/results_log b/TextFooler/output/AT/nt1/H3K79me3/results_log index d9d0f6d9..81e1b46b 100644 --- a/TextFooler/output/AT/nt1/H3K79me3/results_log +++ b/TextFooler/output/AT/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 90.700%, adv accuracy: 12.100%, avg changed rate: 2.295%, num of queries: 108.0 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 90.700%, adv accuracy: 12.100%, avg changed rate: 2.295%, num of queries: 108.0 diff --git a/TextFooler/output/AT/nt1/H3K9ac/results_log b/TextFooler/output/AT/nt1/H3K9ac/results_log index 1f9858c9..7494e4d0 100644 --- a/TextFooler/output/AT/nt1/H3K9ac/results_log +++ b/TextFooler/output/AT/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 89.400%, adv accuracy: 22.000%, avg changed rate: 1.565%, num of queries: 109.4 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 89.400%, adv accuracy: 22.000%, avg changed rate: 1.565%, num of queries: 109.4 diff --git a/TextFooler/output/AT/nt1/H4/results_log b/TextFooler/output/AT/nt1/H4/results_log index e55c8325..2222cd71 100644 --- a/TextFooler/output/AT/nt1/H4/results_log +++ b/TextFooler/output/AT/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 52.500%, avg changed rate: 2.465%, num of queries: 116.1 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 52.500%, avg changed rate: 2.465%, num of queries: 116.1 diff --git a/TextFooler/output/AT/nt1/H4ac/results_log b/TextFooler/output/AT/nt1/H4ac/results_log index 0f34c21a..78a4c9b2 100644 --- a/TextFooler/output/AT/nt1/H4ac/results_log +++ b/TextFooler/output/AT/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 84.400%, adv accuracy: 20.100%, avg changed rate: 1.378%, num of queries: 108.2 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 84.400%, adv accuracy: 20.100%, avg changed rate: 1.378%, num of queries: 108.2 diff --git a/TextFooler/output/AT/nt1/prom_300_all/results_log b/TextFooler/output/AT/nt1/prom_300_all/results_log index abc5a67b..240b54a5 100644 --- a/TextFooler/output/AT/nt1/prom_300_all/results_log +++ b/TextFooler/output/AT/nt1/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.300%, adv accuracy: 35.000%, avg changed rate: 2.632%, num of queries: 72.1 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.300%, adv accuracy: 35.000%, avg changed rate: 2.632%, num of queries: 72.1 diff --git a/TextFooler/output/AT/nt1/prom_300_notata/results_log b/TextFooler/output/AT/nt1/prom_300_notata/results_log index 82ed508c..a7cac0a6 100644 --- a/TextFooler/output/AT/nt1/prom_300_notata/results_log +++ b/TextFooler/output/AT/nt1/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.500%, adv accuracy: 33.700%, avg changed rate: 2.679%, num of queries: 72.0 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.500%, adv accuracy: 33.700%, avg changed rate: 2.679%, num of queries: 72.0 diff --git a/TextFooler/output/AT/nt1/prom_300_tata/results_log b/TextFooler/output/AT/nt1/prom_300_tata/results_log index 9b50414b..709a6841 100644 --- a/TextFooler/output/AT/nt1/prom_300_tata/results_log +++ b/TextFooler/output/AT/nt1/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 81.600%, avg changed rate: 2.893%, num of queries: 72.2 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 81.600%, avg changed rate: 2.893%, num of queries: 72.2 diff --git a/TextFooler/output/AT/nt1/prom_core_all/results_log b/TextFooler/output/AT/nt1/prom_core_all/results_log index 95a8a2e3..f2a86bf1 100644 --- a/TextFooler/output/AT/nt1/prom_core_all/results_log +++ b/TextFooler/output/AT/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 86.600%, adv accuracy: 29.600%, avg changed rate: 4.323%, num of queries: 22.3 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 86.600%, adv accuracy: 29.600%, avg changed rate: 4.323%, num of queries: 22.3 diff --git a/TextFooler/output/AT/nt1/prom_core_notata/results_log b/TextFooler/output/AT/nt1/prom_core_notata/results_log index adf6f531..4b837bea 100644 --- a/TextFooler/output/AT/nt1/prom_core_notata/results_log +++ b/TextFooler/output/AT/nt1/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 31.200%, avg changed rate: 4.301%, num of queries: 22.5 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 31.200%, avg changed rate: 4.301%, num of queries: 22.5 diff --git a/TextFooler/output/AT/nt1/prom_core_tata/results_log b/TextFooler/output/AT/nt1/prom_core_tata/results_log index 6ea805ab..af62f93d 100644 --- a/TextFooler/output/AT/nt1/prom_core_tata/results_log +++ b/TextFooler/output/AT/nt1/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 85.800%, avg changed rate: 5.768%, num of queries: 24.1 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 85.800%, avg changed rate: 5.768%, num of queries: 24.1 diff --git a/TextFooler/output/AT/nt1/tf0/results_log b/TextFooler/output/AT/nt1/tf0/results_log index d5b7382d..f3289b5c 100644 --- a/TextFooler/output/AT/nt1/tf0/results_log +++ b/TextFooler/output/AT/nt1/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 37.800%, avg changed rate: 3.549%, num of queries: 32.0 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 37.800%, avg changed rate: 3.549%, num of queries: 32.0 diff --git a/TextFooler/output/AT/nt1/tf1/results_log b/TextFooler/output/AT/nt1/tf1/results_log index 65f8a5f6..3f646d23 100644 --- a/TextFooler/output/AT/nt1/tf1/results_log +++ b/TextFooler/output/AT/nt1/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 35.200%, avg changed rate: 3.376%, num of queries: 31.6 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 35.200%, avg changed rate: 3.376%, num of queries: 31.6 diff --git a/TextFooler/output/AT/nt1/tf2/results_log b/TextFooler/output/AT/nt1/tf2/results_log index cf62d805..ba72b898 100644 --- a/TextFooler/output/AT/nt1/tf2/results_log +++ b/TextFooler/output/AT/nt1/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 92.500%, adv accuracy: 26.500%, avg changed rate: 3.671%, num of queries: 30.4 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 92.500%, adv accuracy: 26.500%, avg changed rate: 3.671%, num of queries: 30.4 diff --git a/TextFooler/output/AT/nt1/tf3/results_log b/TextFooler/output/AT/nt1/tf3/results_log index a9e6f917..6da5788c 100644 --- a/TextFooler/output/AT/nt1/tf3/results_log +++ b/TextFooler/output/AT/nt1/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 79.900%, adv accuracy: 35.500%, avg changed rate: 3.740%, num of queries: 31.8 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 79.900%, adv accuracy: 35.500%, avg changed rate: 3.740%, num of queries: 31.8 diff --git a/TextFooler/output/AT/nt1/tf4/results_log b/TextFooler/output/AT/nt1/tf4/results_log index c473cbea..c2cbe2a2 100644 --- a/TextFooler/output/AT/nt1/tf4/results_log +++ b/TextFooler/output/AT/nt1/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 35.900%, avg changed rate: 4.402%, num of queries: 31.4 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 35.900%, avg changed rate: 4.402%, num of queries: 31.4 diff --git a/TextFooler/output/AT/nt2/0/results_log b/TextFooler/output/AT/nt2/0/results_log index 43daa0f5..bffb2b56 100644 --- a/TextFooler/output/AT/nt2/0/results_log +++ b/TextFooler/output/AT/nt2/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 63.600%, avg changed rate: 2.233%, num of queries: 156.5 +For target model GUE/0/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 63.600%, avg changed rate: 2.233%, num of queries: 156.5 diff --git a/TextFooler/output/AT/nt2/1/results_log b/TextFooler/output/AT/nt2/1/results_log index c7bb43cc..aa4db991 100644 --- a/TextFooler/output/AT/nt2/1/results_log +++ b/TextFooler/output/AT/nt2/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 0.200%, avg changed rate: 3.071%, num of queries: 184.9 +For target model GUE/1/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 0.200%, avg changed rate: 3.071%, num of queries: 184.9 diff --git a/TextFooler/output/AT/nt2/2/results_log b/TextFooler/output/AT/nt2/2/results_log index 3c462620..fa458633 100644 --- a/TextFooler/output/AT/nt2/2/results_log +++ b/TextFooler/output/AT/nt2/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 98.400%, adv accuracy: 85.300%, avg changed rate: 3.560%, num of queries: 205.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 98.400%, adv accuracy: 85.300%, avg changed rate: 3.560%, num of queries: 205.9 diff --git a/TextFooler/output/AT/nt2/3/results_log b/TextFooler/output/AT/nt2/3/results_log index 1bd2d915..f3032d64 100644 --- a/TextFooler/output/AT/nt2/3/results_log +++ b/TextFooler/output/AT/nt2/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 89.300%, avg changed rate: 2.591%, num of queries: 155.4 +For target model GUE/3/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 89.300%, avg changed rate: 2.591%, num of queries: 155.4 diff --git a/TextFooler/output/AT/nt2/4/results_log b/TextFooler/output/AT/nt2/4/results_log index 5f50fe38..b5707830 100644 --- a/TextFooler/output/AT/nt2/4/results_log +++ b/TextFooler/output/AT/nt2/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 67.800%, adv accuracy: 15.400%, avg changed rate: 2.524%, num of queries: 149.0 +For target model GUE/4/five_percent/cat.csv: original accuracy: 67.800%, adv accuracy: 15.400%, avg changed rate: 2.524%, num of queries: 149.0 diff --git a/TextFooler/output/AT/nt2/H3/results_log b/TextFooler/output/AT/nt2/H3/results_log index 29ff9214..2e2b990a 100644 --- a/TextFooler/output/AT/nt2/H3/results_log +++ b/TextFooler/output/AT/nt2/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 91.600%, adv accuracy: 32.700%, avg changed rate: 1.249%, num of queries: 399.4 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 91.600%, adv accuracy: 32.700%, avg changed rate: 1.249%, num of queries: 399.4 diff --git a/TextFooler/output/AT/nt2/H3K14ac/results_log b/TextFooler/output/AT/nt2/H3K14ac/results_log index b5091ae6..b7e9e5a6 100644 --- a/TextFooler/output/AT/nt2/H3K14ac/results_log +++ b/TextFooler/output/AT/nt2/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 83.200%, adv accuracy: 0.000%, avg changed rate: 1.321%, num of queries: 393.0 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 83.200%, adv accuracy: 0.000%, avg changed rate: 1.321%, num of queries: 393.0 diff --git a/TextFooler/output/AT/nt2/H3K36me3/results_log b/TextFooler/output/AT/nt2/H3K36me3/results_log index f9f6c8eb..4ee3dfc0 100644 --- a/TextFooler/output/AT/nt2/H3K36me3/results_log +++ b/TextFooler/output/AT/nt2/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 0.686%, num of queries: 246.2 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 0.686%, num of queries: 246.2 diff --git a/TextFooler/output/AT/nt2/H3K4me1/results_log b/TextFooler/output/AT/nt2/H3K4me1/results_log index 054d41cb..d0df0429 100644 --- a/TextFooler/output/AT/nt2/H3K4me1/results_log +++ b/TextFooler/output/AT/nt2/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 82.000%, adv accuracy: 0.000%, avg changed rate: 0.870%, num of queries: 298.9 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 82.000%, adv accuracy: 0.000%, avg changed rate: 0.870%, num of queries: 298.9 diff --git a/TextFooler/output/AT/nt2/H3K4me2/results_log b/TextFooler/output/AT/nt2/H3K4me2/results_log index f33ed1ab..3756ed80 100644 --- a/TextFooler/output/AT/nt2/H3K4me2/results_log +++ b/TextFooler/output/AT/nt2/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 77.900%, adv accuracy: 0.000%, avg changed rate: 0.631%, num of queries: 230.9 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 77.900%, adv accuracy: 0.000%, avg changed rate: 0.631%, num of queries: 230.9 diff --git a/TextFooler/output/AT/nt2/H3K4me3/results_log b/TextFooler/output/AT/nt2/H3K4me3/results_log index 39c2e876..10199bc5 100644 --- a/TextFooler/output/AT/nt2/H3K4me3/results_log +++ b/TextFooler/output/AT/nt2/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.600%, adv accuracy: 0.000%, avg changed rate: 0.639%, num of queries: 235.6 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 75.600%, adv accuracy: 0.000%, avg changed rate: 0.639%, num of queries: 235.6 diff --git a/TextFooler/output/AT/nt2/H3K79me3/results_log b/TextFooler/output/AT/nt2/H3K79me3/results_log index 413e699e..571eb239 100644 --- a/TextFooler/output/AT/nt2/H3K79me3/results_log +++ b/TextFooler/output/AT/nt2/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 85.100%, adv accuracy: 0.000%, avg changed rate: 1.267%, num of queries: 390.3 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 85.100%, adv accuracy: 0.000%, avg changed rate: 1.267%, num of queries: 390.3 diff --git a/TextFooler/output/AT/nt2/H3K9ac/results_log b/TextFooler/output/AT/nt2/H3K9ac/results_log index 007a08f0..2deabf94 100644 --- a/TextFooler/output/AT/nt2/H3K9ac/results_log +++ b/TextFooler/output/AT/nt2/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 84.000%, adv accuracy: 0.000%, avg changed rate: 0.973%, num of queries: 312.6 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 84.000%, adv accuracy: 0.000%, avg changed rate: 0.973%, num of queries: 312.6 diff --git a/TextFooler/output/AT/nt2/H4/results_log b/TextFooler/output/AT/nt2/H4/results_log index de0b6581..a4fb1a32 100644 --- a/TextFooler/output/AT/nt2/H4/results_log +++ b/TextFooler/output/AT/nt2/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 34.300%, avg changed rate: 1.131%, num of queries: 365.6 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 34.300%, avg changed rate: 1.131%, num of queries: 365.6 diff --git a/TextFooler/output/AT/nt2/H4ac/results_log b/TextFooler/output/AT/nt2/H4ac/results_log index 2b07b96c..2adc8f99 100644 --- a/TextFooler/output/AT/nt2/H4ac/results_log +++ b/TextFooler/output/AT/nt2/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 87.400%, adv accuracy: 0.000%, avg changed rate: 0.637%, num of queries: 236.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 87.400%, adv accuracy: 0.000%, avg changed rate: 0.637%, num of queries: 236.7 diff --git a/TextFooler/output/AT/nt2/prom_300_all/results_log b/TextFooler/output/AT/nt2/prom_300_all/results_log index 21637c64..7702b095 100644 --- a/TextFooler/output/AT/nt2/prom_300_all/results_log +++ b/TextFooler/output/AT/nt2/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.000%, adv accuracy: 0.000%, avg changed rate: 1.175%, num of queries: 221.6 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.000%, adv accuracy: 0.000%, avg changed rate: 1.175%, num of queries: 221.6 diff --git a/TextFooler/output/AT/nt2/prom_300_notata/results_log b/TextFooler/output/AT/nt2/prom_300_notata/results_log index f055abe0..cbfbe37f 100644 --- a/TextFooler/output/AT/nt2/prom_300_notata/results_log +++ b/TextFooler/output/AT/nt2/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 0.000%, avg changed rate: 1.229%, num of queries: 247.1 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 0.000%, avg changed rate: 1.229%, num of queries: 247.1 diff --git a/TextFooler/output/AT/nt2/prom_300_tata/results_log b/TextFooler/output/AT/nt2/prom_300_tata/results_log index 2d52ddb6..6277bb2e 100644 --- a/TextFooler/output/AT/nt2/prom_300_tata/results_log +++ b/TextFooler/output/AT/nt2/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 72.400%, avg changed rate: 1.081%, num of queries: 202.2 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 72.400%, avg changed rate: 1.081%, num of queries: 202.2 diff --git a/TextFooler/output/AT/nt2/prom_core_all/results_log b/TextFooler/output/AT/nt2/prom_core_all/results_log index 1ed2b6a4..a50103da 100644 --- a/TextFooler/output/AT/nt2/prom_core_all/results_log +++ b/TextFooler/output/AT/nt2/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.400%, adv accuracy: 0.000%, avg changed rate: 1.960%, num of queries: 81.0 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.400%, adv accuracy: 0.000%, avg changed rate: 1.960%, num of queries: 81.0 diff --git a/TextFooler/output/AT/nt2/prom_core_notata/results_log b/TextFooler/output/AT/nt2/prom_core_notata/results_log index cfb05427..67fa1458 100644 --- a/TextFooler/output/AT/nt2/prom_core_notata/results_log +++ b/TextFooler/output/AT/nt2/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 0.000%, avg changed rate: 1.755%, num of queries: 74.2 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 0.000%, avg changed rate: 1.755%, num of queries: 74.2 diff --git a/TextFooler/output/AT/nt2/prom_core_tata/results_log b/TextFooler/output/AT/nt2/prom_core_tata/results_log index cbf17502..4a98f91b 100644 --- a/TextFooler/output/AT/nt2/prom_core_tata/results_log +++ b/TextFooler/output/AT/nt2/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 72.600%, avg changed rate: 3.540%, num of queries: 134.7 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 72.600%, avg changed rate: 3.540%, num of queries: 134.7 diff --git a/TextFooler/output/AT/nt2/tf0/results_log b/TextFooler/output/AT/nt2/tf0/results_log index cf9cdbf9..eae890d0 100644 --- a/TextFooler/output/AT/nt2/tf0/results_log +++ b/TextFooler/output/AT/nt2/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 73.400%, adv accuracy: 0.000%, avg changed rate: 2.705%, num of queries: 152.6 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 73.400%, adv accuracy: 0.000%, avg changed rate: 2.705%, num of queries: 152.6 diff --git a/TextFooler/output/AT/nt2/tf1/results_log b/TextFooler/output/AT/nt2/tf1/results_log index 9457fd48..204e4778 100644 --- a/TextFooler/output/AT/nt2/tf1/results_log +++ b/TextFooler/output/AT/nt2/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 81.800%, adv accuracy: 0.000%, avg changed rate: 1.945%, num of queries: 115.5 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 81.800%, adv accuracy: 0.000%, avg changed rate: 1.945%, num of queries: 115.5 diff --git a/TextFooler/output/AT/nt2/tf2/results_log b/TextFooler/output/AT/nt2/tf2/results_log index 57bd6faf..be246f21 100644 --- a/TextFooler/output/AT/nt2/tf2/results_log +++ b/TextFooler/output/AT/nt2/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 66.200%, adv accuracy: 0.100%, avg changed rate: 2.569%, num of queries: 148.6 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 66.200%, adv accuracy: 0.100%, avg changed rate: 2.569%, num of queries: 148.6 diff --git a/TextFooler/output/AT/nt2/tf3/results_log b/TextFooler/output/AT/nt2/tf3/results_log index 2ee29ffb..93213226 100644 --- a/TextFooler/output/AT/nt2/tf3/results_log +++ b/TextFooler/output/AT/nt2/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 85.400%, adv accuracy: 0.100%, avg changed rate: 1.899%, num of queries: 119.1 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 85.400%, adv accuracy: 0.100%, avg changed rate: 1.899%, num of queries: 119.1 diff --git a/TextFooler/output/AT/nt2/tf4/results_log b/TextFooler/output/AT/nt2/tf4/results_log index 035c17d3..e24b8bbc 100644 --- a/TextFooler/output/AT/nt2/tf4/results_log +++ b/TextFooler/output/AT/nt2/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 2.385%, num of queries: 146.0 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 2.385%, num of queries: 146.0 diff --git a/TextFooler/output/AT/og/0/results_log b/TextFooler/output/AT/og/0/results_log index d50a53a9..d8f14e76 100644 --- a/TextFooler/output/AT/og/0/results_log +++ b/TextFooler/output/AT/og/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 96.400%, adv accuracy: 63.600%, avg changed rate: 2.925%, num of queries: 170.6 +For target model GUE/0/five_percent/cat.csv: original accuracy: 96.400%, adv accuracy: 63.600%, avg changed rate: 2.925%, num of queries: 170.6 diff --git a/TextFooler/output/AT/og/1/results_log b/TextFooler/output/AT/og/1/results_log index a2aeb309..4136dbcb 100644 --- a/TextFooler/output/AT/og/1/results_log +++ b/TextFooler/output/AT/og/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 79.000%, adv accuracy: 1.300%, avg changed rate: 5.867%, num of queries: 331.3 +For target model GUE/1/five_percent/cat.csv: original accuracy: 79.000%, adv accuracy: 1.300%, avg changed rate: 5.867%, num of queries: 331.3 diff --git a/TextFooler/output/AT/og/2/results_log b/TextFooler/output/AT/og/2/results_log index 5b6312e9..20d3f5e3 100644 --- a/TextFooler/output/AT/og/2/results_log +++ b/TextFooler/output/AT/og/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 85.300%, avg changed rate: 4.541%, num of queries: 251.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 85.300%, avg changed rate: 4.541%, num of queries: 251.9 diff --git a/TextFooler/output/AT/og/3/results_log b/TextFooler/output/AT/og/3/results_log index 109ac13e..43430eae 100644 --- a/TextFooler/output/AT/og/3/results_log +++ b/TextFooler/output/AT/og/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 89.400%, avg changed rate: 4.290%, num of queries: 252.2 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 89.400%, avg changed rate: 4.290%, num of queries: 252.2 diff --git a/TextFooler/output/AT/og/4/results_log b/TextFooler/output/AT/og/4/results_log index a87cda9e..2a77ee9f 100644 --- a/TextFooler/output/AT/og/4/results_log +++ b/TextFooler/output/AT/og/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 86.800%, adv accuracy: 15.300%, avg changed rate: 1.947%, num of queries: 120.3 +For target model GUE/4/five_percent/cat.csv: original accuracy: 86.800%, adv accuracy: 15.300%, avg changed rate: 1.947%, num of queries: 120.3 diff --git a/TextFooler/output/AT/og/H3/results_log b/TextFooler/output/AT/og/H3/results_log index ab4ba57e..aa4bd356 100644 --- a/TextFooler/output/AT/og/H3/results_log +++ b/TextFooler/output/AT/og/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 32.600%, avg changed rate: 2.046%, num of queries: 615.6 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 96.600%, adv accuracy: 32.600%, avg changed rate: 2.046%, num of queries: 615.6 diff --git a/TextFooler/output/AT/og/H3K14ac/results_log b/TextFooler/output/AT/og/H3K14ac/results_log index f240e6bb..58237193 100644 --- a/TextFooler/output/AT/og/H3K14ac/results_log +++ b/TextFooler/output/AT/og/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 72.900%, adv accuracy: 0.000%, avg changed rate: 1.205%, num of queries: 405.7 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 72.900%, adv accuracy: 0.000%, avg changed rate: 1.205%, num of queries: 405.7 diff --git a/TextFooler/output/AT/og/H3K36me3/results_log b/TextFooler/output/AT/og/H3K36me3/results_log index 72797c1e..dc42adf9 100644 --- a/TextFooler/output/AT/og/H3K36me3/results_log +++ b/TextFooler/output/AT/og/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 92.400%, adv accuracy: 0.000%, avg changed rate: 0.974%, num of queries: 347.8 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 92.400%, adv accuracy: 0.000%, avg changed rate: 0.974%, num of queries: 347.8 diff --git a/TextFooler/output/AT/og/H3K4me1/results_log b/TextFooler/output/AT/og/H3K4me1/results_log index c68a0a2c..cb9211c2 100644 --- a/TextFooler/output/AT/og/H3K4me1/results_log +++ b/TextFooler/output/AT/og/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 85.100%, adv accuracy: 0.000%, avg changed rate: 0.939%, num of queries: 338.9 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 85.100%, adv accuracy: 0.000%, avg changed rate: 0.939%, num of queries: 338.9 diff --git a/TextFooler/output/AT/og/H3K4me2/results_log b/TextFooler/output/AT/og/H3K4me2/results_log index ab59f29b..dcc600ef 100644 --- a/TextFooler/output/AT/og/H3K4me2/results_log +++ b/TextFooler/output/AT/og/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 73.600%, adv accuracy: 0.000%, avg changed rate: 1.179%, num of queries: 399.0 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 73.600%, adv accuracy: 0.000%, avg changed rate: 1.179%, num of queries: 399.0 diff --git a/TextFooler/output/AT/og/H3K4me3/results_log b/TextFooler/output/AT/og/H3K4me3/results_log index f5aeeb4e..a976b836 100644 --- a/TextFooler/output/AT/og/H3K4me3/results_log +++ b/TextFooler/output/AT/og/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 85.300%, adv accuracy: 0.000%, avg changed rate: 0.881%, num of queries: 324.4 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 85.300%, adv accuracy: 0.000%, avg changed rate: 0.881%, num of queries: 324.4 diff --git a/TextFooler/output/AT/og/H3K79me3/results_log b/TextFooler/output/AT/og/H3K79me3/results_log index df78b63b..c2c5a461 100644 --- a/TextFooler/output/AT/og/H3K79me3/results_log +++ b/TextFooler/output/AT/og/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 88.800%, adv accuracy: 0.000%, avg changed rate: 1.263%, num of queries: 420.0 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 88.800%, adv accuracy: 0.000%, avg changed rate: 1.263%, num of queries: 420.0 diff --git a/TextFooler/output/AT/og/H3K9ac/results_log b/TextFooler/output/AT/og/H3K9ac/results_log index a1a82228..e831e8df 100644 --- a/TextFooler/output/AT/og/H3K9ac/results_log +++ b/TextFooler/output/AT/og/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 81.100%, adv accuracy: 0.000%, avg changed rate: 1.374%, num of queries: 448.0 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 81.100%, adv accuracy: 0.000%, avg changed rate: 1.374%, num of queries: 448.0 diff --git a/TextFooler/output/AT/og/H4/results_log b/TextFooler/output/AT/og/H4/results_log index 454153bb..3b194718 100644 --- a/TextFooler/output/AT/og/H4/results_log +++ b/TextFooler/output/AT/og/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 34.900%, avg changed rate: 3.115%, num of queries: 926.4 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 34.900%, avg changed rate: 3.115%, num of queries: 926.4 diff --git a/TextFooler/output/AT/og/H4ac/results_log b/TextFooler/output/AT/og/H4ac/results_log index ab75b20b..f36e4893 100644 --- a/TextFooler/output/AT/og/H4ac/results_log +++ b/TextFooler/output/AT/og/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 0.767%, num of queries: 296.0 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 0.767%, num of queries: 296.0 diff --git a/TextFooler/output/AT/og/prom_300_all/results_log b/TextFooler/output/AT/og/prom_300_all/results_log index 470e8038..0d52e65b 100644 --- a/TextFooler/output/AT/og/prom_300_all/results_log +++ b/TextFooler/output/AT/og/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 2.326%, num of queries: 411.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 2.326%, num of queries: 411.0 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 2.326%, num of queries: 411.0 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 2.326%, num of queries: 411.0 diff --git a/TextFooler/output/AT/og/prom_300_notata/results_log b/TextFooler/output/AT/og/prom_300_notata/results_log index 45a38905..f7249563 100644 --- a/TextFooler/output/AT/og/prom_300_notata/results_log +++ b/TextFooler/output/AT/og/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 0.000%, avg changed rate: 1.998%, num of queries: 362.0 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 84.300%, adv accuracy: 0.000%, avg changed rate: 1.998%, num of queries: 362.0 diff --git a/TextFooler/output/AT/og/prom_300_tata/results_log b/TextFooler/output/AT/og/prom_300_tata/results_log index 5be07ce9..2ea9d1db 100644 --- a/TextFooler/output/AT/og/prom_300_tata/results_log +++ b/TextFooler/output/AT/og/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 72.400%, avg changed rate: 2.013%, num of queries: 364.7 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 72.400%, avg changed rate: 2.013%, num of queries: 364.7 diff --git a/TextFooler/output/AT/og/prom_core_all/results_log b/TextFooler/output/AT/og/prom_core_all/results_log index c3189571..52bc2abf 100644 --- a/TextFooler/output/AT/og/prom_core_all/results_log +++ b/TextFooler/output/AT/og/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.111%, num of queries: 124.7 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.111%, num of queries: 124.7 diff --git a/TextFooler/output/AT/og/prom_core_notata/results_log b/TextFooler/output/AT/og/prom_core_notata/results_log index fd5c1a52..402b42e8 100644 --- a/TextFooler/output/AT/og/prom_core_notata/results_log +++ b/TextFooler/output/AT/og/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 76.100%, adv accuracy: 0.000%, avg changed rate: 4.139%, num of queries: 160.7 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 76.100%, adv accuracy: 0.000%, avg changed rate: 4.139%, num of queries: 160.7 diff --git a/TextFooler/output/AT/og/prom_core_tata/results_log b/TextFooler/output/AT/og/prom_core_tata/results_log index 31fc5f44..ea1f66b3 100644 --- a/TextFooler/output/AT/og/prom_core_tata/results_log +++ b/TextFooler/output/AT/og/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 72.400%, avg changed rate: 2.172%, num of queries: 95.0 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 72.400%, avg changed rate: 2.172%, num of queries: 95.0 diff --git a/TextFooler/output/AT/og/tf0/results_log b/TextFooler/output/AT/og/tf0/results_log index 79a5ff1f..a5440e50 100644 --- a/TextFooler/output/AT/og/tf0/results_log +++ b/TextFooler/output/AT/og/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 88.300%, adv accuracy: 0.000%, avg changed rate: 2.906%, num of queries: 168.6 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 88.300%, adv accuracy: 0.000%, avg changed rate: 2.906%, num of queries: 168.6 diff --git a/TextFooler/output/AT/og/tf1/results_log b/TextFooler/output/AT/og/tf1/results_log index 223aba64..d2f0aa4c 100644 --- a/TextFooler/output/AT/og/tf1/results_log +++ b/TextFooler/output/AT/og/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 57.500%, adv accuracy: 0.300%, avg changed rate: 5.184%, num of queries: 288.1 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 57.500%, adv accuracy: 0.300%, avg changed rate: 5.184%, num of queries: 288.1 diff --git a/TextFooler/output/AT/og/tf2/results_log b/TextFooler/output/AT/og/tf2/results_log index d8a1c8c8..bdf054a5 100644 --- a/TextFooler/output/AT/og/tf2/results_log +++ b/TextFooler/output/AT/og/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 88.100%, adv accuracy: 0.000%, avg changed rate: 2.637%, num of queries: 155.1 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 88.100%, adv accuracy: 0.000%, avg changed rate: 2.637%, num of queries: 155.1 diff --git a/TextFooler/output/AT/og/tf3/results_log b/TextFooler/output/AT/og/tf3/results_log index 10bf3fcb..a81782e5 100644 --- a/TextFooler/output/AT/og/tf3/results_log +++ b/TextFooler/output/AT/og/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 81.200%, adv accuracy: 0.000%, avg changed rate: 2.672%, num of queries: 157.4 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 81.200%, adv accuracy: 0.000%, avg changed rate: 2.672%, num of queries: 157.4 diff --git a/TextFooler/output/AT/og/tf4/results_log b/TextFooler/output/AT/og/tf4/results_log index 11fd3957..b4ea732e 100644 --- a/TextFooler/output/AT/og/tf4/results_log +++ b/TextFooler/output/AT/og/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 0.400%, avg changed rate: 3.182%, num of queries: 188.7 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 0.400%, avg changed rate: 3.182%, num of queries: 188.7 diff --git a/TextFooler/output/All/dnabert/0/results_log b/TextFooler/output/All/dnabert/0/results_log index 31d4d537..7b56762f 100644 --- a/TextFooler/output/All/dnabert/0/results_log +++ b/TextFooler/output/All/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 89.000%, adv accuracy: 63.600%, avg changed rate: 2.296%, num of queries: 139.7 +For target model GUE/0/five_percent/cat.csv: original accuracy: 89.000%, adv accuracy: 63.600%, avg changed rate: 2.296%, num of queries: 139.7 diff --git a/TextFooler/output/All/dnabert/1/results_log b/TextFooler/output/All/dnabert/1/results_log index 8b286304..b1eca7f8 100644 --- a/TextFooler/output/All/dnabert/1/results_log +++ b/TextFooler/output/All/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 92.900%, adv accuracy: 1.600%, avg changed rate: 2.605%, num of queries: 165.8 +For target model GUE/1/five_percent/cat.csv: original accuracy: 92.900%, adv accuracy: 1.600%, avg changed rate: 2.605%, num of queries: 165.8 diff --git a/TextFooler/output/All/dnabert/2/results_log b/TextFooler/output/All/dnabert/2/results_log index fdf053f4..0076d6b0 100644 --- a/TextFooler/output/All/dnabert/2/results_log +++ b/TextFooler/output/All/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 85.400%, avg changed rate: 3.208%, num of queries: 185.8 +For target model GUE/2/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 85.400%, avg changed rate: 3.208%, num of queries: 185.8 diff --git a/TextFooler/output/All/dnabert/3/results_log b/TextFooler/output/All/dnabert/3/results_log index 8a6be2e2..bd7d8fbf 100644 --- a/TextFooler/output/All/dnabert/3/results_log +++ b/TextFooler/output/All/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 95.500%, adv accuracy: 89.300%, avg changed rate: 3.705%, num of queries: 209.9 +For target model GUE/3/five_percent/cat.csv: original accuracy: 95.500%, adv accuracy: 89.300%, avg changed rate: 3.705%, num of queries: 209.9 diff --git a/TextFooler/output/All/dnabert/4/results_log b/TextFooler/output/All/dnabert/4/results_log index 1824ea79..2c719c20 100644 --- a/TextFooler/output/All/dnabert/4/results_log +++ b/TextFooler/output/All/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 82.400%, adv accuracy: 15.300%, avg changed rate: 1.911%, num of queries: 119.6 +For target model GUE/4/five_percent/cat.csv: original accuracy: 82.400%, adv accuracy: 15.300%, avg changed rate: 1.911%, num of queries: 119.6 diff --git a/TextFooler/output/All/dnabert/H3/results_log b/TextFooler/output/All/dnabert/H3/results_log index eba62a35..65244f5b 100644 --- a/TextFooler/output/All/dnabert/H3/results_log +++ b/TextFooler/output/All/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 34.700%, avg changed rate: 1.442%, num of queries: 628.4 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 34.700%, avg changed rate: 1.442%, num of queries: 628.4 diff --git a/TextFooler/output/All/dnabert/H3K14ac/results_log b/TextFooler/output/All/dnabert/H3K14ac/results_log index fc319b1b..962f7aa0 100644 --- a/TextFooler/output/All/dnabert/H3K14ac/results_log +++ b/TextFooler/output/All/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 70.600%, adv accuracy: 0.000%, avg changed rate: 0.946%, num of queries: 339.4 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 70.600%, adv accuracy: 0.000%, avg changed rate: 0.946%, num of queries: 339.4 diff --git a/TextFooler/output/All/dnabert/H3K36me3/results_log b/TextFooler/output/All/dnabert/H3K36me3/results_log index 338c2e24..a35b9a41 100644 --- a/TextFooler/output/All/dnabert/H3K36me3/results_log +++ b/TextFooler/output/All/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 80.300%, adv accuracy: 0.000%, avg changed rate: 0.788%, num of queries: 299.2 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 80.300%, adv accuracy: 0.000%, avg changed rate: 0.788%, num of queries: 299.2 diff --git a/TextFooler/output/All/dnabert/H3K4me1/results_log b/TextFooler/output/All/dnabert/H3K4me1/results_log index 47322eb0..18dada26 100644 --- a/TextFooler/output/All/dnabert/H3K4me1/results_log +++ b/TextFooler/output/All/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 1.049%, num of queries: 364.3 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 1.049%, num of queries: 364.3 diff --git a/TextFooler/output/All/dnabert/H3K4me2/results_log b/TextFooler/output/All/dnabert/H3K4me2/results_log index 416edec1..386f7222 100644 --- a/TextFooler/output/All/dnabert/H3K4me2/results_log +++ b/TextFooler/output/All/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 67.600%, adv accuracy: 0.000%, avg changed rate: 0.773%, num of queries: 310.2 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 67.600%, adv accuracy: 0.000%, avg changed rate: 0.773%, num of queries: 310.2 diff --git a/TextFooler/output/All/dnabert/H3K4me3/results_log b/TextFooler/output/All/dnabert/H3K4me3/results_log index 6de30148..f11094ef 100644 --- a/TextFooler/output/All/dnabert/H3K4me3/results_log +++ b/TextFooler/output/All/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 71.000%, adv accuracy: 0.000%, avg changed rate: 0.785%, num of queries: 298.1 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 71.000%, adv accuracy: 0.000%, avg changed rate: 0.785%, num of queries: 298.1 diff --git a/TextFooler/output/All/dnabert/H3K79me3/results_log b/TextFooler/output/All/dnabert/H3K79me3/results_log index de079e8c..f9916588 100644 --- a/TextFooler/output/All/dnabert/H3K79me3/results_log +++ b/TextFooler/output/All/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 0.100%, avg changed rate: 1.230%, num of queries: 415.4 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 0.100%, avg changed rate: 1.230%, num of queries: 415.4 diff --git a/TextFooler/output/All/dnabert/H3K9ac/results_log b/TextFooler/output/All/dnabert/H3K9ac/results_log index 80ab3760..9664bd02 100644 --- a/TextFooler/output/All/dnabert/H3K9ac/results_log +++ b/TextFooler/output/All/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 77.200%, adv accuracy: 0.100%, avg changed rate: 1.119%, num of queries: 391.1 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 77.200%, adv accuracy: 0.100%, avg changed rate: 1.119%, num of queries: 391.1 diff --git a/TextFooler/output/All/dnabert/H4/results_log b/TextFooler/output/All/dnabert/H4/results_log index 6f9203e0..07f69bab 100644 --- a/TextFooler/output/All/dnabert/H4/results_log +++ b/TextFooler/output/All/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 36.700%, avg changed rate: 2.342%, num of queries: 860.2 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 36.700%, avg changed rate: 2.342%, num of queries: 860.2 diff --git a/TextFooler/output/All/dnabert/H4ac/results_log b/TextFooler/output/All/dnabert/H4ac/results_log index 1fca8e7b..9ffa6350 100644 --- a/TextFooler/output/All/dnabert/H4ac/results_log +++ b/TextFooler/output/All/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 1.052%, num of queries: 365.6 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 1.052%, num of queries: 365.6 diff --git a/TextFooler/output/All/dnabert/prom_300_all/results_log b/TextFooler/output/All/dnabert/prom_300_all/results_log index c3195f15..b761d306 100644 --- a/TextFooler/output/All/dnabert/prom_300_all/results_log +++ b/TextFooler/output/All/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 95.700%, adv accuracy: 0.000%, avg changed rate: 1.239%, num of queries: 250.7 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 95.700%, adv accuracy: 0.000%, avg changed rate: 1.239%, num of queries: 250.7 diff --git a/TextFooler/output/All/dnabert/prom_300_notata/results_log b/TextFooler/output/All/dnabert/prom_300_notata/results_log index bd28ceb4..78f28b73 100644 --- a/TextFooler/output/All/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/All/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 1.373%, num of queries: 271.2 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.900%, adv accuracy: 0.000%, avg changed rate: 1.373%, num of queries: 271.2 diff --git a/TextFooler/output/All/dnabert/prom_300_tata/results_log b/TextFooler/output/All/dnabert/prom_300_tata/results_log index d26f33b4..7ddb84b8 100644 --- a/TextFooler/output/All/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/All/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.600%, adv accuracy: 72.400%, avg changed rate: 2.118%, num of queries: 380.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.600%, adv accuracy: 72.400%, avg changed rate: 2.118%, num of queries: 380.6 diff --git a/TextFooler/output/All/dnabert/prom_core_all/results_log b/TextFooler/output/All/dnabert/prom_core_all/results_log index dfa15807..b617fdef 100644 --- a/TextFooler/output/All/dnabert/prom_core_all/results_log +++ b/TextFooler/output/All/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 2.776%, num of queries: 113.6 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 2.776%, num of queries: 113.6 diff --git a/TextFooler/output/All/dnabert/prom_core_notata/results_log b/TextFooler/output/All/dnabert/prom_core_notata/results_log index 5d44f50b..01973e6f 100644 --- a/TextFooler/output/All/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/All/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 3.118%, num of queries: 125.8 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 3.118%, num of queries: 125.8 diff --git a/TextFooler/output/All/dnabert/prom_core_tata/results_log b/TextFooler/output/All/dnabert/prom_core_tata/results_log index 927b3dc1..5d72749e 100644 --- a/TextFooler/output/All/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/All/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 72.400%, avg changed rate: 2.767%, num of queries: 113.1 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 72.400%, avg changed rate: 2.767%, num of queries: 113.1 diff --git a/TextFooler/output/All/dnabert/tf0/results_log b/TextFooler/output/All/dnabert/tf0/results_log index 351719a6..2ed548ba 100644 --- a/TextFooler/output/All/dnabert/tf0/results_log +++ b/TextFooler/output/All/dnabert/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 82.000%, adv accuracy: 0.000%, avg changed rate: 2.800%, num of queries: 164.2 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 82.000%, adv accuracy: 0.000%, avg changed rate: 2.800%, num of queries: 164.2 diff --git a/TextFooler/output/All/dnabert/tf1/results_log b/TextFooler/output/All/dnabert/tf1/results_log index b627fc33..f4666da8 100644 --- a/TextFooler/output/All/dnabert/tf1/results_log +++ b/TextFooler/output/All/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 79.900%, adv accuracy: 0.100%, avg changed rate: 2.602%, num of queries: 155.5 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 79.900%, adv accuracy: 0.100%, avg changed rate: 2.602%, num of queries: 155.5 diff --git a/TextFooler/output/All/dnabert/tf2/results_log b/TextFooler/output/All/dnabert/tf2/results_log index de8f8c14..f8b210b6 100644 --- a/TextFooler/output/All/dnabert/tf2/results_log +++ b/TextFooler/output/All/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 2.249%, num of queries: 136.6 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 2.249%, num of queries: 136.6 diff --git a/TextFooler/output/All/dnabert/tf3/results_log b/TextFooler/output/All/dnabert/tf3/results_log index 056b34fe..6c1e6dd2 100644 --- a/TextFooler/output/All/dnabert/tf3/results_log +++ b/TextFooler/output/All/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 75.200%, adv accuracy: 0.000%, avg changed rate: 3.290%, num of queries: 187.8 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 75.200%, adv accuracy: 0.000%, avg changed rate: 3.290%, num of queries: 187.8 diff --git a/TextFooler/output/All/dnabert/tf4/results_log b/TextFooler/output/All/dnabert/tf4/results_log index 4fd5df84..3aff36b8 100644 --- a/TextFooler/output/All/dnabert/tf4/results_log +++ b/TextFooler/output/All/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 88.200%, adv accuracy: 0.700%, avg changed rate: 3.128%, num of queries: 191.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 88.200%, adv accuracy: 0.700%, avg changed rate: 3.128%, num of queries: 191.9 diff --git a/TextFooler/output/All/hyena/0/results_log b/TextFooler/output/All/hyena/0/results_log index 7593ec72..62cb97c5 100644 --- a/TextFooler/output/All/hyena/0/results_log +++ b/TextFooler/output/All/hyena/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 81.400%, adv accuracy: 81.400%, avg changed rate: nan%, num of queries: 152.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 81.400%, adv accuracy: 81.400%, avg changed rate: nan%, num of queries: 152.3 diff --git a/TextFooler/output/All/hyena/1/results_log b/TextFooler/output/All/hyena/1/results_log index a0f076b7..dbbc543c 100644 --- a/TextFooler/output/All/hyena/1/results_log +++ b/TextFooler/output/All/hyena/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 152.6 +For target model GUE/1/five_percent/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 152.6 diff --git a/TextFooler/output/All/hyena/2/results_log b/TextFooler/output/All/hyena/2/results_log index e2385484..2df69f2f 100644 --- a/TextFooler/output/All/hyena/2/results_log +++ b/TextFooler/output/All/hyena/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 92.100%, avg changed rate: nan%, num of queries: 152.0 +For target model GUE/2/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 92.100%, avg changed rate: nan%, num of queries: 152.0 diff --git a/TextFooler/output/All/hyena/3/results_log b/TextFooler/output/All/hyena/3/results_log index fb8a3ec3..3b98d3ea 100644 --- a/TextFooler/output/All/hyena/3/results_log +++ b/TextFooler/output/All/hyena/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 95.100%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/3/five_percent/cat.csv: original accuracy: 95.100%, adv accuracy: 95.100%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/All/hyena/4/results_log b/TextFooler/output/All/hyena/4/results_log index df4371cf..e6f4e31b 100644 --- a/TextFooler/output/All/hyena/4/results_log +++ b/TextFooler/output/All/hyena/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 56.400%, adv accuracy: 42.900%, avg changed rate: 11.111%, num of queries: 140.2 +For target model GUE/4/five_percent/cat.csv: original accuracy: 56.400%, adv accuracy: 42.900%, avg changed rate: 11.111%, num of queries: 140.2 diff --git a/TextFooler/output/All/hyena/H3/results_log b/TextFooler/output/All/hyena/H3/results_log index 5093f35d..9b0dbc26 100644 --- a/TextFooler/output/All/hyena/H3/results_log +++ b/TextFooler/output/All/hyena/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 69.300%, adv accuracy: 68.600%, avg changed rate: 11.886%, num of queries: 750.5 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 69.300%, adv accuracy: 68.600%, avg changed rate: 11.886%, num of queries: 750.5 diff --git a/TextFooler/output/All/hyena/H3K14ac/results_log b/TextFooler/output/All/hyena/H3K14ac/results_log index 95699cdc..5af6ce15 100644 --- a/TextFooler/output/All/hyena/H3K14ac/results_log +++ b/TextFooler/output/All/hyena/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 57.300%, adv accuracy: 54.200%, avg changed rate: 16.303%, num of queries: 742.6 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 57.300%, adv accuracy: 54.200%, avg changed rate: 16.303%, num of queries: 742.6 diff --git a/TextFooler/output/All/hyena/H3K36me3/results_log b/TextFooler/output/All/hyena/H3K36me3/results_log index e85c7a06..ed1d15ec 100644 --- a/TextFooler/output/All/hyena/H3K36me3/results_log +++ b/TextFooler/output/All/hyena/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 8.900%, avg changed rate: 8.185%, num of queries: 608.8 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 8.900%, avg changed rate: 8.185%, num of queries: 608.8 diff --git a/TextFooler/output/All/hyena/H3K4me1/results_log b/TextFooler/output/All/hyena/H3K4me1/results_log index ca3b6cef..10131f59 100644 --- a/TextFooler/output/All/hyena/H3K4me1/results_log +++ b/TextFooler/output/All/hyena/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 47.200%, adv accuracy: 45.700%, avg changed rate: 16.947%, num of queries: 748.8 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 47.200%, adv accuracy: 45.700%, avg changed rate: 16.947%, num of queries: 748.8 diff --git a/TextFooler/output/All/hyena/H3K4me2/results_log b/TextFooler/output/All/hyena/H3K4me2/results_log index 5bb5b0c4..3bd099f9 100644 --- a/TextFooler/output/All/hyena/H3K4me2/results_log +++ b/TextFooler/output/All/hyena/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 58.800%, adv accuracy: 48.300%, avg changed rate: 9.360%, num of queries: 723.1 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 58.800%, adv accuracy: 48.300%, avg changed rate: 9.360%, num of queries: 723.1 diff --git a/TextFooler/output/All/hyena/H3K4me3/results_log b/TextFooler/output/All/hyena/H3K4me3/results_log index cf373dfb..78f5bdf9 100644 --- a/TextFooler/output/All/hyena/H3K4me3/results_log +++ b/TextFooler/output/All/hyena/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 46.800%, adv accuracy: 17.400%, avg changed rate: 12.068%, num of queries: 650.1 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 46.800%, adv accuracy: 17.400%, avg changed rate: 12.068%, num of queries: 650.1 diff --git a/TextFooler/output/All/hyena/H3K79me3/results_log b/TextFooler/output/All/hyena/H3K79me3/results_log index cab0b6e1..b91a56e2 100644 --- a/TextFooler/output/All/hyena/H3K79me3/results_log +++ b/TextFooler/output/All/hyena/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 45.300%, adv accuracy: 33.400%, avg changed rate: 4.867%, num of queries: 702.1 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 45.300%, adv accuracy: 33.400%, avg changed rate: 4.867%, num of queries: 702.1 diff --git a/TextFooler/output/All/hyena/H3K9ac/results_log b/TextFooler/output/All/hyena/H3K9ac/results_log index 2b29f239..2ae3290c 100644 --- a/TextFooler/output/All/hyena/H3K9ac/results_log +++ b/TextFooler/output/All/hyena/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 29.100%, avg changed rate: 13.913%, num of queries: 679.3 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 53.100%, adv accuracy: 29.100%, avg changed rate: 13.913%, num of queries: 679.3 diff --git a/TextFooler/output/All/hyena/H4/results_log b/TextFooler/output/All/hyena/H4/results_log index de659334..a7e2c5c1 100644 --- a/TextFooler/output/All/hyena/H4/results_log +++ b/TextFooler/output/All/hyena/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 68.300%, adv accuracy: 45.400%, avg changed rate: 5.396%, num of queries: 606.5 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 68.300%, adv accuracy: 45.400%, avg changed rate: 5.396%, num of queries: 606.5 diff --git a/TextFooler/output/All/hyena/H4ac/results_log b/TextFooler/output/All/hyena/H4ac/results_log index 2941c957..b24c8f72 100644 --- a/TextFooler/output/All/hyena/H4ac/results_log +++ b/TextFooler/output/All/hyena/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 51.200%, adv accuracy: 2.800%, avg changed rate: 3.637%, num of queries: 551.2 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 51.200%, adv accuracy: 2.800%, avg changed rate: 3.637%, num of queries: 551.2 diff --git a/TextFooler/output/All/hyena/prom_300_all/results_log b/TextFooler/output/All/hyena/prom_300_all/results_log index e18f0ec6..8ae3ac56 100644 --- a/TextFooler/output/All/hyena/prom_300_all/results_log +++ b/TextFooler/output/All/hyena/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.000%, adv accuracy: 27.900%, avg changed rate: 15.579%, num of queries: 422.4 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.000%, adv accuracy: 27.900%, avg changed rate: 15.579%, num of queries: 422.4 diff --git a/TextFooler/output/All/hyena/prom_300_notata/results_log b/TextFooler/output/All/hyena/prom_300_notata/results_log index a50bb528..6d965d3a 100644 --- a/TextFooler/output/All/hyena/prom_300_notata/results_log +++ b/TextFooler/output/All/hyena/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 45.000%, adv accuracy: 33.300%, avg changed rate: 11.197%, num of queries: 428.7 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 45.000%, adv accuracy: 33.300%, avg changed rate: 11.197%, num of queries: 428.7 diff --git a/TextFooler/output/All/hyena/prom_300_tata/results_log b/TextFooler/output/All/hyena/prom_300_tata/results_log index 893d6438..ac1624af 100644 --- a/TextFooler/output/All/hyena/prom_300_tata/results_log +++ b/TextFooler/output/All/hyena/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 85.100%, avg changed rate: 15.741%, num of queries: 442.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 85.100%, avg changed rate: 15.741%, num of queries: 442.6 diff --git a/TextFooler/output/All/hyena/prom_core_all/results_log b/TextFooler/output/All/hyena/prom_core_all/results_log index 189d16ca..9af3642f 100644 --- a/TextFooler/output/All/hyena/prom_core_all/results_log +++ b/TextFooler/output/All/hyena/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.300%, adv accuracy: 47.300%, avg changed rate: nan%, num of queries: 105.6 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 47.300%, adv accuracy: 47.300%, avg changed rate: nan%, num of queries: 105.6 diff --git a/TextFooler/output/All/hyena/prom_core_notata/results_log b/TextFooler/output/All/hyena/prom_core_notata/results_log index c7675b27..5bfcc03b 100644 --- a/TextFooler/output/All/hyena/prom_core_notata/results_log +++ b/TextFooler/output/All/hyena/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 105.4 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 105.4 diff --git a/TextFooler/output/All/hyena/prom_core_tata/results_log b/TextFooler/output/All/hyena/prom_core_tata/results_log index ac1662ee..5d1054af 100644 --- a/TextFooler/output/All/hyena/prom_core_tata/results_log +++ b/TextFooler/output/All/hyena/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 104.3 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.000%, adv accuracy: 86.000%, avg changed rate: nan%, num of queries: 104.3 diff --git a/TextFooler/output/All/hyena/tf0/results_log b/TextFooler/output/All/hyena/tf0/results_log index 4758141e..8505e98c 100644 --- a/TextFooler/output/All/hyena/tf0/results_log +++ b/TextFooler/output/All/hyena/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.4 diff --git a/TextFooler/output/All/hyena/tf1/results_log b/TextFooler/output/All/hyena/tf1/results_log index f5bd2b85..fcabb127 100644 --- a/TextFooler/output/All/hyena/tf1/results_log +++ b/TextFooler/output/All/hyena/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 48.900%, adv accuracy: 48.900%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/All/hyena/tf2/results_log b/TextFooler/output/All/hyena/tf2/results_log index 59362ce3..5f04e6d2 100644 --- a/TextFooler/output/All/hyena/tf2/results_log +++ b/TextFooler/output/All/hyena/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 49.700%, adv accuracy: 49.700%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/All/hyena/tf3/results_log b/TextFooler/output/All/hyena/tf3/results_log index 133bdd3b..8eaa47ca 100644 --- a/TextFooler/output/All/hyena/tf3/results_log +++ b/TextFooler/output/All/hyena/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/All/hyena/tf4/results_log b/TextFooler/output/All/hyena/tf4/results_log index b3b54b6f..1d5afa63 100644 --- a/TextFooler/output/All/hyena/tf4/results_log +++ b/TextFooler/output/All/hyena/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 49.800%, avg changed rate: nan%, num of queries: 152.4 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 49.800%, adv accuracy: 49.800%, avg changed rate: nan%, num of queries: 152.4 diff --git a/TextFooler/output/All/nt1/0/results_log b/TextFooler/output/All/nt1/0/results_log index 57b6aad8..c64e4432 100644 --- a/TextFooler/output/All/nt1/0/results_log +++ b/TextFooler/output/All/nt1/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 89.600%, adv accuracy: 67.600%, avg changed rate: 3.236%, num of queries: 28.1 +For target model GUE/0/five_percent/cat.csv: original accuracy: 89.600%, adv accuracy: 67.600%, avg changed rate: 3.236%, num of queries: 28.1 diff --git a/TextFooler/output/All/nt1/1/results_log b/TextFooler/output/All/nt1/1/results_log index 16f9eb8f..6dfe82bd 100644 --- a/TextFooler/output/All/nt1/1/results_log +++ b/TextFooler/output/All/nt1/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 23.600%, avg changed rate: 3.652%, num of queries: 29.1 +For target model GUE/1/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 23.600%, avg changed rate: 3.652%, num of queries: 29.1 diff --git a/TextFooler/output/All/nt1/2/results_log b/TextFooler/output/All/nt1/2/results_log index 3f53d0a1..6ce28600 100644 --- a/TextFooler/output/All/nt1/2/results_log +++ b/TextFooler/output/All/nt1/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 89.200%, avg changed rate: 3.842%, num of queries: 30.1 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 89.200%, avg changed rate: 3.842%, num of queries: 30.1 diff --git a/TextFooler/output/All/nt1/3/results_log b/TextFooler/output/All/nt1/3/results_log index 559777bb..8251bf60 100644 --- a/TextFooler/output/All/nt1/3/results_log +++ b/TextFooler/output/All/nt1/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 91.100%, avg changed rate: 3.972%, num of queries: 29.2 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 91.100%, avg changed rate: 3.972%, num of queries: 29.2 diff --git a/TextFooler/output/All/nt1/4/results_log b/TextFooler/output/All/nt1/4/results_log index ad44a3be..8a24cbbb 100644 --- a/TextFooler/output/All/nt1/4/results_log +++ b/TextFooler/output/All/nt1/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 76.900%, adv accuracy: 26.000%, avg changed rate: 3.352%, num of queries: 28.4 +For target model GUE/4/five_percent/cat.csv: original accuracy: 76.900%, adv accuracy: 26.000%, avg changed rate: 3.352%, num of queries: 28.4 diff --git a/TextFooler/output/All/nt1/H3/results_log b/TextFooler/output/All/nt1/H3/results_log index 563ff1c9..f6193cc2 100644 --- a/TextFooler/output/All/nt1/H3/results_log +++ b/TextFooler/output/All/nt1/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 92.000%, adv accuracy: 40.100%, avg changed rate: 2.043%, num of queries: 106.0 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 92.000%, adv accuracy: 40.100%, avg changed rate: 2.043%, num of queries: 106.0 diff --git a/TextFooler/output/All/nt1/H3K14ac/results_log b/TextFooler/output/All/nt1/H3K14ac/results_log index a42f5c04..eb06b686 100644 --- a/TextFooler/output/All/nt1/H3K14ac/results_log +++ b/TextFooler/output/All/nt1/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 15.100%, avg changed rate: 0.890%, num of queries: 103.0 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 15.100%, avg changed rate: 0.890%, num of queries: 103.0 diff --git a/TextFooler/output/All/nt1/H3K36me3/results_log b/TextFooler/output/All/nt1/H3K36me3/results_log index 7cd11e3b..6db06b12 100644 --- a/TextFooler/output/All/nt1/H3K36me3/results_log +++ b/TextFooler/output/All/nt1/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 79.000%, adv accuracy: 1.800%, avg changed rate: 1.222%, num of queries: 95.4 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 79.000%, adv accuracy: 1.800%, avg changed rate: 1.222%, num of queries: 95.4 diff --git a/TextFooler/output/All/nt1/H3K4me1/results_log b/TextFooler/output/All/nt1/H3K4me1/results_log index 11a54d2b..7ac368c6 100644 --- a/TextFooler/output/All/nt1/H3K4me1/results_log +++ b/TextFooler/output/All/nt1/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 81.300%, adv accuracy: 4.000%, avg changed rate: 1.601%, num of queries: 99.6 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 81.300%, adv accuracy: 4.000%, avg changed rate: 1.601%, num of queries: 99.6 diff --git a/TextFooler/output/All/nt1/H3K4me2/results_log b/TextFooler/output/All/nt1/H3K4me2/results_log index 31f3ecd7..04f5e3d3 100644 --- a/TextFooler/output/All/nt1/H3K4me2/results_log +++ b/TextFooler/output/All/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 70.400%, adv accuracy: 1.500%, avg changed rate: 0.711%, num of queries: 91.8 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 70.400%, adv accuracy: 1.500%, avg changed rate: 0.711%, num of queries: 91.8 diff --git a/TextFooler/output/All/nt1/H3K4me3/results_log b/TextFooler/output/All/nt1/H3K4me3/results_log index 3f265f70..f1c6cf1a 100644 --- a/TextFooler/output/All/nt1/H3K4me3/results_log +++ b/TextFooler/output/All/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 70.500%, adv accuracy: 6.600%, avg changed rate: 1.143%, num of queries: 100.6 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 70.500%, adv accuracy: 6.600%, avg changed rate: 1.143%, num of queries: 100.6 diff --git a/TextFooler/output/All/nt1/H3K79me3/results_log b/TextFooler/output/All/nt1/H3K79me3/results_log index a976c5d8..2acaf69b 100644 --- a/TextFooler/output/All/nt1/H3K79me3/results_log +++ b/TextFooler/output/All/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 17.000%, avg changed rate: 1.570%, num of queries: 107.1 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 82.600%, adv accuracy: 17.000%, avg changed rate: 1.570%, num of queries: 107.1 diff --git a/TextFooler/output/All/nt1/H3K9ac/results_log b/TextFooler/output/All/nt1/H3K9ac/results_log index 894af774..c1a01396 100644 --- a/TextFooler/output/All/nt1/H3K9ac/results_log +++ b/TextFooler/output/All/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 82.100%, adv accuracy: 24.900%, avg changed rate: 1.608%, num of queries: 112.1 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 82.100%, adv accuracy: 24.900%, avg changed rate: 1.608%, num of queries: 112.1 diff --git a/TextFooler/output/All/nt1/H4/results_log b/TextFooler/output/All/nt1/H4/results_log index f1f41284..5138cc98 100644 --- a/TextFooler/output/All/nt1/H4/results_log +++ b/TextFooler/output/All/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 95.800%, adv accuracy: 45.800%, avg changed rate: 2.413%, num of queries: 110.9 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 95.800%, adv accuracy: 45.800%, avg changed rate: 2.413%, num of queries: 110.9 diff --git a/TextFooler/output/All/nt1/H4ac/results_log b/TextFooler/output/All/nt1/H4ac/results_log index 4b6ffa3d..dde33f6e 100644 --- a/TextFooler/output/All/nt1/H4ac/results_log +++ b/TextFooler/output/All/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 72.000%, adv accuracy: 17.000%, avg changed rate: 1.559%, num of queries: 109.0 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 72.000%, adv accuracy: 17.000%, avg changed rate: 1.559%, num of queries: 109.0 diff --git a/TextFooler/output/All/nt1/prom_300_all/results_log b/TextFooler/output/All/nt1/prom_300_all/results_log index 7347b495..22c04f9c 100644 --- a/TextFooler/output/All/nt1/prom_300_all/results_log +++ b/TextFooler/output/All/nt1/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 45.900%, adv accuracy: 10.900%, avg changed rate: 1.257%, num of queries: 64.4 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 45.900%, adv accuracy: 10.900%, avg changed rate: 1.257%, num of queries: 64.4 diff --git a/TextFooler/output/All/nt1/prom_300_notata/results_log b/TextFooler/output/All/nt1/prom_300_notata/results_log index d8a7aa01..cdacc1b2 100644 --- a/TextFooler/output/All/nt1/prom_300_notata/results_log +++ b/TextFooler/output/All/nt1/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 24.700%, avg changed rate: 3.029%, num of queries: 70.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 97.400%, adv accuracy: 24.700%, avg changed rate: 3.029%, num of queries: 70.9 diff --git a/TextFooler/output/All/nt1/prom_300_tata/results_log b/TextFooler/output/All/nt1/prom_300_tata/results_log index 07d59da1..1d705e4d 100644 --- a/TextFooler/output/All/nt1/prom_300_tata/results_log +++ b/TextFooler/output/All/nt1/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 77.400%, avg changed rate: 2.934%, num of queries: 68.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 77.400%, avg changed rate: 2.934%, num of queries: 68.6 diff --git a/TextFooler/output/All/nt1/prom_core_all/results_log b/TextFooler/output/All/nt1/prom_core_all/results_log index 9f74e3f3..7b4ccc1e 100644 --- a/TextFooler/output/All/nt1/prom_core_all/results_log +++ b/TextFooler/output/All/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 81.000%, adv accuracy: 20.500%, avg changed rate: 3.993%, num of queries: 21.4 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 81.000%, adv accuracy: 20.500%, avg changed rate: 3.993%, num of queries: 21.4 diff --git a/TextFooler/output/All/nt1/prom_core_notata/results_log b/TextFooler/output/All/nt1/prom_core_notata/results_log index 4ea36916..16df046e 100644 --- a/TextFooler/output/All/nt1/prom_core_notata/results_log +++ b/TextFooler/output/All/nt1/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 84.800%, adv accuracy: 27.200%, avg changed rate: 4.368%, num of queries: 22.7 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 84.800%, adv accuracy: 27.200%, avg changed rate: 4.368%, num of queries: 22.7 diff --git a/TextFooler/output/All/nt1/prom_core_tata/results_log b/TextFooler/output/All/nt1/prom_core_tata/results_log index d9d21ba8..13cc5696 100644 --- a/TextFooler/output/All/nt1/prom_core_tata/results_log +++ b/TextFooler/output/All/nt1/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.100%, adv accuracy: 85.400%, avg changed rate: 4.922%, num of queries: 23.8 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.100%, adv accuracy: 85.400%, avg changed rate: 4.922%, num of queries: 23.8 diff --git a/TextFooler/output/All/nt1/tf0/results_log b/TextFooler/output/All/nt1/tf0/results_log index 20eadd64..939e7b0c 100644 --- a/TextFooler/output/All/nt1/tf0/results_log +++ b/TextFooler/output/All/nt1/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 81.300%, adv accuracy: 9.500%, avg changed rate: 2.482%, num of queries: 27.1 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 81.300%, adv accuracy: 9.500%, avg changed rate: 2.482%, num of queries: 27.1 diff --git a/TextFooler/output/All/nt1/tf1/results_log b/TextFooler/output/All/nt1/tf1/results_log index aa746ab8..a2f485ec 100644 --- a/TextFooler/output/All/nt1/tf1/results_log +++ b/TextFooler/output/All/nt1/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 70.600%, adv accuracy: 19.900%, avg changed rate: 2.271%, num of queries: 28.9 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 70.600%, adv accuracy: 19.900%, avg changed rate: 2.271%, num of queries: 28.9 diff --git a/TextFooler/output/All/nt1/tf2/results_log b/TextFooler/output/All/nt1/tf2/results_log index 2f3f277b..262b666a 100644 --- a/TextFooler/output/All/nt1/tf2/results_log +++ b/TextFooler/output/All/nt1/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 11.000%, avg changed rate: 1.956%, num of queries: 26.4 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 11.000%, avg changed rate: 1.956%, num of queries: 26.4 diff --git a/TextFooler/output/All/nt1/tf3/results_log b/TextFooler/output/All/nt1/tf3/results_log index 669c4dfa..9822b9a7 100644 --- a/TextFooler/output/All/nt1/tf3/results_log +++ b/TextFooler/output/All/nt1/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 73.300%, adv accuracy: 29.000%, avg changed rate: 3.715%, num of queries: 31.3 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 73.300%, adv accuracy: 29.000%, avg changed rate: 3.715%, num of queries: 31.3 diff --git a/TextFooler/output/All/nt1/tf4/results_log b/TextFooler/output/All/nt1/tf4/results_log index b0ab26ad..6cf83bb1 100644 --- a/TextFooler/output/All/nt1/tf4/results_log +++ b/TextFooler/output/All/nt1/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 92.700%, adv accuracy: 29.700%, avg changed rate: 4.004%, num of queries: 30.6 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 92.700%, adv accuracy: 29.700%, avg changed rate: 4.004%, num of queries: 30.6 diff --git a/TextFooler/output/All/nt2/0/results_log b/TextFooler/output/All/nt2/0/results_log index 30160d60..e5b37ff7 100644 --- a/TextFooler/output/All/nt2/0/results_log +++ b/TextFooler/output/All/nt2/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 92.300%, adv accuracy: 63.600%, avg changed rate: 1.425%, num of queries: 89.1 +For target model GUE/0/five_percent/cat.csv: original accuracy: 92.300%, adv accuracy: 63.600%, avg changed rate: 1.425%, num of queries: 89.1 diff --git a/TextFooler/output/All/nt2/1/results_log b/TextFooler/output/All/nt2/1/results_log index cd9255aa..80bfaba3 100644 --- a/TextFooler/output/All/nt2/1/results_log +++ b/TextFooler/output/All/nt2/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 0.000%, avg changed rate: 1.245%, num of queries: 81.1 +For target model GUE/1/five_percent/cat.csv: original accuracy: 94.500%, adv accuracy: 0.000%, avg changed rate: 1.245%, num of queries: 81.1 diff --git a/TextFooler/output/All/nt2/2/results_log b/TextFooler/output/All/nt2/2/results_log index a4660068..3b977f1a 100644 --- a/TextFooler/output/All/nt2/2/results_log +++ b/TextFooler/output/All/nt2/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 98.400%, adv accuracy: 85.300%, avg changed rate: 1.806%, num of queries: 106.0 +For target model GUE/2/five_percent/cat.csv: original accuracy: 98.400%, adv accuracy: 85.300%, avg changed rate: 1.806%, num of queries: 106.0 diff --git a/TextFooler/output/All/nt2/3/results_log b/TextFooler/output/All/nt2/3/results_log index f5b0720d..f4a9fdee 100644 --- a/TextFooler/output/All/nt2/3/results_log +++ b/TextFooler/output/All/nt2/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 89.300%, avg changed rate: 1.901%, num of queries: 117.7 +For target model GUE/3/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 89.300%, avg changed rate: 1.901%, num of queries: 117.7 diff --git a/TextFooler/output/All/nt2/4/results_log b/TextFooler/output/All/nt2/4/results_log index 04b161b7..62862277 100644 --- a/TextFooler/output/All/nt2/4/results_log +++ b/TextFooler/output/All/nt2/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 15.300%, avg changed rate: 1.392%, num of queries: 87.0 +For target model GUE/4/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 15.300%, avg changed rate: 1.392%, num of queries: 87.0 diff --git a/TextFooler/output/All/nt2/H3/results_log b/TextFooler/output/All/nt2/H3/results_log index c37356be..e06beb24 100644 --- a/TextFooler/output/All/nt2/H3/results_log +++ b/TextFooler/output/All/nt2/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 93.900%, adv accuracy: 32.600%, avg changed rate: 0.626%, num of queries: 256.6 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 93.900%, adv accuracy: 32.600%, avg changed rate: 0.626%, num of queries: 256.6 diff --git a/TextFooler/output/All/nt2/H3K14ac/results_log b/TextFooler/output/All/nt2/H3K14ac/results_log index 12c45ad8..b27c2d9e 100644 --- a/TextFooler/output/All/nt2/H3K14ac/results_log +++ b/TextFooler/output/All/nt2/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 76.500%, adv accuracy: 0.000%, avg changed rate: 0.280%, num of queries: 151.6 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 76.500%, adv accuracy: 0.000%, avg changed rate: 0.280%, num of queries: 151.6 diff --git a/TextFooler/output/All/nt2/H3K36me3/results_log b/TextFooler/output/All/nt2/H3K36me3/results_log index 21dca1f5..c16c35a7 100644 --- a/TextFooler/output/All/nt2/H3K36me3/results_log +++ b/TextFooler/output/All/nt2/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 83.800%, adv accuracy: 0.000%, avg changed rate: 0.325%, num of queries: 163.3 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 83.800%, adv accuracy: 0.000%, avg changed rate: 0.325%, num of queries: 163.3 diff --git a/TextFooler/output/All/nt2/H3K4me1/results_log b/TextFooler/output/All/nt2/H3K4me1/results_log index 4c1a4f6c..6ab71782 100644 --- a/TextFooler/output/All/nt2/H3K4me1/results_log +++ b/TextFooler/output/All/nt2/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 80.100%, adv accuracy: 0.000%, avg changed rate: 0.491%, num of queries: 202.7 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 80.100%, adv accuracy: 0.000%, avg changed rate: 0.491%, num of queries: 202.7 diff --git a/TextFooler/output/All/nt2/H3K4me2/results_log b/TextFooler/output/All/nt2/H3K4me2/results_log index 87fc4ca0..7ecc6a3f 100644 --- a/TextFooler/output/All/nt2/H3K4me2/results_log +++ b/TextFooler/output/All/nt2/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 69.000%, adv accuracy: 0.000%, avg changed rate: 0.368%, num of queries: 171.1 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 69.000%, adv accuracy: 0.000%, avg changed rate: 0.368%, num of queries: 171.1 diff --git a/TextFooler/output/All/nt2/H3K4me3/results_log b/TextFooler/output/All/nt2/H3K4me3/results_log index e9009a9a..d8785078 100644 --- a/TextFooler/output/All/nt2/H3K4me3/results_log +++ b/TextFooler/output/All/nt2/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 72.100%, adv accuracy: 0.000%, avg changed rate: 0.537%, num of queries: 210.2 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 72.100%, adv accuracy: 0.000%, avg changed rate: 0.537%, num of queries: 210.2 diff --git a/TextFooler/output/All/nt2/H3K79me3/results_log b/TextFooler/output/All/nt2/H3K79me3/results_log index a1cef1aa..958a21d5 100644 --- a/TextFooler/output/All/nt2/H3K79me3/results_log +++ b/TextFooler/output/All/nt2/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 0.336%, num of queries: 181.6 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 0.336%, num of queries: 181.6 diff --git a/TextFooler/output/All/nt2/H3K9ac/results_log b/TextFooler/output/All/nt2/H3K9ac/results_log index b3e0e357..b8566d0d 100644 --- a/TextFooler/output/All/nt2/H3K9ac/results_log +++ b/TextFooler/output/All/nt2/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 79.500%, adv accuracy: 0.000%, avg changed rate: 0.577%, num of queries: 218.7 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 79.500%, adv accuracy: 0.000%, avg changed rate: 0.577%, num of queries: 218.7 diff --git a/TextFooler/output/All/nt2/H4/results_log b/TextFooler/output/All/nt2/H4/results_log index e0f2a6dc..83fe5832 100644 --- a/TextFooler/output/All/nt2/H4/results_log +++ b/TextFooler/output/All/nt2/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 94.400%, adv accuracy: 34.300%, avg changed rate: 0.540%, num of queries: 216.3 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 94.400%, adv accuracy: 34.300%, avg changed rate: 0.540%, num of queries: 216.3 diff --git a/TextFooler/output/All/nt2/H4ac/results_log b/TextFooler/output/All/nt2/H4ac/results_log index 1f491db4..09d0f53c 100644 --- a/TextFooler/output/All/nt2/H4ac/results_log +++ b/TextFooler/output/All/nt2/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 77.800%, adv accuracy: 0.000%, avg changed rate: 0.369%, num of queries: 172.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 77.800%, adv accuracy: 0.000%, avg changed rate: 0.369%, num of queries: 172.7 diff --git a/TextFooler/output/All/nt2/prom_300_all/results_log b/TextFooler/output/All/nt2/prom_300_all/results_log index 4ae13d5b..e378e742 100644 --- a/TextFooler/output/All/nt2/prom_300_all/results_log +++ b/TextFooler/output/All/nt2/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 0.792%, num of queries: 169.7 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 0.792%, num of queries: 169.7 diff --git a/TextFooler/output/All/nt2/prom_300_notata/results_log b/TextFooler/output/All/nt2/prom_300_notata/results_log index 9f34f353..9017f9bc 100644 --- a/TextFooler/output/All/nt2/prom_300_notata/results_log +++ b/TextFooler/output/All/nt2/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 0.000%, avg changed rate: 0.961%, num of queries: 202.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 0.000%, avg changed rate: 0.961%, num of queries: 202.9 diff --git a/TextFooler/output/All/nt2/prom_300_tata/results_log b/TextFooler/output/All/nt2/prom_300_tata/results_log index a26b194e..6e7f9c93 100644 --- a/TextFooler/output/All/nt2/prom_300_tata/results_log +++ b/TextFooler/output/All/nt2/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.700%, adv accuracy: 72.400%, avg changed rate: 1.026%, num of queries: 193.1 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 95.700%, adv accuracy: 72.400%, avg changed rate: 1.026%, num of queries: 193.1 diff --git a/TextFooler/output/All/nt2/prom_core_all/results_log b/TextFooler/output/All/nt2/prom_core_all/results_log index dbe7122f..0e3fcb06 100644 --- a/TextFooler/output/All/nt2/prom_core_all/results_log +++ b/TextFooler/output/All/nt2/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 0.000%, avg changed rate: 1.551%, num of queries: 70.6 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 0.000%, avg changed rate: 1.551%, num of queries: 70.6 diff --git a/TextFooler/output/All/nt2/prom_core_notata/results_log b/TextFooler/output/All/nt2/prom_core_notata/results_log index b21d7006..b9215bca 100644 --- a/TextFooler/output/All/nt2/prom_core_notata/results_log +++ b/TextFooler/output/All/nt2/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 81.700%, adv accuracy: 0.000%, avg changed rate: 1.736%, num of queries: 72.5 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 81.700%, adv accuracy: 0.000%, avg changed rate: 1.736%, num of queries: 72.5 diff --git a/TextFooler/output/All/nt2/prom_core_tata/results_log b/TextFooler/output/All/nt2/prom_core_tata/results_log index db75620f..af1d2f72 100644 --- a/TextFooler/output/All/nt2/prom_core_tata/results_log +++ b/TextFooler/output/All/nt2/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 72.400%, avg changed rate: 2.103%, num of queries: 82.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 95.900%, adv accuracy: 72.400%, avg changed rate: 2.103%, num of queries: 82.9 diff --git a/TextFooler/output/All/nt2/tf0/results_log b/TextFooler/output/All/nt2/tf0/results_log index 1dc6bdc3..cc5a2fc6 100644 --- a/TextFooler/output/All/nt2/tf0/results_log +++ b/TextFooler/output/All/nt2/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.100%, adv accuracy: 0.000%, avg changed rate: 1.414%, num of queries: 169.7 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.100%, adv accuracy: 0.000%, avg changed rate: 1.414%, num of queries: 169.7 diff --git a/TextFooler/output/All/nt2/tf1/results_log b/TextFooler/output/All/nt2/tf1/results_log index 6cc7cab2..54c3a4de 100644 --- a/TextFooler/output/All/nt2/tf1/results_log +++ b/TextFooler/output/All/nt2/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 0.000%, avg changed rate: 1.371%, num of queries: 103.8 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 0.000%, avg changed rate: 1.371%, num of queries: 103.8 diff --git a/TextFooler/output/All/nt2/tf2/results_log b/TextFooler/output/All/nt2/tf2/results_log index 256703d1..100aaca4 100644 --- a/TextFooler/output/All/nt2/tf2/results_log +++ b/TextFooler/output/All/nt2/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 86.300%, adv accuracy: 0.000%, avg changed rate: 1.426%, num of queries: 116.5 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 86.300%, adv accuracy: 0.000%, avg changed rate: 1.426%, num of queries: 116.5 diff --git a/TextFooler/output/All/nt2/tf3/results_log b/TextFooler/output/All/nt2/tf3/results_log index 763ac708..3b0c397d 100644 --- a/TextFooler/output/All/nt2/tf3/results_log +++ b/TextFooler/output/All/nt2/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 81.500%, adv accuracy: 0.000%, avg changed rate: 1.424%, num of queries: 89.8 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 81.500%, adv accuracy: 0.000%, avg changed rate: 1.424%, num of queries: 89.8 diff --git a/TextFooler/output/All/nt2/tf4/results_log b/TextFooler/output/All/nt2/tf4/results_log index fdfe6eb2..9b2e7a0c 100644 --- a/TextFooler/output/All/nt2/tf4/results_log +++ b/TextFooler/output/All/nt2/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 92.400%, adv accuracy: 0.000%, avg changed rate: 1.838%, num of queries: 112.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 92.400%, adv accuracy: 0.000%, avg changed rate: 1.838%, num of queries: 112.9 diff --git a/TextFooler/output/All/og/0/results_log b/TextFooler/output/All/og/0/results_log index 6be0d3c1..235698aa 100644 --- a/TextFooler/output/All/og/0/results_log +++ b/TextFooler/output/All/og/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 84.500%, adv accuracy: 63.600%, avg changed rate: 3.146%, num of queries: 181.1 +For target model GUE/0/five_percent/cat.csv: original accuracy: 84.500%, adv accuracy: 63.600%, avg changed rate: 3.146%, num of queries: 181.1 diff --git a/TextFooler/output/All/og/1/results_log b/TextFooler/output/All/og/1/results_log index 8c574f56..b049ebf6 100644 --- a/TextFooler/output/All/og/1/results_log +++ b/TextFooler/output/All/og/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 59.900%, adv accuracy: 2.200%, avg changed rate: 8.255%, num of queries: 462.1 +For target model GUE/1/five_percent/cat.csv: original accuracy: 59.900%, adv accuracy: 2.200%, avg changed rate: 8.255%, num of queries: 462.1 diff --git a/TextFooler/output/All/og/2/results_log b/TextFooler/output/All/og/2/results_log index 17c0cb95..8b967f35 100644 --- a/TextFooler/output/All/og/2/results_log +++ b/TextFooler/output/All/og/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 85.300%, avg changed rate: 2.911%, num of queries: 170.7 +For target model GUE/2/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 85.300%, avg changed rate: 2.911%, num of queries: 170.7 diff --git a/TextFooler/output/All/og/3/results_log b/TextFooler/output/All/og/3/results_log index cf51089d..5c23ce00 100644 --- a/TextFooler/output/All/og/3/results_log +++ b/TextFooler/output/All/og/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 89.300%, avg changed rate: 3.539%, num of queries: 203.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 89.300%, avg changed rate: 3.539%, num of queries: 203.5 diff --git a/TextFooler/output/All/og/4/results_log b/TextFooler/output/All/og/4/results_log index 6714717e..34472e9d 100644 --- a/TextFooler/output/All/og/4/results_log +++ b/TextFooler/output/All/og/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 15.300%, avg changed rate: 2.361%, num of queries: 141.2 +For target model GUE/4/five_percent/cat.csv: original accuracy: 79.300%, adv accuracy: 15.300%, avg changed rate: 2.361%, num of queries: 141.2 diff --git a/TextFooler/output/All/og/H3/results_log b/TextFooler/output/All/og/H3/results_log index 25432ca5..64e00247 100644 --- a/TextFooler/output/All/og/H3/results_log +++ b/TextFooler/output/All/og/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 87.300%, adv accuracy: 32.600%, avg changed rate: 2.454%, num of queries: 717.5 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 87.300%, adv accuracy: 32.600%, avg changed rate: 2.454%, num of queries: 717.5 diff --git a/TextFooler/output/All/og/H3K14ac/results_log b/TextFooler/output/All/og/H3K14ac/results_log index 6b8357ef..33d7cf33 100644 --- a/TextFooler/output/All/og/H3K14ac/results_log +++ b/TextFooler/output/All/og/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 83.700%, adv accuracy: 0.000%, avg changed rate: 0.580%, num of queries: 249.7 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 83.700%, adv accuracy: 0.000%, avg changed rate: 0.580%, num of queries: 249.7 diff --git a/TextFooler/output/All/og/H3K36me3/results_log b/TextFooler/output/All/og/H3K36me3/results_log index e22fb5ba..896c6c12 100644 --- a/TextFooler/output/All/og/H3K36me3/results_log +++ b/TextFooler/output/All/og/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 0.595%, num of queries: 253.2 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 78.700%, adv accuracy: 0.000%, avg changed rate: 0.595%, num of queries: 253.2 diff --git a/TextFooler/output/All/og/H3K4me1/results_log b/TextFooler/output/All/og/H3K4me1/results_log index cb532237..c0b1955a 100644 --- a/TextFooler/output/All/og/H3K4me1/results_log +++ b/TextFooler/output/All/og/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 71.500%, adv accuracy: 0.000%, avg changed rate: 0.502%, num of queries: 229.7 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 71.500%, adv accuracy: 0.000%, avg changed rate: 0.502%, num of queries: 229.7 diff --git a/TextFooler/output/All/og/H3K4me2/results_log b/TextFooler/output/All/og/H3K4me2/results_log index 4eccc911..e381cd40 100644 --- a/TextFooler/output/All/og/H3K4me2/results_log +++ b/TextFooler/output/All/og/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 68.700%, adv accuracy: 0.000%, avg changed rate: 1.058%, num of queries: 368.8 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 68.700%, adv accuracy: 0.000%, avg changed rate: 1.058%, num of queries: 368.8 diff --git a/TextFooler/output/All/og/H3K4me3/results_log b/TextFooler/output/All/og/H3K4me3/results_log index cd846633..315d9f7e 100644 --- a/TextFooler/output/All/og/H3K4me3/results_log +++ b/TextFooler/output/All/og/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 63.100%, adv accuracy: 0.000%, avg changed rate: 1.848%, num of queries: 566.1 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 63.100%, adv accuracy: 0.000%, avg changed rate: 1.848%, num of queries: 566.1 diff --git a/TextFooler/output/All/og/H3K79me3/results_log b/TextFooler/output/All/og/H3K79me3/results_log index 4ef17258..ba141c3a 100644 --- a/TextFooler/output/All/og/H3K79me3/results_log +++ b/TextFooler/output/All/og/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 0.827%, num of queries: 310.8 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 76.400%, adv accuracy: 0.000%, avg changed rate: 0.827%, num of queries: 310.8 diff --git a/TextFooler/output/All/og/H3K9ac/results_log b/TextFooler/output/All/og/H3K9ac/results_log index baf094c0..95f06048 100644 --- a/TextFooler/output/All/og/H3K9ac/results_log +++ b/TextFooler/output/All/og/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 75.500%, adv accuracy: 0.000%, avg changed rate: 0.956%, num of queries: 343.4 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 75.500%, adv accuracy: 0.000%, avg changed rate: 0.956%, num of queries: 343.4 diff --git a/TextFooler/output/All/og/H4/results_log b/TextFooler/output/All/og/H4/results_log index 454199dd..748c2871 100644 --- a/TextFooler/output/All/og/H4/results_log +++ b/TextFooler/output/All/og/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 95.000%, adv accuracy: 34.300%, avg changed rate: 1.103%, num of queries: 381.3 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 95.000%, adv accuracy: 34.300%, avg changed rate: 1.103%, num of queries: 381.3 diff --git a/TextFooler/output/All/og/H4ac/results_log b/TextFooler/output/All/og/H4ac/results_log index 5280be11..750159a8 100644 --- a/TextFooler/output/All/og/H4ac/results_log +++ b/TextFooler/output/All/og/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 71.900%, adv accuracy: 0.000%, avg changed rate: 0.833%, num of queries: 312.5 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 71.900%, adv accuracy: 0.000%, avg changed rate: 0.833%, num of queries: 312.5 diff --git a/TextFooler/output/All/og/prom_300_all/results_log b/TextFooler/output/All/og/prom_300_all/results_log index 41a520a4..be032329 100644 --- a/TextFooler/output/All/og/prom_300_all/results_log +++ b/TextFooler/output/All/og/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 88.500%, adv accuracy: 0.000%, avg changed rate: 1.053%, num of queries: 220.6 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 88.500%, adv accuracy: 0.000%, avg changed rate: 1.053%, num of queries: 220.6 diff --git a/TextFooler/output/All/og/prom_300_notata/results_log b/TextFooler/output/All/og/prom_300_notata/results_log index b6e10f85..cbefa6fe 100644 --- a/TextFooler/output/All/og/prom_300_notata/results_log +++ b/TextFooler/output/All/og/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 73.000%, adv accuracy: 0.000%, avg changed rate: 1.309%, num of queries: 258.7 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 73.000%, adv accuracy: 0.000%, avg changed rate: 1.309%, num of queries: 258.7 diff --git a/TextFooler/output/All/og/prom_300_tata/results_log b/TextFooler/output/All/og/prom_300_tata/results_log index a8987277..6c84d8c1 100644 --- a/TextFooler/output/All/og/prom_300_tata/results_log +++ b/TextFooler/output/All/og/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 72.400%, avg changed rate: 1.670%, num of queries: 313.0 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 72.400%, avg changed rate: 1.670%, num of queries: 313.0 diff --git a/TextFooler/output/All/og/prom_core_all/results_log b/TextFooler/output/All/og/prom_core_all/results_log index 23d0f382..c4ea2814 100644 --- a/TextFooler/output/All/og/prom_core_all/results_log +++ b/TextFooler/output/All/og/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 53.700%, adv accuracy: 0.900%, avg changed rate: 9.072%, num of queries: 338.5 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 53.700%, adv accuracy: 0.900%, avg changed rate: 9.072%, num of queries: 338.5 diff --git a/TextFooler/output/All/og/prom_core_notata/results_log b/TextFooler/output/All/og/prom_core_notata/results_log index b7947bff..650a4304 100644 --- a/TextFooler/output/All/og/prom_core_notata/results_log +++ b/TextFooler/output/All/og/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 61.200%, adv accuracy: 0.000%, avg changed rate: 4.788%, num of queries: 183.3 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 61.200%, adv accuracy: 0.000%, avg changed rate: 4.788%, num of queries: 183.3 diff --git a/TextFooler/output/All/og/prom_core_tata/results_log b/TextFooler/output/All/og/prom_core_tata/results_log index 16b6733a..05577b7f 100644 --- a/TextFooler/output/All/og/prom_core_tata/results_log +++ b/TextFooler/output/All/og/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 72.500%, avg changed rate: 4.373%, num of queries: 173.3 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 72.500%, avg changed rate: 4.373%, num of queries: 173.3 diff --git a/TextFooler/output/All/og/tf0/results_log b/TextFooler/output/All/og/tf0/results_log index a0f9b28d..99b80bbe 100644 --- a/TextFooler/output/All/og/tf0/results_log +++ b/TextFooler/output/All/og/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 78.400%, adv accuracy: 0.000%, avg changed rate: 3.093%, num of queries: 178.2 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 78.400%, adv accuracy: 0.000%, avg changed rate: 3.093%, num of queries: 178.2 diff --git a/TextFooler/output/All/og/tf1/results_log b/TextFooler/output/All/og/tf1/results_log index a3441ee6..bfbd872a 100644 --- a/TextFooler/output/All/og/tf1/results_log +++ b/TextFooler/output/All/og/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 75.700%, adv accuracy: 0.000%, avg changed rate: 2.629%, num of queries: 154.7 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 75.700%, adv accuracy: 0.000%, avg changed rate: 2.629%, num of queries: 154.7 diff --git a/TextFooler/output/All/og/tf2/results_log b/TextFooler/output/All/og/tf2/results_log index 5bd6cff5..bdce2df3 100644 --- a/TextFooler/output/All/og/tf2/results_log +++ b/TextFooler/output/All/og/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 71.500%, adv accuracy: 0.000%, avg changed rate: 4.035%, num of queries: 225.6 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 71.500%, adv accuracy: 0.000%, avg changed rate: 4.035%, num of queries: 225.6 diff --git a/TextFooler/output/All/og/tf3/results_log b/TextFooler/output/All/og/tf3/results_log index ab931400..cd082916 100644 --- a/TextFooler/output/All/og/tf3/results_log +++ b/TextFooler/output/All/og/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 59.200%, adv accuracy: 0.000%, avg changed rate: 2.750%, num of queries: 161.4 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 59.200%, adv accuracy: 0.000%, avg changed rate: 2.750%, num of queries: 161.4 diff --git a/TextFooler/output/All/og/tf4/results_log b/TextFooler/output/All/og/tf4/results_log index 7e9248bf..7a8f01c1 100644 --- a/TextFooler/output/All/og/tf4/results_log +++ b/TextFooler/output/All/og/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 89.200%, adv accuracy: 0.100%, avg changed rate: 2.916%, num of queries: 170.7 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 89.200%, adv accuracy: 0.100%, avg changed rate: 2.916%, num of queries: 170.7 diff --git a/TextFooler/output/FreeLB/dnabert/0/results_log b/TextFooler/output/FreeLB/dnabert/0/results_log index 70a21302..3c1dd271 100644 --- a/TextFooler/output/FreeLB/dnabert/0/results_log +++ b/TextFooler/output/FreeLB/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 65.500%, avg changed rate: 3.584%, num of queries: 268.9 +For target model GUE/0/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 65.500%, avg changed rate: 3.584%, num of queries: 268.9 diff --git a/TextFooler/output/FreeLB/dnabert/1/results_log b/TextFooler/output/FreeLB/dnabert/1/results_log index 596ef06e..fb216ec1 100644 --- a/TextFooler/output/FreeLB/dnabert/1/results_log +++ b/TextFooler/output/FreeLB/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 97.800%, adv accuracy: 0.000%, avg changed rate: 3.114%, num of queries: 178.3 +For target model GUE/1/five_percent/cat.csv: original accuracy: 97.800%, adv accuracy: 0.000%, avg changed rate: 3.114%, num of queries: 178.3 diff --git a/TextFooler/output/FreeLB/dnabert/2/results_log b/TextFooler/output/FreeLB/dnabert/2/results_log index f5a0c434..979bca8b 100644 --- a/TextFooler/output/FreeLB/dnabert/2/results_log +++ b/TextFooler/output/FreeLB/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.900%, adv accuracy: 85.800%, avg changed rate: 3.616%, num of queries: 230.7 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.900%, adv accuracy: 85.800%, avg changed rate: 3.616%, num of queries: 230.7 diff --git a/TextFooler/output/FreeLB/dnabert/3/results_log b/TextFooler/output/FreeLB/dnabert/3/results_log index 275d41be..08ffcbb0 100644 --- a/TextFooler/output/FreeLB/dnabert/3/results_log +++ b/TextFooler/output/FreeLB/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 89.800%, avg changed rate: 3.505%, num of queries: 248.6 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 89.800%, avg changed rate: 3.505%, num of queries: 248.6 diff --git a/TextFooler/output/FreeLB/dnabert/4/results_log b/TextFooler/output/FreeLB/dnabert/4/results_log index 4e6b6942..ed1602f1 100644 --- a/TextFooler/output/FreeLB/dnabert/4/results_log +++ b/TextFooler/output/FreeLB/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 15.300%, avg changed rate: 2.036%, num of queries: 127.0 +For target model GUE/4/five_percent/cat.csv: original accuracy: 94.000%, adv accuracy: 15.300%, avg changed rate: 2.036%, num of queries: 127.0 diff --git a/TextFooler/output/FreeLB/dnabert/H3/results_log b/TextFooler/output/FreeLB/dnabert/H3/results_log index c8f853df..ffe3e627 100644 --- a/TextFooler/output/FreeLB/dnabert/H3/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 33.100%, avg changed rate: 3.202%, num of queries: 943.6 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 97.700%, adv accuracy: 33.100%, avg changed rate: 3.202%, num of queries: 943.6 diff --git a/TextFooler/output/FreeLB/dnabert/H3K14ac/results_log b/TextFooler/output/FreeLB/dnabert/H3K14ac/results_log index 5b051e1d..b43bf1e3 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K14ac/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 0.100%, avg changed rate: 0.988%, num of queries: 372.2 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 0.100%, avg changed rate: 0.988%, num of queries: 372.2 diff --git a/TextFooler/output/FreeLB/dnabert/H3K36me3/results_log b/TextFooler/output/FreeLB/dnabert/H3K36me3/results_log index be38b0d1..0d3070a7 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K36me3/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 0.000%, avg changed rate: 0.968%, num of queries: 350.7 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 94.100%, adv accuracy: 0.000%, avg changed rate: 0.968%, num of queries: 350.7 diff --git a/TextFooler/output/FreeLB/dnabert/H3K4me1/results_log b/TextFooler/output/FreeLB/dnabert/H3K4me1/results_log index 77a54077..1e93a5c1 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K4me1/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 85.600%, adv accuracy: 0.000%, avg changed rate: 0.942%, num of queries: 337.6 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 85.600%, adv accuracy: 0.000%, avg changed rate: 0.942%, num of queries: 337.6 diff --git a/TextFooler/output/FreeLB/dnabert/H3K4me2/results_log b/TextFooler/output/FreeLB/dnabert/H3K4me2/results_log index 89e3d59f..dd2cf72d 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K4me2/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 88.900%, adv accuracy: 0.000%, avg changed rate: 1.008%, num of queries: 354.3 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 88.900%, adv accuracy: 0.000%, avg changed rate: 1.008%, num of queries: 354.3 diff --git a/TextFooler/output/FreeLB/dnabert/H3K4me3/results_log b/TextFooler/output/FreeLB/dnabert/H3K4me3/results_log index a3f2df9e..1c7adff7 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K4me3/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 89.500%, adv accuracy: 0.000%, avg changed rate: 0.773%, num of queries: 296.8 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 89.500%, adv accuracy: 0.000%, avg changed rate: 0.773%, num of queries: 296.8 diff --git a/TextFooler/output/FreeLB/dnabert/H3K79me3/results_log b/TextFooler/output/FreeLB/dnabert/H3K79me3/results_log index 79f94292..4116d858 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K79me3/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 0.000%, avg changed rate: 1.644%, num of queries: 513.1 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 93.600%, adv accuracy: 0.000%, avg changed rate: 1.644%, num of queries: 513.1 diff --git a/TextFooler/output/FreeLB/dnabert/H3K9ac/results_log b/TextFooler/output/FreeLB/dnabert/H3K9ac/results_log index 20a46904..c30817c5 100644 --- a/TextFooler/output/FreeLB/dnabert/H3K9ac/results_log +++ b/TextFooler/output/FreeLB/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.767%, num of queries: 544.3 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.767%, num of queries: 544.3 diff --git a/TextFooler/output/FreeLB/dnabert/H4/results_log b/TextFooler/output/FreeLB/dnabert/H4/results_log index 45f6229c..2914b6d6 100644 --- a/TextFooler/output/FreeLB/dnabert/H4/results_log +++ b/TextFooler/output/FreeLB/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 34.300%, avg changed rate: 2.429%, num of queries: 709.5 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 34.300%, avg changed rate: 2.429%, num of queries: 709.5 diff --git a/TextFooler/output/FreeLB/dnabert/H4ac/results_log b/TextFooler/output/FreeLB/dnabert/H4ac/results_log index 1bcd648c..f4ecf0d0 100644 --- a/TextFooler/output/FreeLB/dnabert/H4ac/results_log +++ b/TextFooler/output/FreeLB/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 0.000%, avg changed rate: 1.001%, num of queries: 352.4 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 0.000%, avg changed rate: 1.001%, num of queries: 352.4 diff --git a/TextFooler/output/FreeLB/dnabert/prom_300_all/results_log b/TextFooler/output/FreeLB/dnabert/prom_300_all/results_log index 9b5bfcd4..bbbcfa3e 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_300_all/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 0.000%, avg changed rate: 1.928%, num of queries: 356.2 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 0.000%, avg changed rate: 1.928%, num of queries: 356.2 diff --git a/TextFooler/output/FreeLB/dnabert/prom_300_notata/results_log b/TextFooler/output/FreeLB/dnabert/prom_300_notata/results_log index 09b49d55..4114a77e 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 3.000%, avg changed rate: 2.777%, num of queries: 567.6 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 3.000%, avg changed rate: 2.777%, num of queries: 567.6 diff --git a/TextFooler/output/FreeLB/dnabert/prom_300_tata/results_log b/TextFooler/output/FreeLB/dnabert/prom_300_tata/results_log index 14de03f5..c07dfdc1 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.100%, adv accuracy: 72.500%, avg changed rate: 3.514%, num of queries: 599.9 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.100%, adv accuracy: 72.500%, avg changed rate: 3.514%, num of queries: 599.9 diff --git a/TextFooler/output/FreeLB/dnabert/prom_core_all/results_log b/TextFooler/output/FreeLB/dnabert/prom_core_all/results_log index ba4129b8..a4a2c846 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_core_all/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 2.787%, num of queries: 115.7 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 2.787%, num of queries: 115.7 diff --git a/TextFooler/output/FreeLB/dnabert/prom_core_notata/results_log b/TextFooler/output/FreeLB/dnabert/prom_core_notata/results_log index aec0054c..7c1d3ac1 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 89.500%, adv accuracy: 0.900%, avg changed rate: 3.068%, num of queries: 132.2 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 89.500%, adv accuracy: 0.900%, avg changed rate: 3.068%, num of queries: 132.2 diff --git a/TextFooler/output/FreeLB/dnabert/prom_core_tata/results_log b/TextFooler/output/FreeLB/dnabert/prom_core_tata/results_log index 9f3cfba3..3376b61e 100644 --- a/TextFooler/output/FreeLB/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 72.700%, avg changed rate: 2.172%, num of queries: 100.0 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 72.700%, avg changed rate: 2.172%, num of queries: 100.0 diff --git a/TextFooler/output/FreeLB/dnabert/tf0/results_log b/TextFooler/output/FreeLB/dnabert/tf0/results_log index 2663f594..951d3383 100644 --- a/TextFooler/output/FreeLB/dnabert/tf0/results_log +++ b/TextFooler/output/FreeLB/dnabert/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 90.300%, adv accuracy: 0.200%, avg changed rate: 3.313%, num of queries: 192.8 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 90.300%, adv accuracy: 0.200%, avg changed rate: 3.313%, num of queries: 192.8 diff --git a/TextFooler/output/FreeLB/dnabert/tf1/results_log b/TextFooler/output/FreeLB/dnabert/tf1/results_log index 793f0c71..a8d8eaaa 100644 --- a/TextFooler/output/FreeLB/dnabert/tf1/results_log +++ b/TextFooler/output/FreeLB/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 83.900%, adv accuracy: 0.000%, avg changed rate: 3.277%, num of queries: 188.4 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 83.900%, adv accuracy: 0.000%, avg changed rate: 3.277%, num of queries: 188.4 diff --git a/TextFooler/output/FreeLB/dnabert/tf2/results_log b/TextFooler/output/FreeLB/dnabert/tf2/results_log index a1aa92d4..10622228 100644 --- a/TextFooler/output/FreeLB/dnabert/tf2/results_log +++ b/TextFooler/output/FreeLB/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 2.666%, num of queries: 159.6 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 2.666%, num of queries: 159.6 diff --git a/TextFooler/output/FreeLB/dnabert/tf3/results_log b/TextFooler/output/FreeLB/dnabert/tf3/results_log index 64a63f4b..8500c87d 100644 --- a/TextFooler/output/FreeLB/dnabert/tf3/results_log +++ b/TextFooler/output/FreeLB/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.300%, avg changed rate: 2.873%, num of queries: 171.3 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.300%, avg changed rate: 2.873%, num of queries: 171.3 diff --git a/TextFooler/output/FreeLB/dnabert/tf4/results_log b/TextFooler/output/FreeLB/dnabert/tf4/results_log index 45f0d0dc..da649c23 100644 --- a/TextFooler/output/FreeLB/dnabert/tf4/results_log +++ b/TextFooler/output/FreeLB/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 98.300%, adv accuracy: 0.700%, avg changed rate: 3.498%, num of queries: 206.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 98.300%, adv accuracy: 0.700%, avg changed rate: 3.498%, num of queries: 206.9 diff --git a/TextFooler/output/FreeLB/hyena/0/results_log b/TextFooler/output/FreeLB/hyena/0/results_log index ef2a12de..67be6d76 100644 --- a/TextFooler/output/FreeLB/hyena/0/results_log +++ b/TextFooler/output/FreeLB/hyena/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/0/five_percent/cat.csv: original accuracy: 82.200%, adv accuracy: 82.200%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/FreeLB/hyena/1/results_log b/TextFooler/output/FreeLB/hyena/1/results_log index 6417383d..06d8f828 100644 --- a/TextFooler/output/FreeLB/hyena/1/results_log +++ b/TextFooler/output/FreeLB/hyena/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 51.800%, adv accuracy: 10.200%, avg changed rate: 10.860%, num of queries: 117.7 +For target model GUE/1/five_percent/cat.csv: original accuracy: 51.800%, adv accuracy: 10.200%, avg changed rate: 10.860%, num of queries: 117.7 diff --git a/TextFooler/output/FreeLB/hyena/2/results_log b/TextFooler/output/FreeLB/hyena/2/results_log index cc71552b..7c40de0d 100644 --- a/TextFooler/output/FreeLB/hyena/2/results_log +++ b/TextFooler/output/FreeLB/hyena/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 +For target model GUE/2/five_percent/cat.csv: original accuracy: 93.200%, adv accuracy: 93.200%, avg changed rate: nan%, num of queries: 151.9 diff --git a/TextFooler/output/FreeLB/hyena/3/results_log b/TextFooler/output/FreeLB/hyena/3/results_log index a71b29b0..6ef4739c 100644 --- a/TextFooler/output/FreeLB/hyena/3/results_log +++ b/TextFooler/output/FreeLB/hyena/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 94.800%, adv accuracy: 90.000%, avg changed rate: 9.158%, num of queries: 116.4 +For target model GUE/3/five_percent/cat.csv: original accuracy: 94.800%, adv accuracy: 90.000%, avg changed rate: 9.158%, num of queries: 116.4 diff --git a/TextFooler/output/FreeLB/hyena/4/results_log b/TextFooler/output/FreeLB/hyena/4/results_log index c675bb62..f61cc8ab 100644 --- a/TextFooler/output/FreeLB/hyena/4/results_log +++ b/TextFooler/output/FreeLB/hyena/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 58.800%, adv accuracy: 47.500%, avg changed rate: 14.203%, num of queries: 143.4 +For target model GUE/4/five_percent/cat.csv: original accuracy: 58.800%, adv accuracy: 47.500%, avg changed rate: 14.203%, num of queries: 143.4 diff --git a/TextFooler/output/FreeLB/hyena/H3/results_log b/TextFooler/output/FreeLB/hyena/H3/results_log index 4d03a0fd..23f0d3d4 100644 --- a/TextFooler/output/FreeLB/hyena/H3/results_log +++ b/TextFooler/output/FreeLB/hyena/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 63.400%, adv accuracy: 63.400%, avg changed rate: nan%, num of queries: 749.7 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 63.400%, adv accuracy: 63.400%, avg changed rate: nan%, num of queries: 749.7 diff --git a/TextFooler/output/FreeLB/hyena/H3K14ac/results_log b/TextFooler/output/FreeLB/hyena/H3K14ac/results_log index 6aa90c1b..14d503f8 100644 --- a/TextFooler/output/FreeLB/hyena/H3K14ac/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 57.300%, adv accuracy: 56.200%, avg changed rate: 23.073%, num of queries: 747.9 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 57.300%, adv accuracy: 56.200%, avg changed rate: 23.073%, num of queries: 747.9 diff --git a/TextFooler/output/FreeLB/hyena/H3K36me3/results_log b/TextFooler/output/FreeLB/hyena/H3K36me3/results_log index 47627561..f316312f 100644 --- a/TextFooler/output/FreeLB/hyena/H3K36me3/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 56.200%, adv accuracy: 39.900%, avg changed rate: 11.410%, num of queries: 712.4 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 56.200%, adv accuracy: 39.900%, avg changed rate: 11.410%, num of queries: 712.4 diff --git a/TextFooler/output/FreeLB/hyena/H3K4me1/results_log b/TextFooler/output/FreeLB/hyena/H3K4me1/results_log index ac776458..4612160f 100644 --- a/TextFooler/output/FreeLB/hyena/H3K4me1/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 47.600%, adv accuracy: 35.800%, avg changed rate: 6.005%, num of queries: 707.2 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 47.600%, adv accuracy: 35.800%, avg changed rate: 6.005%, num of queries: 707.2 diff --git a/TextFooler/output/FreeLB/hyena/H3K4me2/results_log b/TextFooler/output/FreeLB/hyena/H3K4me2/results_log index 7b11faaf..e251917e 100644 --- a/TextFooler/output/FreeLB/hyena/H3K4me2/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 57.600%, adv accuracy: 31.000%, avg changed rate: 6.111%, num of queries: 653.8 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 57.600%, adv accuracy: 31.000%, avg changed rate: 6.111%, num of queries: 653.8 diff --git a/TextFooler/output/FreeLB/hyena/H3K4me3/results_log b/TextFooler/output/FreeLB/hyena/H3K4me3/results_log index 1c8014f9..385b2917 100644 --- a/TextFooler/output/FreeLB/hyena/H3K4me3/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 53.400%, adv accuracy: 53.400%, avg changed rate: nan%, num of queries: 751.5 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 53.400%, adv accuracy: 53.400%, avg changed rate: nan%, num of queries: 751.5 diff --git a/TextFooler/output/FreeLB/hyena/H3K79me3/results_log b/TextFooler/output/FreeLB/hyena/H3K79me3/results_log index 1dd62bd6..8094fe50 100644 --- a/TextFooler/output/FreeLB/hyena/H3K79me3/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 48.000%, adv accuracy: 9.800%, avg changed rate: 8.693%, num of queries: 601.8 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 48.000%, adv accuracy: 9.800%, avg changed rate: 8.693%, num of queries: 601.8 diff --git a/TextFooler/output/FreeLB/hyena/H3K9ac/results_log b/TextFooler/output/FreeLB/hyena/H3K9ac/results_log index 177896f5..a858d591 100644 --- a/TextFooler/output/FreeLB/hyena/H3K9ac/results_log +++ b/TextFooler/output/FreeLB/hyena/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 52.400%, adv accuracy: 9.400%, avg changed rate: 8.449%, num of queries: 617.0 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 52.400%, adv accuracy: 9.400%, avg changed rate: 8.449%, num of queries: 617.0 diff --git a/TextFooler/output/FreeLB/hyena/H4/results_log b/TextFooler/output/FreeLB/hyena/H4/results_log index a471aca4..602baa9f 100644 --- a/TextFooler/output/FreeLB/hyena/H4/results_log +++ b/TextFooler/output/FreeLB/hyena/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 70.500%, adv accuracy: 63.800%, avg changed rate: 21.352%, num of queries: 734.5 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 70.500%, adv accuracy: 63.800%, avg changed rate: 21.352%, num of queries: 734.5 diff --git a/TextFooler/output/FreeLB/hyena/H4ac/results_log b/TextFooler/output/FreeLB/hyena/H4ac/results_log index 7cab5675..ce557f72 100644 --- a/TextFooler/output/FreeLB/hyena/H4ac/results_log +++ b/TextFooler/output/FreeLB/hyena/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 51.900%, adv accuracy: 1.700%, avg changed rate: 3.204%, num of queries: 550.8 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 51.900%, adv accuracy: 1.700%, avg changed rate: 3.204%, num of queries: 550.8 diff --git a/TextFooler/output/FreeLB/hyena/prom_300_all/results_log b/TextFooler/output/FreeLB/hyena/prom_300_all/results_log index 73d37619..e40c029e 100644 --- a/TextFooler/output/FreeLB/hyena/prom_300_all/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.300%, adv accuracy: 38.500%, avg changed rate: 18.192%, num of queries: 433.2 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 50.300%, adv accuracy: 38.500%, avg changed rate: 18.192%, num of queries: 433.2 diff --git a/TextFooler/output/FreeLB/hyena/prom_300_notata/results_log b/TextFooler/output/FreeLB/hyena/prom_300_notata/results_log index 9283f0ec..9fb40d00 100644 --- a/TextFooler/output/FreeLB/hyena/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 50.700%, adv accuracy: 50.700%, avg changed rate: nan%, num of queries: 451.6 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 50.700%, adv accuracy: 50.700%, avg changed rate: nan%, num of queries: 451.6 diff --git a/TextFooler/output/FreeLB/hyena/prom_300_tata/results_log b/TextFooler/output/FreeLB/hyena/prom_300_tata/results_log index 9f3d4cb6..b2674569 100644 --- a/TextFooler/output/FreeLB/hyena/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 85.600%, adv accuracy: 80.000%, avg changed rate: 15.595%, num of queries: 416.4 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 85.600%, adv accuracy: 80.000%, avg changed rate: 15.595%, num of queries: 416.4 diff --git a/TextFooler/output/FreeLB/hyena/prom_core_all/results_log b/TextFooler/output/FreeLB/hyena/prom_core_all/results_log index 0d60d2a5..d291daca 100644 --- a/TextFooler/output/FreeLB/hyena/prom_core_all/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 53.600%, adv accuracy: 35.600%, avg changed rate: 8.246%, num of queries: 96.3 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 53.600%, adv accuracy: 35.600%, avg changed rate: 8.246%, num of queries: 96.3 diff --git a/TextFooler/output/FreeLB/hyena/prom_core_notata/results_log b/TextFooler/output/FreeLB/hyena/prom_core_notata/results_log index 5e354660..3b2fbcda 100644 --- a/TextFooler/output/FreeLB/hyena/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.500%, adv accuracy: 48.200%, avg changed rate: 8.571%, num of queries: 105.4 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 48.500%, adv accuracy: 48.200%, avg changed rate: 8.571%, num of queries: 105.4 diff --git a/TextFooler/output/FreeLB/hyena/prom_core_tata/results_log b/TextFooler/output/FreeLB/hyena/prom_core_tata/results_log index 878e22cc..f33a0b84 100644 --- a/TextFooler/output/FreeLB/hyena/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB/hyena/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.800%, adv accuracy: 82.200%, avg changed rate: 24.783%, num of queries: 97.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 86.800%, adv accuracy: 82.200%, avg changed rate: 24.783%, num of queries: 97.9 diff --git a/TextFooler/output/FreeLB/hyena/tf0/results_log b/TextFooler/output/FreeLB/hyena/tf0/results_log index a7cda175..4f06b71e 100644 --- a/TextFooler/output/FreeLB/hyena/tf0/results_log +++ b/TextFooler/output/FreeLB/hyena/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 49.300%, adv accuracy: 11.500%, avg changed rate: 7.193%, num of queries: 121.5 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 49.300%, adv accuracy: 11.500%, avg changed rate: 7.193%, num of queries: 121.5 diff --git a/TextFooler/output/FreeLB/hyena/tf1/results_log b/TextFooler/output/FreeLB/hyena/tf1/results_log index 1d6b704e..dc8d2296 100644 --- a/TextFooler/output/FreeLB/hyena/tf1/results_log +++ b/TextFooler/output/FreeLB/hyena/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 55.600%, adv accuracy: 10.800%, avg changed rate: 8.294%, num of queries: 119.5 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 55.600%, adv accuracy: 10.800%, avg changed rate: 8.294%, num of queries: 119.5 diff --git a/TextFooler/output/FreeLB/hyena/tf2/results_log b/TextFooler/output/FreeLB/hyena/tf2/results_log index eb13aefe..ce4662b9 100644 --- a/TextFooler/output/FreeLB/hyena/tf2/results_log +++ b/TextFooler/output/FreeLB/hyena/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 50.300%, adv accuracy: 48.100%, avg changed rate: 21.017%, num of queries: 150.4 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 50.300%, adv accuracy: 48.100%, avg changed rate: 21.017%, num of queries: 150.4 diff --git a/TextFooler/output/FreeLB/hyena/tf3/results_log b/TextFooler/output/FreeLB/hyena/tf3/results_log index 133bdd3b..8eaa47ca 100644 --- a/TextFooler/output/FreeLB/hyena/tf3/results_log +++ b/TextFooler/output/FreeLB/hyena/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 47.700%, adv accuracy: 47.700%, avg changed rate: nan%, num of queries: 153.2 diff --git a/TextFooler/output/FreeLB/hyena/tf4/results_log b/TextFooler/output/FreeLB/hyena/tf4/results_log index 6472384d..14860e6c 100644 --- a/TextFooler/output/FreeLB/hyena/tf4/results_log +++ b/TextFooler/output/FreeLB/hyena/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 42.600%, adv accuracy: 6.000%, avg changed rate: 8.659%, num of queries: 116.3 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 42.600%, adv accuracy: 6.000%, avg changed rate: 8.659%, num of queries: 116.3 diff --git a/TextFooler/output/FreeLB/nt1/0/results_log b/TextFooler/output/FreeLB/nt1/0/results_log index b178caf9..5e0b1117 100644 --- a/TextFooler/output/FreeLB/nt1/0/results_log +++ b/TextFooler/output/FreeLB/nt1/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 74.300%, avg changed rate: 4.764%, num of queries: 31.6 -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 74.300%, avg changed rate: 4.764%, num of queries: 31.6 +For target model GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 74.300%, avg changed rate: 4.764%, num of queries: 31.6 +For target model GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 74.300%, avg changed rate: 4.764%, num of queries: 31.6 diff --git a/TextFooler/output/FreeLB/nt1/1/results_log b/TextFooler/output/FreeLB/nt1/1/results_log index 8bd64485..fb35c7b7 100644 --- a/TextFooler/output/FreeLB/nt1/1/results_log +++ b/TextFooler/output/FreeLB/nt1/1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 55.800%, avg changed rate: 4.145%, num of queries: 32.9 -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 55.800%, avg changed rate: 4.145%, num of queries: 32.9 +For target model GUE/1/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 55.800%, avg changed rate: 4.145%, num of queries: 32.9 +For target model GUE/1/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 55.800%, avg changed rate: 4.145%, num of queries: 32.9 diff --git a/TextFooler/output/FreeLB/nt1/2/results_log b/TextFooler/output/FreeLB/nt1/2/results_log index b1ae39aa..3e4eb14e 100644 --- a/TextFooler/output/FreeLB/nt1/2/results_log +++ b/TextFooler/output/FreeLB/nt1/2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 92.200%, avg changed rate: 5.405%, num of queries: 33.3 -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 92.200%, avg changed rate: 5.405%, num of queries: 33.3 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 92.200%, avg changed rate: 5.405%, num of queries: 33.3 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 92.200%, avg changed rate: 5.405%, num of queries: 33.3 diff --git a/TextFooler/output/FreeLB/nt1/3/results_log b/TextFooler/output/FreeLB/nt1/3/results_log index 8184692c..97e99d4a 100644 --- a/TextFooler/output/FreeLB/nt1/3/results_log +++ b/TextFooler/output/FreeLB/nt1/3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.600%, avg changed rate: 5.726%, num of queries: 33.4 -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.600%, avg changed rate: 5.726%, num of queries: 33.4 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.600%, avg changed rate: 5.726%, num of queries: 33.4 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 93.600%, avg changed rate: 5.726%, num of queries: 33.4 diff --git a/TextFooler/output/FreeLB/nt1/4/results_log b/TextFooler/output/FreeLB/nt1/4/results_log index c1901792..9b05216c 100644 --- a/TextFooler/output/FreeLB/nt1/4/results_log +++ b/TextFooler/output/FreeLB/nt1/4/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 +For target model GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 +For target model GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 +For target model GUE/4/five_percent/cat.csv: original accuracy: 97.100%, adv accuracy: 30.800%, avg changed rate: 3.972%, num of queries: 29.7 diff --git a/TextFooler/output/FreeLB/nt1/H3/results_log b/TextFooler/output/FreeLB/nt1/H3/results_log index 59e50a42..7712d4e4 100644 --- a/TextFooler/output/FreeLB/nt1/H3/results_log +++ b/TextFooler/output/FreeLB/nt1/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 97.300%, adv accuracy: 25.000%, avg changed rate: 3.080%, num of queries: 117.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 97.800%, adv accuracy: 48.000%, avg changed rate: 2.925%, num of queries: 116.1 +For target model GUE/H3/cat.csv: original accuracy: 97.300%, adv accuracy: 25.000%, avg changed rate: 3.080%, num of queries: 117.8 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 97.800%, adv accuracy: 48.000%, avg changed rate: 2.925%, num of queries: 116.1 diff --git a/TextFooler/output/FreeLB/nt1/H3K14ac/results_log b/TextFooler/output/FreeLB/nt1/H3K14ac/results_log index faf3538c..3a95555d 100644 --- a/TextFooler/output/FreeLB/nt1/H3K14ac/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 87.000%, adv accuracy: 20.100%, avg changed rate: 1.661%, num of queries: 109.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 19.000%, avg changed rate: 1.637%, num of queries: 108.5 +For target model GUE/H3K14ac/cat.csv: original accuracy: 87.000%, adv accuracy: 20.100%, avg changed rate: 1.661%, num of queries: 109.5 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 87.500%, adv accuracy: 19.000%, avg changed rate: 1.637%, num of queries: 108.5 diff --git a/TextFooler/output/FreeLB/nt1/H3K36me3/results_log b/TextFooler/output/FreeLB/nt1/H3K36me3/results_log index 0e5713c0..8818ee49 100644 --- a/TextFooler/output/FreeLB/nt1/H3K36me3/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 87.400%, adv accuracy: 9.000%, avg changed rate: 2.107%, num of queries: 105.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 89.600%, adv accuracy: 11.500%, avg changed rate: 2.130%, num of queries: 106.9 +For target model GUE/H3K36me3/cat.csv: original accuracy: 87.400%, adv accuracy: 9.000%, avg changed rate: 2.107%, num of queries: 105.5 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 89.600%, adv accuracy: 11.500%, avg changed rate: 2.130%, num of queries: 106.9 diff --git a/TextFooler/output/FreeLB/nt1/H3K4me1/results_log b/TextFooler/output/FreeLB/nt1/H3K4me1/results_log index 92755586..9be524de 100644 --- a/TextFooler/output/FreeLB/nt1/H3K4me1/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 86.300%, adv accuracy: 10.700%, avg changed rate: 1.699%, num of queries: 103.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 88.600%, adv accuracy: 11.300%, avg changed rate: 1.716%, num of queries: 104.6 +For target model GUE/H3K4me1/cat.csv: original accuracy: 86.300%, adv accuracy: 10.700%, avg changed rate: 1.699%, num of queries: 103.8 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 88.600%, adv accuracy: 11.300%, avg changed rate: 1.716%, num of queries: 104.6 diff --git a/TextFooler/output/FreeLB/nt1/H3K4me2/results_log b/TextFooler/output/FreeLB/nt1/H3K4me2/results_log index b8fd13d6..95c86536 100644 --- a/TextFooler/output/FreeLB/nt1/H3K4me2/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 86.500%, adv accuracy: 17.300%, avg changed rate: 1.676%, num of queries: 107.8 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 86.500%, adv accuracy: 17.300%, avg changed rate: 1.676%, num of queries: 107.8 diff --git a/TextFooler/output/FreeLB/nt1/H3K4me3/results_log b/TextFooler/output/FreeLB/nt1/H3K4me3/results_log index d3b87ef3..9f78b0a2 100644 --- a/TextFooler/output/FreeLB/nt1/H3K4me3/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 81.800%, adv accuracy: 7.800%, avg changed rate: 1.782%, num of queries: 103.2 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 81.800%, adv accuracy: 7.800%, avg changed rate: 1.782%, num of queries: 103.2 diff --git a/TextFooler/output/FreeLB/nt1/H3K79me3/results_log b/TextFooler/output/FreeLB/nt1/H3K79me3/results_log index 0aa3da51..07aa6452 100644 --- a/TextFooler/output/FreeLB/nt1/H3K79me3/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 92.000%, adv accuracy: 20.400%, avg changed rate: 2.104%, num of queries: 111.0 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 92.000%, adv accuracy: 20.400%, avg changed rate: 2.104%, num of queries: 111.0 diff --git a/TextFooler/output/FreeLB/nt1/H3K9ac/results_log b/TextFooler/output/FreeLB/nt1/H3K9ac/results_log index f033a1ff..95b6c601 100644 --- a/TextFooler/output/FreeLB/nt1/H3K9ac/results_log +++ b/TextFooler/output/FreeLB/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 91.400%, adv accuracy: 37.500%, avg changed rate: 1.364%, num of queries: 116.9 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 91.400%, adv accuracy: 37.500%, avg changed rate: 1.364%, num of queries: 116.9 diff --git a/TextFooler/output/FreeLB/nt1/H4/results_log b/TextFooler/output/FreeLB/nt1/H4/results_log index 0b05b754..19c2293b 100644 --- a/TextFooler/output/FreeLB/nt1/H4/results_log +++ b/TextFooler/output/FreeLB/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 61.600%, avg changed rate: 2.764%, num of queries: 123.4 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 98.000%, adv accuracy: 61.600%, avg changed rate: 2.764%, num of queries: 123.4 diff --git a/TextFooler/output/FreeLB/nt1/H4ac/results_log b/TextFooler/output/FreeLB/nt1/H4ac/results_log index edb0dede..5519beea 100644 --- a/TextFooler/output/FreeLB/nt1/H4ac/results_log +++ b/TextFooler/output/FreeLB/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 83.100%, adv accuracy: 29.200%, avg changed rate: 1.479%, num of queries: 114.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 83.100%, adv accuracy: 29.200%, avg changed rate: 1.479%, num of queries: 114.7 diff --git a/TextFooler/output/FreeLB/nt1/prom_300_all/results_log b/TextFooler/output/FreeLB/nt1/prom_300_all/results_log index 9fe6504d..d8b8a526 100644 --- a/TextFooler/output/FreeLB/nt1/prom_300_all/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 35.400%, avg changed rate: 2.791%, num of queries: 72.7 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 35.400%, avg changed rate: 2.791%, num of queries: 72.7 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 35.400%, avg changed rate: 2.791%, num of queries: 72.7 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.900%, adv accuracy: 35.400%, avg changed rate: 2.791%, num of queries: 72.7 diff --git a/TextFooler/output/FreeLB/nt1/prom_300_notata/results_log b/TextFooler/output/FreeLB/nt1/prom_300_notata/results_log index 2749caaf..f702e052 100644 --- a/TextFooler/output/FreeLB/nt1/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 31.000%, avg changed rate: 2.955%, num of queries: 72.1 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 31.000%, avg changed rate: 2.955%, num of queries: 72.1 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 31.000%, avg changed rate: 2.955%, num of queries: 72.1 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.200%, adv accuracy: 31.000%, avg changed rate: 2.955%, num of queries: 72.1 diff --git a/TextFooler/output/FreeLB/nt1/prom_300_tata/results_log b/TextFooler/output/FreeLB/nt1/prom_300_tata/results_log index 09803b7a..6289308b 100644 --- a/TextFooler/output/FreeLB/nt1/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 84.900%, avg changed rate: 3.438%, num of queries: 76.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 84.900%, avg changed rate: 3.438%, num of queries: 76.3 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 84.900%, avg changed rate: 3.438%, num of queries: 76.3 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 99.800%, adv accuracy: 84.900%, avg changed rate: 3.438%, num of queries: 76.3 diff --git a/TextFooler/output/FreeLB/nt1/prom_core_all/results_log b/TextFooler/output/FreeLB/nt1/prom_core_all/results_log index 4a71d430..55d2895e 100644 --- a/TextFooler/output/FreeLB/nt1/prom_core_all/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 41.600%, avg changed rate: 4.639%, num of queries: 23.7 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 41.600%, avg changed rate: 4.639%, num of queries: 23.7 diff --git a/TextFooler/output/FreeLB/nt1/prom_core_notata/results_log b/TextFooler/output/FreeLB/nt1/prom_core_notata/results_log index 7845d14e..b5df44c5 100644 --- a/TextFooler/output/FreeLB/nt1/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.000%, adv accuracy: 43.800%, avg changed rate: 4.599%, num of queries: 23.8 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.000%, adv accuracy: 43.800%, avg changed rate: 4.599%, num of queries: 23.8 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.000%, adv accuracy: 43.800%, avg changed rate: 4.599%, num of queries: 23.8 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.000%, adv accuracy: 43.800%, avg changed rate: 4.599%, num of queries: 23.8 diff --git a/TextFooler/output/FreeLB/nt1/prom_core_tata/results_log b/TextFooler/output/FreeLB/nt1/prom_core_tata/results_log index acf07b02..8e9b4865 100644 --- a/TextFooler/output/FreeLB/nt1/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB/nt1/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 88.900%, avg changed rate: 5.874%, num of queries: 24.9 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 88.900%, avg changed rate: 5.874%, num of queries: 24.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 88.900%, avg changed rate: 5.874%, num of queries: 24.9 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 88.900%, avg changed rate: 5.874%, num of queries: 24.9 diff --git a/TextFooler/output/FreeLB/nt1/tf0/results_log b/TextFooler/output/FreeLB/nt1/tf0/results_log index d059d329..de04827e 100644 --- a/TextFooler/output/FreeLB/nt1/tf0/results_log +++ b/TextFooler/output/FreeLB/nt1/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 33.800%, avg changed rate: 4.054%, num of queries: 31.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 33.800%, avg changed rate: 4.054%, num of queries: 31.7 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 33.800%, avg changed rate: 4.054%, num of queries: 31.7 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 93.800%, adv accuracy: 33.800%, avg changed rate: 4.054%, num of queries: 31.7 diff --git a/TextFooler/output/FreeLB/nt1/tf1/results_log b/TextFooler/output/FreeLB/nt1/tf1/results_log index a1ba414b..9d13992a 100644 --- a/TextFooler/output/FreeLB/nt1/tf1/results_log +++ b/TextFooler/output/FreeLB/nt1/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 31.200%, avg changed rate: 4.092%, num of queries: 31.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 31.200%, avg changed rate: 4.092%, num of queries: 31.5 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 31.200%, avg changed rate: 4.092%, num of queries: 31.5 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 31.200%, avg changed rate: 4.092%, num of queries: 31.5 diff --git a/TextFooler/output/FreeLB/nt1/tf2/results_log b/TextFooler/output/FreeLB/nt1/tf2/results_log index f91949a1..3ff4c7a8 100644 --- a/TextFooler/output/FreeLB/nt1/tf2/results_log +++ b/TextFooler/output/FreeLB/nt1/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 31.400%, avg changed rate: 3.963%, num of queries: 31.2 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 31.400%, avg changed rate: 3.963%, num of queries: 31.2 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 31.400%, avg changed rate: 3.963%, num of queries: 31.2 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 31.400%, avg changed rate: 3.963%, num of queries: 31.2 diff --git a/TextFooler/output/FreeLB/nt1/tf3/results_log b/TextFooler/output/FreeLB/nt1/tf3/results_log index a803993f..63143d33 100644 --- a/TextFooler/output/FreeLB/nt1/tf3/results_log +++ b/TextFooler/output/FreeLB/nt1/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 25.700%, avg changed rate: 3.806%, num of queries: 30.4 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 25.700%, avg changed rate: 3.806%, num of queries: 30.4 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 25.700%, avg changed rate: 3.806%, num of queries: 30.4 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 91.300%, adv accuracy: 25.700%, avg changed rate: 3.806%, num of queries: 30.4 diff --git a/TextFooler/output/FreeLB/nt1/tf4/results_log b/TextFooler/output/FreeLB/nt1/tf4/results_log index e05dd831..10ec45ca 100644 --- a/TextFooler/output/FreeLB/nt1/tf4/results_log +++ b/TextFooler/output/FreeLB/nt1/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 38.600%, avg changed rate: 4.825%, num of queries: 31.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 38.600%, avg changed rate: 4.825%, num of queries: 31.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 38.600%, avg changed rate: 4.825%, num of queries: 31.9 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 38.600%, avg changed rate: 4.825%, num of queries: 31.9 diff --git a/TextFooler/output/FreeLB/nt2/0/results_log b/TextFooler/output/FreeLB/nt2/0/results_log index 0a1d4906..c6743b4f 100644 --- a/TextFooler/output/FreeLB/nt2/0/results_log +++ b/TextFooler/output/FreeLB/nt2/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 63.600%, avg changed rate: 2.199%, num of queries: 153.4 +For target model GUE/0/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 63.600%, avg changed rate: 2.199%, num of queries: 153.4 diff --git a/TextFooler/output/FreeLB/nt2/1/results_log b/TextFooler/output/FreeLB/nt2/1/results_log index 5b14ef00..465d0342 100644 --- a/TextFooler/output/FreeLB/nt2/1/results_log +++ b/TextFooler/output/FreeLB/nt2/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 0.000%, avg changed rate: 2.891%, num of queries: 192.3 +For target model GUE/1/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 0.000%, avg changed rate: 2.891%, num of queries: 192.3 diff --git a/TextFooler/output/FreeLB/nt2/2/results_log b/TextFooler/output/FreeLB/nt2/2/results_log index 14ed1f3c..e85aa158 100644 --- a/TextFooler/output/FreeLB/nt2/2/results_log +++ b/TextFooler/output/FreeLB/nt2/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 85.700%, avg changed rate: 4.300%, num of queries: 259.4 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 85.700%, avg changed rate: 4.300%, num of queries: 259.4 diff --git a/TextFooler/output/FreeLB/nt2/3/results_log b/TextFooler/output/FreeLB/nt2/3/results_log index c2ea50c1..10e5bcff 100644 --- a/TextFooler/output/FreeLB/nt2/3/results_log +++ b/TextFooler/output/FreeLB/nt2/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 89.300%, avg changed rate: 2.432%, num of queries: 153.7 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.600%, adv accuracy: 89.300%, avg changed rate: 2.432%, num of queries: 153.7 diff --git a/TextFooler/output/FreeLB/nt2/4/results_log b/TextFooler/output/FreeLB/nt2/4/results_log index 11cc9023..e9470817 100644 --- a/TextFooler/output/FreeLB/nt2/4/results_log +++ b/TextFooler/output/FreeLB/nt2/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 91.800%, adv accuracy: 15.300%, avg changed rate: 1.562%, num of queries: 102.4 +For target model GUE/4/five_percent/cat.csv: original accuracy: 91.800%, adv accuracy: 15.300%, avg changed rate: 1.562%, num of queries: 102.4 diff --git a/TextFooler/output/FreeLB/nt2/H3/results_log b/TextFooler/output/FreeLB/nt2/H3/results_log index 96d8a9b0..96097744 100644 --- a/TextFooler/output/FreeLB/nt2/H3/results_log +++ b/TextFooler/output/FreeLB/nt2/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 32.600%, avg changed rate: 1.128%, num of queries: 397.9 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 32.600%, avg changed rate: 1.128%, num of queries: 397.9 diff --git a/TextFooler/output/FreeLB/nt2/H3K14ac/results_log b/TextFooler/output/FreeLB/nt2/H3K14ac/results_log index 7dbdff95..496cedba 100644 --- a/TextFooler/output/FreeLB/nt2/H3K14ac/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 0.923%, num of queries: 347.3 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 0.923%, num of queries: 347.3 diff --git a/TextFooler/output/FreeLB/nt2/H3K36me3/results_log b/TextFooler/output/FreeLB/nt2/H3K36me3/results_log index 4fa4709c..485de09f 100644 --- a/TextFooler/output/FreeLB/nt2/H3K36me3/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 91.400%, adv accuracy: 0.000%, avg changed rate: 0.522%, num of queries: 250.3 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 91.400%, adv accuracy: 0.000%, avg changed rate: 0.522%, num of queries: 250.3 diff --git a/TextFooler/output/FreeLB/nt2/H3K4me1/results_log b/TextFooler/output/FreeLB/nt2/H3K4me1/results_log index 197f1a83..b5344849 100644 --- a/TextFooler/output/FreeLB/nt2/H3K4me1/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 0.557%, num of queries: 221.6 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 87.700%, adv accuracy: 0.000%, avg changed rate: 0.557%, num of queries: 221.6 diff --git a/TextFooler/output/FreeLB/nt2/H3K4me2/results_log b/TextFooler/output/FreeLB/nt2/H3K4me2/results_log index b4511efc..0ddd954d 100644 --- a/TextFooler/output/FreeLB/nt2/H3K4me2/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 0.646%, num of queries: 270.7 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 0.646%, num of queries: 270.7 diff --git a/TextFooler/output/FreeLB/nt2/H3K4me3/results_log b/TextFooler/output/FreeLB/nt2/H3K4me3/results_log index b42e93fa..366182fa 100644 --- a/TextFooler/output/FreeLB/nt2/H3K4me3/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 86.500%, adv accuracy: 0.000%, avg changed rate: 0.532%, num of queries: 233.6 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 86.500%, adv accuracy: 0.000%, avg changed rate: 0.532%, num of queries: 233.6 diff --git a/TextFooler/output/FreeLB/nt2/H3K79me3/results_log b/TextFooler/output/FreeLB/nt2/H3K79me3/results_log index a77c8586..5157fd4e 100644 --- a/TextFooler/output/FreeLB/nt2/H3K79me3/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.000%, avg changed rate: 0.564%, num of queries: 241.0 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 88.000%, adv accuracy: 0.000%, avg changed rate: 0.564%, num of queries: 241.0 diff --git a/TextFooler/output/FreeLB/nt2/H3K9ac/results_log b/TextFooler/output/FreeLB/nt2/H3K9ac/results_log index 26948044..91e66559 100644 --- a/TextFooler/output/FreeLB/nt2/H3K9ac/results_log +++ b/TextFooler/output/FreeLB/nt2/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 0.100%, avg changed rate: 0.619%, num of queries: 253.5 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 92.800%, adv accuracy: 0.100%, avg changed rate: 0.619%, num of queries: 253.5 diff --git a/TextFooler/output/FreeLB/nt2/H4/results_log b/TextFooler/output/FreeLB/nt2/H4/results_log index fd61ff09..68c20173 100644 --- a/TextFooler/output/FreeLB/nt2/H4/results_log +++ b/TextFooler/output/FreeLB/nt2/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 34.300%, avg changed rate: 0.877%, num of queries: 297.4 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 34.300%, avg changed rate: 0.877%, num of queries: 297.4 diff --git a/TextFooler/output/FreeLB/nt2/H4ac/results_log b/TextFooler/output/FreeLB/nt2/H4ac/results_log index 07a88edc..d312f3ad 100644 --- a/TextFooler/output/FreeLB/nt2/H4ac/results_log +++ b/TextFooler/output/FreeLB/nt2/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 0.000%, avg changed rate: 0.556%, num of queries: 232.7 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 0.000%, avg changed rate: 0.556%, num of queries: 232.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 0.000%, avg changed rate: 0.556%, num of queries: 232.7 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 77.000%, adv accuracy: 0.000%, avg changed rate: 0.556%, num of queries: 232.7 diff --git a/TextFooler/output/FreeLB/nt2/prom_300_all/results_log b/TextFooler/output/FreeLB/nt2/prom_300_all/results_log index 8ab50d56..0014f528 100644 --- a/TextFooler/output/FreeLB/nt2/prom_300_all/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 0.700%, avg changed rate: 1.913%, num of queries: 364.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 0.700%, avg changed rate: 1.913%, num of queries: 364.0 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 0.700%, avg changed rate: 1.913%, num of queries: 364.0 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.800%, adv accuracy: 0.700%, avg changed rate: 1.913%, num of queries: 364.0 diff --git a/TextFooler/output/FreeLB/nt2/prom_300_notata/results_log b/TextFooler/output/FreeLB/nt2/prom_300_notata/results_log index 53feb158..22e33aa2 100644 --- a/TextFooler/output/FreeLB/nt2/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 0.000%, avg changed rate: 1.327%, num of queries: 260.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 0.000%, avg changed rate: 1.327%, num of queries: 260.6 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 0.000%, avg changed rate: 1.327%, num of queries: 260.6 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 99.400%, adv accuracy: 0.000%, avg changed rate: 1.327%, num of queries: 260.6 diff --git a/TextFooler/output/FreeLB/nt2/prom_300_tata/results_log b/TextFooler/output/FreeLB/nt2/prom_300_tata/results_log index 2962d467..514df9b6 100644 --- a/TextFooler/output/FreeLB/nt2/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 72.400%, avg changed rate: 1.411%, num of queries: 255.1 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 72.400%, avg changed rate: 1.411%, num of queries: 255.1 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 72.400%, avg changed rate: 1.411%, num of queries: 255.1 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 72.400%, avg changed rate: 1.411%, num of queries: 255.1 diff --git a/TextFooler/output/FreeLB/nt2/prom_core_all/results_log b/TextFooler/output/FreeLB/nt2/prom_core_all/results_log index a565ab1d..b1eb08f0 100644 --- a/TextFooler/output/FreeLB/nt2/prom_core_all/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 85.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 85.0 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 85.0 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 94.200%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 85.0 diff --git a/TextFooler/output/FreeLB/nt2/prom_core_notata/results_log b/TextFooler/output/FreeLB/nt2/prom_core_notata/results_log index 8b517ccc..9874c7aa 100644 --- a/TextFooler/output/FreeLB/nt2/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 2.288%, num of queries: 91.0 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 2.288%, num of queries: 91.0 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 2.288%, num of queries: 91.0 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 2.288%, num of queries: 91.0 diff --git a/TextFooler/output/FreeLB/nt2/prom_core_tata/results_log b/TextFooler/output/FreeLB/nt2/prom_core_tata/results_log index 0e0e80ce..87103fc9 100644 --- a/TextFooler/output/FreeLB/nt2/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB/nt2/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 72.400%, avg changed rate: 2.056%, num of queries: 81.4 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 72.400%, avg changed rate: 2.056%, num of queries: 81.4 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 72.400%, avg changed rate: 2.056%, num of queries: 81.4 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 72.400%, avg changed rate: 2.056%, num of queries: 81.4 diff --git a/TextFooler/output/FreeLB/nt2/tf0/results_log b/TextFooler/output/FreeLB/nt2/tf0/results_log index 04832bec..b966828f 100644 --- a/TextFooler/output/FreeLB/nt2/tf0/results_log +++ b/TextFooler/output/FreeLB/nt2/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 2.185%, num of queries: 131.2 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 2.185%, num of queries: 131.2 diff --git a/TextFooler/output/FreeLB/nt2/tf1/results_log b/TextFooler/output/FreeLB/nt2/tf1/results_log index 1c05c906..a5f438d1 100644 --- a/TextFooler/output/FreeLB/nt2/tf1/results_log +++ b/TextFooler/output/FreeLB/nt2/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 1.967%, num of queries: 121.2 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 86.900%, adv accuracy: 0.000%, avg changed rate: 1.967%, num of queries: 121.2 diff --git a/TextFooler/output/FreeLB/nt2/tf2/results_log b/TextFooler/output/FreeLB/nt2/tf2/results_log index fc4883f7..b5aa6561 100644 --- a/TextFooler/output/FreeLB/nt2/tf2/results_log +++ b/TextFooler/output/FreeLB/nt2/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 92.500%, adv accuracy: 0.000%, avg changed rate: 1.866%, num of queries: 132.1 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 92.500%, adv accuracy: 0.000%, avg changed rate: 1.866%, num of queries: 132.1 diff --git a/TextFooler/output/FreeLB/nt2/tf3/results_log b/TextFooler/output/FreeLB/nt2/tf3/results_log index ed4e39ec..5a3d1ded 100644 --- a/TextFooler/output/FreeLB/nt2/tf3/results_log +++ b/TextFooler/output/FreeLB/nt2/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 1.746%, num of queries: 115.1 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 93.300%, adv accuracy: 0.000%, avg changed rate: 1.746%, num of queries: 115.1 diff --git a/TextFooler/output/FreeLB/nt2/tf4/results_log b/TextFooler/output/FreeLB/nt2/tf4/results_log index 57e0f3f0..954c516e 100644 --- a/TextFooler/output/FreeLB/nt2/tf4/results_log +++ b/TextFooler/output/FreeLB/nt2/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 2.560%, num of queries: 164.7 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 2.560%, num of queries: 164.7 diff --git a/TextFooler/output/FreeLB/og/0/results_log b/TextFooler/output/FreeLB/og/0/results_log index 38e55305..6594db66 100644 --- a/TextFooler/output/FreeLB/og/0/results_log +++ b/TextFooler/output/FreeLB/og/0/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 -For target model /projects/p32013/DNABERT-meta/GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 +For target model GUE/0/five_percent/cat.csv: original accuracy: 98.700%, adv accuracy: 63.600%, avg changed rate: 2.973%, num of queries: 172.3 diff --git a/TextFooler/output/FreeLB/og/1/results_log b/TextFooler/output/FreeLB/og/1/results_log index 32cd1682..15c030f8 100644 --- a/TextFooler/output/FreeLB/og/1/results_log +++ b/TextFooler/output/FreeLB/og/1/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 -For target model /projects/p32013/DNABERT-meta/GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 +For target model GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 +For target model GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 +For target model GUE/1/five_percent/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.208%, num of queries: 133.2 diff --git a/TextFooler/output/FreeLB/og/2/results_log b/TextFooler/output/FreeLB/og/2/results_log index 972e9eac..126bd9f9 100644 --- a/TextFooler/output/FreeLB/og/2/results_log +++ b/TextFooler/output/FreeLB/og/2/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 -For target model /projects/p32013/DNABERT-meta/GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 +For target model GUE/2/five_percent/cat.csv: original accuracy: 99.500%, adv accuracy: 85.300%, avg changed rate: 3.640%, num of queries: 209.6 diff --git a/TextFooler/output/FreeLB/og/3/results_log b/TextFooler/output/FreeLB/og/3/results_log index 7476d174..fdd57260 100644 --- a/TextFooler/output/FreeLB/og/3/results_log +++ b/TextFooler/output/FreeLB/og/3/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 -For target model /projects/p32013/DNABERT-meta/GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 +For target model GUE/3/five_percent/cat.csv: original accuracy: 99.700%, adv accuracy: 89.300%, avg changed rate: 3.218%, num of queries: 189.5 diff --git a/TextFooler/output/FreeLB/og/4/results_log b/TextFooler/output/FreeLB/og/4/results_log index 58522214..4a136b03 100644 --- a/TextFooler/output/FreeLB/og/4/results_log +++ b/TextFooler/output/FreeLB/og/4/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 -For target model /projects/p32013/DNABERT-meta/GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 +For target model GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 +For target model GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 +For target model GUE/4/five_percent/cat.csv: original accuracy: 53.200%, adv accuracy: 15.300%, avg changed rate: 2.625%, num of queries: 154.6 diff --git a/TextFooler/output/FreeLB/og/H3/results_log b/TextFooler/output/FreeLB/og/H3/results_log index 1279f6ce..cd512060 100644 --- a/TextFooler/output/FreeLB/og/H3/results_log +++ b/TextFooler/output/FreeLB/og/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 95.900%, adv accuracy: 0.000%, avg changed rate: 2.155%, num of queries: 642.3 -For target model /projects/p32013/DNABERT-meta/GUE/H3/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 32.600%, avg changed rate: 1.944%, num of queries: 590.1 +For target model GUE/H3/cat.csv: original accuracy: 95.900%, adv accuracy: 0.000%, avg changed rate: 2.155%, num of queries: 642.3 +For target model GUE/H3/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 32.600%, avg changed rate: 1.944%, num of queries: 590.1 diff --git a/TextFooler/output/FreeLB/og/H3K14ac/results_log b/TextFooler/output/FreeLB/og/H3K14ac/results_log index 5efd410b..0612d41c 100644 --- a/TextFooler/output/FreeLB/og/H3K14ac/results_log +++ b/TextFooler/output/FreeLB/og/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.284%, num of queries: 425.4 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 0.000%, avg changed rate: 1.326%, num of queries: 435.9 +For target model GUE/H3K14ac/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.284%, num of queries: 425.4 +For target model GUE/H3K14ac/five_percent/cat.csv: original accuracy: 98.200%, adv accuracy: 0.000%, avg changed rate: 1.326%, num of queries: 435.9 diff --git a/TextFooler/output/FreeLB/og/H3K36me3/results_log b/TextFooler/output/FreeLB/og/H3K36me3/results_log index 5e725b15..1ecf1b92 100644 --- a/TextFooler/output/FreeLB/og/H3K36me3/results_log +++ b/TextFooler/output/FreeLB/og/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/five_percent/cat.csv: original accuracy: 95.800%, adv accuracy: 0.000%, avg changed rate: 0.888%, num of queries: 326.1 +For target model GUE/H3K36me3/five_percent/cat.csv: original accuracy: 95.800%, adv accuracy: 0.000%, avg changed rate: 0.888%, num of queries: 326.1 diff --git a/TextFooler/output/FreeLB/og/H3K4me1/results_log b/TextFooler/output/FreeLB/og/H3K4me1/results_log index 57065338..55a93f8e 100644 --- a/TextFooler/output/FreeLB/og/H3K4me1/results_log +++ b/TextFooler/output/FreeLB/og/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 0.936%, num of queries: 338.3 +For target model GUE/H3K4me1/five_percent/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 0.936%, num of queries: 338.3 diff --git a/TextFooler/output/FreeLB/og/H3K4me2/results_log b/TextFooler/output/FreeLB/og/H3K4me2/results_log index 3f259435..76ed3102 100644 --- a/TextFooler/output/FreeLB/og/H3K4me2/results_log +++ b/TextFooler/output/FreeLB/og/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/five_percent/cat.csv: original accuracy: 37.400%, adv accuracy: 0.000%, avg changed rate: 0.526%, num of queries: 235.6 +For target model GUE/H3K4me2/five_percent/cat.csv: original accuracy: 37.400%, adv accuracy: 0.000%, avg changed rate: 0.526%, num of queries: 235.6 diff --git a/TextFooler/output/FreeLB/og/H3K4me3/results_log b/TextFooler/output/FreeLB/og/H3K4me3/results_log index 046f3950..08270d9f 100644 --- a/TextFooler/output/FreeLB/og/H3K4me3/results_log +++ b/TextFooler/output/FreeLB/og/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 0.000%, avg changed rate: 1.199%, num of queries: 404.5 +For target model GUE/H3K4me3/five_percent/cat.csv: original accuracy: 96.000%, adv accuracy: 0.000%, avg changed rate: 1.199%, num of queries: 404.5 diff --git a/TextFooler/output/FreeLB/og/H3K79me3/results_log b/TextFooler/output/FreeLB/og/H3K79me3/results_log index e7d4ce90..f37b4d4a 100644 --- a/TextFooler/output/FreeLB/og/H3K79me3/results_log +++ b/TextFooler/output/FreeLB/og/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.795%, num of queries: 552.8 +For target model GUE/H3K79me3/five_percent/cat.csv: original accuracy: 92.100%, adv accuracy: 0.000%, avg changed rate: 1.795%, num of queries: 552.8 diff --git a/TextFooler/output/FreeLB/og/H3K9ac/results_log b/TextFooler/output/FreeLB/og/H3K9ac/results_log index 2a310f3f..44c82caf 100644 --- a/TextFooler/output/FreeLB/og/H3K9ac/results_log +++ b/TextFooler/output/FreeLB/og/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/five_percent/cat.csv: original accuracy: 82.700%, adv accuracy: 0.000%, avg changed rate: 1.014%, num of queries: 357.9 +For target model GUE/H3K9ac/five_percent/cat.csv: original accuracy: 82.700%, adv accuracy: 0.000%, avg changed rate: 1.014%, num of queries: 357.9 diff --git a/TextFooler/output/FreeLB/og/H4/results_log b/TextFooler/output/FreeLB/og/H4/results_log index ac40dcfc..832a1727 100644 --- a/TextFooler/output/FreeLB/og/H4/results_log +++ b/TextFooler/output/FreeLB/og/H4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 35.000%, avg changed rate: 3.450%, num of queries: 1012.4 -For target model /projects/p32013/DNABERT-meta/GUE/H4/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 35.000%, avg changed rate: 3.450%, num of queries: 1012.4 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 35.000%, avg changed rate: 3.450%, num of queries: 1012.4 +For target model GUE/H4/five_percent/cat.csv: original accuracy: 99.300%, adv accuracy: 35.000%, avg changed rate: 3.450%, num of queries: 1012.4 diff --git a/TextFooler/output/FreeLB/og/H4ac/results_log b/TextFooler/output/FreeLB/og/H4ac/results_log index 56d004d3..78431420 100644 --- a/TextFooler/output/FreeLB/og/H4ac/results_log +++ b/TextFooler/output/FreeLB/og/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 0.957%, num of queries: 343.3 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 0.957%, num of queries: 343.3 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 0.957%, num of queries: 343.3 +For target model GUE/H4ac/five_percent/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 0.957%, num of queries: 343.3 diff --git a/TextFooler/output/FreeLB/og/prom_300_all/results_log b/TextFooler/output/FreeLB/og/prom_300_all/results_log index ccf37634..1b7d7407 100644 --- a/TextFooler/output/FreeLB/og/prom_300_all/results_log +++ b/TextFooler/output/FreeLB/og/prom_300_all/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 +For target model GUE/prom_300_all/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 0.000%, avg changed rate: 2.228%, num of queries: 396.5 diff --git a/TextFooler/output/FreeLB/og/prom_300_notata/results_log b/TextFooler/output/FreeLB/og/prom_300_notata/results_log index c73e73a0..81cc793c 100644 --- a/TextFooler/output/FreeLB/og/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB/og/prom_300_notata/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 +For target model GUE/prom_300_notata/five_percent/cat.csv: original accuracy: 98.600%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 344.9 diff --git a/TextFooler/output/FreeLB/og/prom_300_tata/results_log b/TextFooler/output/FreeLB/og/prom_300_tata/results_log index 81f0f86b..fd992729 100644 --- a/TextFooler/output/FreeLB/og/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB/og/prom_300_tata/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 +For target model GUE/prom_300_tata/five_percent/cat.csv: original accuracy: 98.100%, adv accuracy: 72.400%, avg changed rate: 1.359%, num of queries: 266.6 diff --git a/TextFooler/output/FreeLB/og/prom_core_all/results_log b/TextFooler/output/FreeLB/og/prom_core_all/results_log index 8daad81f..162276ab 100644 --- a/TextFooler/output/FreeLB/og/prom_core_all/results_log +++ b/TextFooler/output/FreeLB/og/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 3.272%, num of queries: 130.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 3.272%, num of queries: 130.3 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 3.272%, num of queries: 130.3 +For target model GUE/prom_core_all/five_percent/cat.csv: original accuracy: 93.400%, adv accuracy: 0.000%, avg changed rate: 3.272%, num of queries: 130.3 diff --git a/TextFooler/output/FreeLB/og/prom_core_notata/results_log b/TextFooler/output/FreeLB/og/prom_core_notata/results_log index 0c567a8e..22c23e81 100644 --- a/TextFooler/output/FreeLB/og/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB/og/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 0.000%, avg changed rate: 3.906%, num of queries: 152.7 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 0.000%, avg changed rate: 3.906%, num of queries: 152.7 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 0.000%, avg changed rate: 3.906%, num of queries: 152.7 +For target model GUE/prom_core_notata/five_percent/cat.csv: original accuracy: 96.700%, adv accuracy: 0.000%, avg changed rate: 3.906%, num of queries: 152.7 diff --git a/TextFooler/output/FreeLB/og/prom_core_tata/results_log b/TextFooler/output/FreeLB/og/prom_core_tata/results_log index 8ffc28da..086d7f15 100644 --- a/TextFooler/output/FreeLB/og/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB/og/prom_core_tata/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 +For target model GUE/prom_core_tata/five_percent/cat.csv: original accuracy: 99.000%, adv accuracy: 72.400%, avg changed rate: 3.899%, num of queries: 154.2 diff --git a/TextFooler/output/FreeLB/og/tf0/results_log b/TextFooler/output/FreeLB/og/tf0/results_log index c0264165..8c0d2e79 100644 --- a/TextFooler/output/FreeLB/og/tf0/results_log +++ b/TextFooler/output/FreeLB/og/tf0/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 +For target model GUE/tf0/five_percent/cat.csv: original accuracy: 86.200%, adv accuracy: 0.000%, avg changed rate: 3.586%, num of queries: 202.9 diff --git a/TextFooler/output/FreeLB/og/tf1/results_log b/TextFooler/output/FreeLB/og/tf1/results_log index e52559fe..d893b26a 100644 --- a/TextFooler/output/FreeLB/og/tf1/results_log +++ b/TextFooler/output/FreeLB/og/tf1/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 +For target model GUE/tf1/five_percent/cat.csv: original accuracy: 45.800%, adv accuracy: 0.000%, avg changed rate: 2.160%, num of queries: 130.8 diff --git a/TextFooler/output/FreeLB/og/tf2/results_log b/TextFooler/output/FreeLB/og/tf2/results_log index d3817d98..34a8575d 100644 --- a/TextFooler/output/FreeLB/og/tf2/results_log +++ b/TextFooler/output/FreeLB/og/tf2/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 +For target model GUE/tf2/five_percent/cat.csv: original accuracy: 96.800%, adv accuracy: 0.000%, avg changed rate: 3.256%, num of queries: 186.5 diff --git a/TextFooler/output/FreeLB/og/tf3/results_log b/TextFooler/output/FreeLB/og/tf3/results_log index 0136e025..b9b7f3bb 100644 --- a/TextFooler/output/FreeLB/og/tf3/results_log +++ b/TextFooler/output/FreeLB/og/tf3/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 +For target model GUE/tf3/five_percent/cat.csv: original accuracy: 61.600%, adv accuracy: 0.000%, avg changed rate: 2.499%, num of queries: 148.7 diff --git a/TextFooler/output/FreeLB/og/tf4/results_log b/TextFooler/output/FreeLB/og/tf4/results_log index c704919c..ef968d8f 100644 --- a/TextFooler/output/FreeLB/og/tf4/results_log +++ b/TextFooler/output/FreeLB/og/tf4/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 +For target model GUE/tf4/five_percent/cat.csv: original accuracy: 97.200%, adv accuracy: 0.000%, avg changed rate: 3.999%, num of queries: 224.5 diff --git a/TextFooler/output/FreeLB1/dnabert/0/results_log b/TextFooler/output/FreeLB1/dnabert/0/results_log index bbe40deb..81d891f5 100644 --- a/TextFooler/output/FreeLB1/dnabert/0/results_log +++ b/TextFooler/output/FreeLB1/dnabert/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 55.900%, adv accuracy: 7.400%, avg changed rate: 8.090%, num of queries: 525.2 -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 98.300%, adv accuracy: 5.800%, avg changed rate: 3.486%, num of queries: 265.5 +For target model GUE/0/cat.csv: original accuracy: 55.900%, adv accuracy: 7.400%, avg changed rate: 8.090%, num of queries: 525.2 +For target model GUE/0/cat.csv: original accuracy: 98.300%, adv accuracy: 5.800%, avg changed rate: 3.486%, num of queries: 265.5 diff --git a/TextFooler/output/FreeLB1/dnabert/1/results_log b/TextFooler/output/FreeLB1/dnabert/1/results_log index b87b918d..504aa7ce 100644 --- a/TextFooler/output/FreeLB1/dnabert/1/results_log +++ b/TextFooler/output/FreeLB1/dnabert/1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 16.200%, avg changed rate: 4.520%, num of queries: 495.9 -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 97.200%, adv accuracy: 0.200%, avg changed rate: 2.946%, num of queries: 171.0 +For target model GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 16.200%, avg changed rate: 4.520%, num of queries: 495.9 +For target model GUE/1/cat.csv: original accuracy: 97.200%, adv accuracy: 0.200%, avg changed rate: 2.946%, num of queries: 171.0 diff --git a/TextFooler/output/FreeLB1/dnabert/2/results_log b/TextFooler/output/FreeLB1/dnabert/2/results_log index 1753adcf..495dd457 100644 --- a/TextFooler/output/FreeLB1/dnabert/2/results_log +++ b/TextFooler/output/FreeLB1/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 99.000%, adv accuracy: 3.700%, avg changed rate: 3.762%, num of queries: 240.8 +For target model GUE/2/cat.csv: original accuracy: 99.000%, adv accuracy: 3.700%, avg changed rate: 3.762%, num of queries: 240.8 diff --git a/TextFooler/output/FreeLB1/dnabert/3/results_log b/TextFooler/output/FreeLB1/dnabert/3/results_log index c91ae2b5..abe02564 100644 --- a/TextFooler/output/FreeLB1/dnabert/3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 99.300%, adv accuracy: 3.700%, avg changed rate: 3.563%, num of queries: 243.1 +For target model GUE/3/cat.csv: original accuracy: 99.300%, adv accuracy: 3.700%, avg changed rate: 3.563%, num of queries: 243.1 diff --git a/TextFooler/output/FreeLB1/dnabert/4/results_log b/TextFooler/output/FreeLB1/dnabert/4/results_log index f95639c9..51fa5495 100644 --- a/TextFooler/output/FreeLB1/dnabert/4/results_log +++ b/TextFooler/output/FreeLB1/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 2.018%, num of queries: 126.7 +For target model GUE/4/cat.csv: original accuracy: 93.900%, adv accuracy: 0.000%, avg changed rate: 2.018%, num of queries: 126.7 diff --git a/TextFooler/output/FreeLB1/dnabert/H3/results_log b/TextFooler/output/FreeLB1/dnabert/H3/results_log index bf5a397a..4b2ebd98 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 3.000%, adv accuracy: 0.000%, avg changed rate: 2.240%, num of queries: 677.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 48.300%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 166.6 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 97.600%, adv accuracy: 0.500%, avg changed rate: 3.477%, num of queries: 1002.5 +For target model GUE/H3/cat.csv: original accuracy: 3.000%, adv accuracy: 0.000%, avg changed rate: 2.240%, num of queries: 677.2 +For target model GUE/H3/cat.csv: original accuracy: 48.300%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 166.6 +For target model GUE/H3/cat.csv: original accuracy: 97.600%, adv accuracy: 0.500%, avg changed rate: 3.477%, num of queries: 1002.5 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K14ac/results_log b/TextFooler/output/FreeLB1/dnabert/H3K14ac/results_log index 63592645..496b7308 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K14ac/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K14ac/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 45.900%, adv accuracy: 0.000%, avg changed rate: 0.278%, num of queries: 172.9 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 58.800%, adv accuracy: 0.000%, avg changed rate: 0.233%, num of queries: 160.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 90.800%, adv accuracy: 0.200%, avg changed rate: 1.077%, num of queries: 399.6 +For target model GUE/H3K14ac/cat.csv: original accuracy: 45.900%, adv accuracy: 0.000%, avg changed rate: 0.278%, num of queries: 172.9 +For target model GUE/H3K14ac/cat.csv: original accuracy: 58.800%, adv accuracy: 0.000%, avg changed rate: 0.233%, num of queries: 160.7 +For target model GUE/H3K14ac/cat.csv: original accuracy: 90.800%, adv accuracy: 0.200%, avg changed rate: 1.077%, num of queries: 399.6 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K36me3/results_log b/TextFooler/output/FreeLB1/dnabert/H3K36me3/results_log index 4217569c..a12cfa9e 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K36me3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K36me3/results_log @@ -1,3 +1,3 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 54.500%, adv accuracy: 0.000%, avg changed rate: 0.249%, num of queries: 165.3 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 73.900%, adv accuracy: 0.000%, avg changed rate: 0.567%, num of queries: 245.0 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 92.000%, adv accuracy: 0.100%, avg changed rate: 0.940%, num of queries: 349.8 +For target model GUE/H3K36me3/cat.csv: original accuracy: 54.500%, adv accuracy: 0.000%, avg changed rate: 0.249%, num of queries: 165.3 +For target model GUE/H3K36me3/cat.csv: original accuracy: 73.900%, adv accuracy: 0.000%, avg changed rate: 0.567%, num of queries: 245.0 +For target model GUE/H3K36me3/cat.csv: original accuracy: 92.000%, adv accuracy: 0.100%, avg changed rate: 0.940%, num of queries: 349.8 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K4me1/results_log b/TextFooler/output/FreeLB1/dnabert/H3K4me1/results_log index dd85bcca..1b872cdc 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K4me1/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 3.500%, adv accuracy: 0.000%, avg changed rate: 0.480%, num of queries: 221.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 0.962%, num of queries: 342.8 +For target model GUE/H3K4me1/cat.csv: original accuracy: 3.500%, adv accuracy: 0.000%, avg changed rate: 0.480%, num of queries: 221.8 +For target model GUE/H3K4me1/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 0.962%, num of queries: 342.8 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K4me2/results_log b/TextFooler/output/FreeLB1/dnabert/H3K4me2/results_log index 441de141..47f17b53 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K4me2/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K4me2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 53.600%, adv accuracy: 0.000%, avg changed rate: 0.248%, num of queries: 164.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 1.031%, num of queries: 360.6 +For target model GUE/H3K4me2/cat.csv: original accuracy: 53.600%, adv accuracy: 0.000%, avg changed rate: 0.248%, num of queries: 164.7 +For target model GUE/H3K4me2/cat.csv: original accuracy: 85.900%, adv accuracy: 0.000%, avg changed rate: 1.031%, num of queries: 360.6 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K4me3/results_log b/TextFooler/output/FreeLB1/dnabert/H3K4me3/results_log index cc5efc48..f67f52f7 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K4me3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K4me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 96.300%, adv accuracy: 43.100%, avg changed rate: 7.187%, num of queries: 3355.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 89.400%, adv accuracy: 0.000%, avg changed rate: 0.725%, num of queries: 285.2 +For target model GUE/H3K4me3/cat.csv: original accuracy: 96.300%, adv accuracy: 43.100%, avg changed rate: 7.187%, num of queries: 3355.2 +For target model GUE/H3K4me3/cat.csv: original accuracy: 89.400%, adv accuracy: 0.000%, avg changed rate: 0.725%, num of queries: 285.2 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K79me3/results_log b/TextFooler/output/FreeLB1/dnabert/H3K79me3/results_log index 486e5363..54ae471c 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K79me3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 47.800%, adv accuracy: 0.000%, avg changed rate: 0.294%, num of queries: 180.0 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 92.600%, adv accuracy: 0.000%, avg changed rate: 1.760%, num of queries: 542.2 +For target model GUE/H3K79me3/cat.csv: original accuracy: 47.800%, adv accuracy: 0.000%, avg changed rate: 0.294%, num of queries: 180.0 +For target model GUE/H3K79me3/cat.csv: original accuracy: 92.600%, adv accuracy: 0.000%, avg changed rate: 1.760%, num of queries: 542.2 diff --git a/TextFooler/output/FreeLB1/dnabert/H3K9ac/results_log b/TextFooler/output/FreeLB1/dnabert/H3K9ac/results_log index 020231bc..1ebe38b2 100644 --- a/TextFooler/output/FreeLB1/dnabert/H3K9ac/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H3K9ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 53.100%, adv accuracy: 0.000%, avg changed rate: 0.273%, num of queries: 171.0 -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 91.100%, adv accuracy: 0.000%, avg changed rate: 1.692%, num of queries: 525.6 +For target model GUE/H3K9ac/cat.csv: original accuracy: 53.100%, adv accuracy: 0.000%, avg changed rate: 0.273%, num of queries: 171.0 +For target model GUE/H3K9ac/cat.csv: original accuracy: 91.100%, adv accuracy: 0.000%, avg changed rate: 1.692%, num of queries: 525.6 diff --git a/TextFooler/output/FreeLB1/dnabert/H4/results_log b/TextFooler/output/FreeLB1/dnabert/H4/results_log index d0cff17e..c07e9d60 100644 --- a/TextFooler/output/FreeLB1/dnabert/H4/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 53.000%, adv accuracy: 0.000%, avg changed rate: 0.255%, num of queries: 165.6 -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 97.600%, adv accuracy: 0.000%, avg changed rate: 2.455%, num of queries: 716.4 +For target model GUE/H4/cat.csv: original accuracy: 53.000%, adv accuracy: 0.000%, avg changed rate: 0.255%, num of queries: 165.6 +For target model GUE/H4/cat.csv: original accuracy: 97.600%, adv accuracy: 0.000%, avg changed rate: 2.455%, num of queries: 716.4 diff --git a/TextFooler/output/FreeLB1/dnabert/H4ac/results_log b/TextFooler/output/FreeLB1/dnabert/H4ac/results_log index 2cdf55d4..f57da345 100644 --- a/TextFooler/output/FreeLB1/dnabert/H4ac/results_log +++ b/TextFooler/output/FreeLB1/dnabert/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 53.900%, adv accuracy: 0.000%, avg changed rate: 0.242%, num of queries: 164.0 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 1.040%, num of queries: 362.3 +For target model GUE/H4ac/cat.csv: original accuracy: 53.900%, adv accuracy: 0.000%, avg changed rate: 0.242%, num of queries: 164.0 +For target model GUE/H4ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 1.040%, num of queries: 362.3 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_300_all/results_log b/TextFooler/output/FreeLB1/dnabert/prom_300_all/results_log index 63ef74bb..1c721333 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_300_all/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 52.500%, adv accuracy: 42.900%, avg changed rate: 3.948%, num of queries: 2769.5 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 98.200%, adv accuracy: 0.000%, avg changed rate: 1.925%, num of queries: 354.9 +For target model GUE/prom_300_all/cat.csv: original accuracy: 52.500%, adv accuracy: 42.900%, avg changed rate: 3.948%, num of queries: 2769.5 +For target model GUE/prom_300_all/cat.csv: original accuracy: 98.200%, adv accuracy: 0.000%, avg changed rate: 1.925%, num of queries: 354.9 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_300_notata/results_log b/TextFooler/output/FreeLB1/dnabert/prom_300_notata/results_log index f72a35c6..1d141e92 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 98.900%, adv accuracy: 69.200%, avg changed rate: 1.312%, num of queries: 2368.2 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 98.400%, adv accuracy: 5.000%, avg changed rate: 2.781%, num of queries: 626.0 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 98.900%, adv accuracy: 69.200%, avg changed rate: 1.312%, num of queries: 2368.2 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 98.400%, adv accuracy: 5.000%, avg changed rate: 2.781%, num of queries: 626.0 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_300_tata/results_log b/TextFooler/output/FreeLB1/dnabert/prom_300_tata/results_log index 14b6aa0e..705f2784 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 91.700%, adv accuracy: 19.000%, avg changed rate: 1.755%, num of queries: 937.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 97.300%, adv accuracy: 1.000%, avg changed rate: 3.157%, num of queries: 562.8 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 91.700%, adv accuracy: 19.000%, avg changed rate: 1.755%, num of queries: 937.6 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 97.300%, adv accuracy: 1.000%, avg changed rate: 3.157%, num of queries: 562.8 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_core_all/results_log b/TextFooler/output/FreeLB1/dnabert/prom_core_all/results_log index 07247477..948a86ae 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_core_all/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 105.9 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 2.810%, num of queries: 117.2 +For target model GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 0.000%, avg changed rate: 2.116%, num of queries: 105.9 +For target model GUE/prom_core_all/cat.csv: original accuracy: 90.900%, adv accuracy: 0.000%, avg changed rate: 2.810%, num of queries: 117.2 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_core_notata/results_log b/TextFooler/output/FreeLB1/dnabert/prom_core_notata/results_log index b24c135f..a3571c49 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 50.700%, adv accuracy: 0.000%, avg changed rate: 1.691%, num of queries: 78.4 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 89.300%, adv accuracy: 1.300%, avg changed rate: 3.216%, num of queries: 139.9 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 50.700%, adv accuracy: 0.000%, avg changed rate: 1.691%, num of queries: 78.4 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 89.300%, adv accuracy: 1.300%, avg changed rate: 3.216%, num of queries: 139.9 diff --git a/TextFooler/output/FreeLB1/dnabert/prom_core_tata/results_log b/TextFooler/output/FreeLB1/dnabert/prom_core_tata/results_log index 2e955493..d9e6f957 100644 --- a/TextFooler/output/FreeLB1/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB1/dnabert/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 6.300%, adv accuracy: 0.000%, avg changed rate: 1.587%, num of queries: 71.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 98.400%, adv accuracy: 1.400%, avg changed rate: 2.240%, num of queries: 104.1 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 6.300%, adv accuracy: 0.000%, avg changed rate: 1.587%, num of queries: 71.6 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 98.400%, adv accuracy: 1.400%, avg changed rate: 2.240%, num of queries: 104.1 diff --git a/TextFooler/output/FreeLB1/dnabert/tf0/results_log b/TextFooler/output/FreeLB1/dnabert/tf0/results_log index 029b2338..d777657f 100644 --- a/TextFooler/output/FreeLB1/dnabert/tf0/results_log +++ b/TextFooler/output/FreeLB1/dnabert/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 59.100%, adv accuracy: 0.000%, avg changed rate: 1.886%, num of queries: 134.5 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 89.100%, adv accuracy: 0.300%, avg changed rate: 3.442%, num of queries: 200.3 +For target model GUE/tf0/cat.csv: original accuracy: 59.100%, adv accuracy: 0.000%, avg changed rate: 1.886%, num of queries: 134.5 +For target model GUE/tf0/cat.csv: original accuracy: 89.100%, adv accuracy: 0.300%, avg changed rate: 3.442%, num of queries: 200.3 diff --git a/TextFooler/output/FreeLB1/dnabert/tf1/results_log b/TextFooler/output/FreeLB1/dnabert/tf1/results_log index ea88b000..9be91085 100644 --- a/TextFooler/output/FreeLB1/dnabert/tf1/results_log +++ b/TextFooler/output/FreeLB1/dnabert/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 58.500%, adv accuracy: 0.000%, avg changed rate: 1.285%, num of queries: 87.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 84.100%, adv accuracy: 0.000%, avg changed rate: 3.326%, num of queries: 190.9 +For target model GUE/tf1/cat.csv: original accuracy: 58.500%, adv accuracy: 0.000%, avg changed rate: 1.285%, num of queries: 87.9 +For target model GUE/tf1/cat.csv: original accuracy: 84.100%, adv accuracy: 0.000%, avg changed rate: 3.326%, num of queries: 190.9 diff --git a/TextFooler/output/FreeLB1/dnabert/tf2/results_log b/TextFooler/output/FreeLB1/dnabert/tf2/results_log index 9e709ab9..23cb509c 100644 --- a/TextFooler/output/FreeLB1/dnabert/tf2/results_log +++ b/TextFooler/output/FreeLB1/dnabert/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 52.700%, adv accuracy: 0.000%, avg changed rate: 1.388%, num of queries: 95.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 2.652%, num of queries: 158.2 +For target model GUE/tf2/cat.csv: original accuracy: 52.700%, adv accuracy: 0.000%, avg changed rate: 1.388%, num of queries: 95.0 +For target model GUE/tf2/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 2.652%, num of queries: 158.2 diff --git a/TextFooler/output/FreeLB1/dnabert/tf3/results_log b/TextFooler/output/FreeLB1/dnabert/tf3/results_log index e3782b43..b5f14838 100644 --- a/TextFooler/output/FreeLB1/dnabert/tf3/results_log +++ b/TextFooler/output/FreeLB1/dnabert/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 49.600%, adv accuracy: 41.000%, avg changed rate: 11.904%, num of queries: 1005.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 90.300%, adv accuracy: 0.100%, avg changed rate: 2.981%, num of queries: 174.8 +For target model GUE/tf3/cat.csv: original accuracy: 49.600%, adv accuracy: 41.000%, avg changed rate: 11.904%, num of queries: 1005.0 +For target model GUE/tf3/cat.csv: original accuracy: 90.300%, adv accuracy: 0.100%, avg changed rate: 2.981%, num of queries: 174.8 diff --git a/TextFooler/output/FreeLB1/dnabert/tf4/results_log b/TextFooler/output/FreeLB1/dnabert/tf4/results_log index 2495e443..a8b268c0 100644 --- a/TextFooler/output/FreeLB1/dnabert/tf4/results_log +++ b/TextFooler/output/FreeLB1/dnabert/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 98.100%, adv accuracy: 12.100%, avg changed rate: 5.807%, num of queries: 431.9 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 98.400%, adv accuracy: 0.800%, avg changed rate: 3.360%, num of queries: 202.6 +For target model GUE/tf4/cat.csv: original accuracy: 98.100%, adv accuracy: 12.100%, avg changed rate: 5.807%, num of queries: 431.9 +For target model GUE/tf4/cat.csv: original accuracy: 98.400%, adv accuracy: 0.800%, avg changed rate: 3.360%, num of queries: 202.6 diff --git a/TextFooler/output/FreeLB1/nt1/0/results_log b/TextFooler/output/FreeLB1/nt1/0/results_log index 725f2bf9..b5e2755a 100644 --- a/TextFooler/output/FreeLB1/nt1/0/results_log +++ b/TextFooler/output/FreeLB1/nt1/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 97.400%, adv accuracy: 30.300%, avg changed rate: 4.669%, num of queries: 31.4 +For target model GUE/0/cat.csv: original accuracy: 97.400%, adv accuracy: 30.300%, avg changed rate: 4.669%, num of queries: 31.4 diff --git a/TextFooler/output/FreeLB1/nt1/1/results_log b/TextFooler/output/FreeLB1/nt1/1/results_log index d60b3178..d695db25 100644 --- a/TextFooler/output/FreeLB1/nt1/1/results_log +++ b/TextFooler/output/FreeLB1/nt1/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 94.700%, adv accuracy: 52.600%, avg changed rate: 4.461%, num of queries: 32.7 +For target model GUE/1/cat.csv: original accuracy: 94.700%, adv accuracy: 52.600%, avg changed rate: 4.461%, num of queries: 32.7 diff --git a/TextFooler/output/FreeLB1/nt1/2/results_log b/TextFooler/output/FreeLB1/nt1/2/results_log index ca60fe8f..d0aed7e8 100644 --- a/TextFooler/output/FreeLB1/nt1/2/results_log +++ b/TextFooler/output/FreeLB1/nt1/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 98.200%, adv accuracy: 40.900%, avg changed rate: 6.077%, num of queries: 33.7 +For target model GUE/2/cat.csv: original accuracy: 98.200%, adv accuracy: 40.900%, avg changed rate: 6.077%, num of queries: 33.7 diff --git a/TextFooler/output/FreeLB1/nt1/3/results_log b/TextFooler/output/FreeLB1/nt1/3/results_log index 6105249c..77c98c78 100644 --- a/TextFooler/output/FreeLB1/nt1/3/results_log +++ b/TextFooler/output/FreeLB1/nt1/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 97.100%, adv accuracy: 45.400%, avg changed rate: 5.508%, num of queries: 33.4 +For target model GUE/3/cat.csv: original accuracy: 97.100%, adv accuracy: 45.400%, avg changed rate: 5.508%, num of queries: 33.4 diff --git a/TextFooler/output/FreeLB1/nt1/4/results_log b/TextFooler/output/FreeLB1/nt1/4/results_log index d31819a3..85ec027d 100644 --- a/TextFooler/output/FreeLB1/nt1/4/results_log +++ b/TextFooler/output/FreeLB1/nt1/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 95.600%, adv accuracy: 22.700%, avg changed rate: 4.144%, num of queries: 30.2 +For target model GUE/4/cat.csv: original accuracy: 95.600%, adv accuracy: 22.700%, avg changed rate: 4.144%, num of queries: 30.2 diff --git a/TextFooler/output/FreeLB1/nt1/H3/results_log b/TextFooler/output/FreeLB1/nt1/H3/results_log index 433ea658..7e5b10ae 100644 --- a/TextFooler/output/FreeLB1/nt1/H3/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 147.4 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 48.500%, adv accuracy: 48.400%, avg changed rate: 5.400%, num of queries: 148.1 +For target model GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 147.4 +For target model GUE/H3/cat.csv: original accuracy: 48.500%, adv accuracy: 48.400%, avg changed rate: 5.400%, num of queries: 148.1 diff --git a/TextFooler/output/FreeLB1/nt1/H3K14ac/results_log b/TextFooler/output/FreeLB1/nt1/H3K14ac/results_log index ceab350e..7824bfa3 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K14ac/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 60.900%, adv accuracy: 40.700%, avg changed rate: 2.455%, num of queries: 133.4 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 63.900%, adv accuracy: 33.800%, avg changed rate: 2.304%, num of queries: 127.3 +For target model GUE/H3K14ac/cat.csv: original accuracy: 60.900%, adv accuracy: 40.700%, avg changed rate: 2.455%, num of queries: 133.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 63.900%, adv accuracy: 33.800%, avg changed rate: 2.304%, num of queries: 127.3 diff --git a/TextFooler/output/FreeLB1/nt1/H3K36me3/results_log b/TextFooler/output/FreeLB1/nt1/H3K36me3/results_log index 9c626aa9..f20e6cf7 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K36me3/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 55.400%, adv accuracy: 55.400%, avg changed rate: nan%, num of queries: 148.1 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 3.500%, adv accuracy: 0.100%, avg changed rate: 1.159%, num of queries: 97.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 55.400%, adv accuracy: 55.400%, avg changed rate: nan%, num of queries: 148.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 3.500%, adv accuracy: 0.100%, avg changed rate: 1.159%, num of queries: 97.1 diff --git a/TextFooler/output/FreeLB1/nt1/H3K4me1/results_log b/TextFooler/output/FreeLB1/nt1/H3K4me1/results_log index abd06f2c..4c618f11 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K4me1/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 7.900%, adv accuracy: 0.400%, avg changed rate: 0.792%, num of queries: 94.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 86.300%, adv accuracy: 10.700%, avg changed rate: 1.699%, num of queries: 103.8 +For target model GUE/H3K4me1/cat.csv: original accuracy: 7.900%, adv accuracy: 0.400%, avg changed rate: 0.792%, num of queries: 94.5 +For target model GUE/H3K4me1/cat.csv: original accuracy: 86.300%, adv accuracy: 10.700%, avg changed rate: 1.699%, num of queries: 103.8 diff --git a/TextFooler/output/FreeLB1/nt1/H3K4me2/results_log b/TextFooler/output/FreeLB1/nt1/H3K4me2/results_log index 2f5616df..5db8b830 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K4me2/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K4me2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 95.400%, adv accuracy: 33.900%, avg changed rate: 2.206%, num of queries: 119.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 83.600%, adv accuracy: 18.800%, avg changed rate: 1.669%, num of queries: 109.1 +For target model GUE/H3K4me2/cat.csv: original accuracy: 95.400%, adv accuracy: 33.900%, avg changed rate: 2.206%, num of queries: 119.2 +For target model GUE/H3K4me2/cat.csv: original accuracy: 83.600%, adv accuracy: 18.800%, avg changed rate: 1.669%, num of queries: 109.1 diff --git a/TextFooler/output/FreeLB1/nt1/H3K4me3/results_log b/TextFooler/output/FreeLB1/nt1/H3K4me3/results_log index abc8d892..1464e3e7 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K4me3/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K4me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 46.900%, adv accuracy: 5.200%, avg changed rate: 1.973%, num of queries: 105.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 79.100%, adv accuracy: 7.300%, avg changed rate: 1.541%, num of queries: 101.4 +For target model GUE/H3K4me3/cat.csv: original accuracy: 46.900%, adv accuracy: 5.200%, avg changed rate: 1.973%, num of queries: 105.7 +For target model GUE/H3K4me3/cat.csv: original accuracy: 79.100%, adv accuracy: 7.300%, avg changed rate: 1.541%, num of queries: 101.4 diff --git a/TextFooler/output/FreeLB1/nt1/H3K79me3/results_log b/TextFooler/output/FreeLB1/nt1/H3K79me3/results_log index ffc0e803..3371cacd 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K79me3/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 52.900%, adv accuracy: 52.900%, avg changed rate: nan%, num of queries: 148.3 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 90.900%, adv accuracy: 23.400%, avg changed rate: 1.966%, num of queries: 112.2 +For target model GUE/H3K79me3/cat.csv: original accuracy: 52.900%, adv accuracy: 52.900%, avg changed rate: nan%, num of queries: 148.3 +For target model GUE/H3K79me3/cat.csv: original accuracy: 90.900%, adv accuracy: 23.400%, avg changed rate: 1.966%, num of queries: 112.2 diff --git a/TextFooler/output/FreeLB1/nt1/H3K9ac/results_log b/TextFooler/output/FreeLB1/nt1/H3K9ac/results_log index 29ef6233..9e816343 100644 --- a/TextFooler/output/FreeLB1/nt1/H3K9ac/results_log +++ b/TextFooler/output/FreeLB1/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 88.500%, adv accuracy: 35.300%, avg changed rate: 1.419%, num of queries: 116.9 +For target model GUE/H3K9ac/cat.csv: original accuracy: 88.500%, adv accuracy: 35.300%, avg changed rate: 1.419%, num of queries: 116.9 diff --git a/TextFooler/output/FreeLB1/nt1/H4/results_log b/TextFooler/output/FreeLB1/nt1/H4/results_log index b41e1b38..9828cb25 100644 --- a/TextFooler/output/FreeLB1/nt1/H4/results_log +++ b/TextFooler/output/FreeLB1/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 96.400%, adv accuracy: 38.400%, avg changed rate: 2.658%, num of queries: 121.7 +For target model GUE/H4/cat.csv: original accuracy: 96.400%, adv accuracy: 38.400%, avg changed rate: 2.658%, num of queries: 121.7 diff --git a/TextFooler/output/FreeLB1/nt1/H4ac/results_log b/TextFooler/output/FreeLB1/nt1/H4ac/results_log index c7293631..c8cd8c93 100644 --- a/TextFooler/output/FreeLB1/nt1/H4ac/results_log +++ b/TextFooler/output/FreeLB1/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 83.800%, adv accuracy: 27.400%, avg changed rate: 1.504%, num of queries: 113.6 +For target model GUE/H4ac/cat.csv: original accuracy: 83.800%, adv accuracy: 27.400%, avg changed rate: 1.504%, num of queries: 113.6 diff --git a/TextFooler/output/FreeLB1/nt1/prom_300_all/results_log b/TextFooler/output/FreeLB1/nt1/prom_300_all/results_log index 72ea43bd..38476a9c 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_300_all/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 98.300%, adv accuracy: 34.300%, avg changed rate: 2.881%, num of queries: 73.2 +For target model GUE/prom_300_all/cat.csv: original accuracy: 98.300%, adv accuracy: 34.300%, avg changed rate: 2.881%, num of queries: 73.2 diff --git a/TextFooler/output/FreeLB1/nt1/prom_300_notata/results_log b/TextFooler/output/FreeLB1/nt1/prom_300_notata/results_log index a5668b49..bbbb75c9 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 98.700%, adv accuracy: 31.700%, avg changed rate: 3.007%, num of queries: 72.2 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 98.700%, adv accuracy: 31.700%, avg changed rate: 3.007%, num of queries: 72.2 diff --git a/TextFooler/output/FreeLB1/nt1/prom_300_tata/results_log b/TextFooler/output/FreeLB1/nt1/prom_300_tata/results_log index 05f1e053..61636962 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 98.500%, adv accuracy: 42.500%, avg changed rate: 3.182%, num of queries: 75.0 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 98.500%, adv accuracy: 42.500%, avg changed rate: 3.182%, num of queries: 75.0 diff --git a/TextFooler/output/FreeLB1/nt1/prom_core_all/results_log b/TextFooler/output/FreeLB1/nt1/prom_core_all/results_log index f0c1b855..fe222733 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_core_all/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 93.100%, adv accuracy: 43.500%, avg changed rate: 4.542%, num of queries: 23.8 +For target model GUE/prom_core_all/cat.csv: original accuracy: 93.100%, adv accuracy: 43.500%, avg changed rate: 4.542%, num of queries: 23.8 diff --git a/TextFooler/output/FreeLB1/nt1/prom_core_notata/results_log b/TextFooler/output/FreeLB1/nt1/prom_core_notata/results_log index ae00026e..30fa30ad 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 94.000%, adv accuracy: 44.000%, avg changed rate: 4.549%, num of queries: 23.8 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 94.000%, adv accuracy: 44.000%, avg changed rate: 4.549%, num of queries: 23.8 diff --git a/TextFooler/output/FreeLB1/nt1/prom_core_tata/results_log b/TextFooler/output/FreeLB1/nt1/prom_core_tata/results_log index a2a4dc1b..b51ca30f 100644 --- a/TextFooler/output/FreeLB1/nt1/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB1/nt1/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 98.200%, adv accuracy: 64.700%, avg changed rate: 6.149%, num of queries: 25.2 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 98.200%, adv accuracy: 64.700%, avg changed rate: 6.149%, num of queries: 25.2 diff --git a/TextFooler/output/FreeLB1/nt1/tf0/results_log b/TextFooler/output/FreeLB1/nt1/tf0/results_log index 1935a140..4925f101 100644 --- a/TextFooler/output/FreeLB1/nt1/tf0/results_log +++ b/TextFooler/output/FreeLB1/nt1/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 93.300%, adv accuracy: 33.800%, avg changed rate: 3.974%, num of queries: 31.7 +For target model GUE/tf0/cat.csv: original accuracy: 93.300%, adv accuracy: 33.800%, avg changed rate: 3.974%, num of queries: 31.7 diff --git a/TextFooler/output/FreeLB1/nt1/tf1/results_log b/TextFooler/output/FreeLB1/nt1/tf1/results_log index a3358f73..fb1c3ad1 100644 --- a/TextFooler/output/FreeLB1/nt1/tf1/results_log +++ b/TextFooler/output/FreeLB1/nt1/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 92.600%, adv accuracy: 33.600%, avg changed rate: 3.975%, num of queries: 31.6 +For target model GUE/tf1/cat.csv: original accuracy: 92.600%, adv accuracy: 33.600%, avg changed rate: 3.975%, num of queries: 31.6 diff --git a/TextFooler/output/FreeLB1/nt1/tf2/results_log b/TextFooler/output/FreeLB1/nt1/tf2/results_log index 04d812b4..3e5ef6d5 100644 --- a/TextFooler/output/FreeLB1/nt1/tf2/results_log +++ b/TextFooler/output/FreeLB1/nt1/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 97.000%, adv accuracy: 36.000%, avg changed rate: 4.035%, num of queries: 31.5 +For target model GUE/tf2/cat.csv: original accuracy: 97.000%, adv accuracy: 36.000%, avg changed rate: 4.035%, num of queries: 31.5 diff --git a/TextFooler/output/FreeLB1/nt1/tf3/results_log b/TextFooler/output/FreeLB1/nt1/tf3/results_log index b481816e..4e3f087d 100644 --- a/TextFooler/output/FreeLB1/nt1/tf3/results_log +++ b/TextFooler/output/FreeLB1/nt1/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 91.600%, adv accuracy: 29.400%, avg changed rate: 3.825%, num of queries: 30.6 +For target model GUE/tf3/cat.csv: original accuracy: 91.600%, adv accuracy: 29.400%, avg changed rate: 3.825%, num of queries: 30.6 diff --git a/TextFooler/output/FreeLB1/nt1/tf4/results_log b/TextFooler/output/FreeLB1/nt1/tf4/results_log index 710405a9..d9d726df 100644 --- a/TextFooler/output/FreeLB1/nt1/tf4/results_log +++ b/TextFooler/output/FreeLB1/nt1/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 98.800%, adv accuracy: 37.500%, avg changed rate: 5.023%, num of queries: 32.0 +For target model GUE/tf4/cat.csv: original accuracy: 98.800%, adv accuracy: 37.500%, avg changed rate: 5.023%, num of queries: 32.0 diff --git a/TextFooler/output/FreeLB1/nt2/0/results_log b/TextFooler/output/FreeLB1/nt2/0/results_log index 6e79266e..a54c311d 100644 --- a/TextFooler/output/FreeLB1/nt2/0/results_log +++ b/TextFooler/output/FreeLB1/nt2/0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 31.800%, adv accuracy: 0.000%, avg changed rate: 1.024%, num of queries: 72.8 -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 98.800%, adv accuracy: 0.100%, avg changed rate: 2.070%, num of queries: 144.8 +For target model GUE/0/cat.csv: original accuracy: 31.800%, adv accuracy: 0.000%, avg changed rate: 1.024%, num of queries: 72.8 +For target model GUE/0/cat.csv: original accuracy: 98.800%, adv accuracy: 0.100%, avg changed rate: 2.070%, num of queries: 144.8 diff --git a/TextFooler/output/FreeLB1/nt2/1/results_log b/TextFooler/output/FreeLB1/nt2/1/results_log index ced536b4..b64fb466 100644 --- a/TextFooler/output/FreeLB1/nt2/1/results_log +++ b/TextFooler/output/FreeLB1/nt2/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 97.600%, adv accuracy: 0.000%, avg changed rate: 2.838%, num of queries: 188.0 +For target model GUE/1/cat.csv: original accuracy: 97.600%, adv accuracy: 0.000%, avg changed rate: 2.838%, num of queries: 188.0 diff --git a/TextFooler/output/FreeLB1/nt2/2/results_log b/TextFooler/output/FreeLB1/nt2/2/results_log index 3701d9ee..06ac4a34 100644 --- a/TextFooler/output/FreeLB1/nt2/2/results_log +++ b/TextFooler/output/FreeLB1/nt2/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 98.200%, adv accuracy: 1.300%, avg changed rate: 4.084%, num of queries: 243.1 +For target model GUE/2/cat.csv: original accuracy: 98.200%, adv accuracy: 1.300%, avg changed rate: 4.084%, num of queries: 243.1 diff --git a/TextFooler/output/FreeLB1/nt2/3/results_log b/TextFooler/output/FreeLB1/nt2/3/results_log index cb74c3bd..763cb6ce 100644 --- a/TextFooler/output/FreeLB1/nt2/3/results_log +++ b/TextFooler/output/FreeLB1/nt2/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 98.900%, adv accuracy: 0.700%, avg changed rate: 2.728%, num of queries: 174.5 +For target model GUE/3/cat.csv: original accuracy: 98.900%, adv accuracy: 0.700%, avg changed rate: 2.728%, num of queries: 174.5 diff --git a/TextFooler/output/FreeLB1/nt2/4/results_log b/TextFooler/output/FreeLB1/nt2/4/results_log index 8848ab09..2a2cb6fd 100644 --- a/TextFooler/output/FreeLB1/nt2/4/results_log +++ b/TextFooler/output/FreeLB1/nt2/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 90.500%, adv accuracy: 0.000%, avg changed rate: 1.536%, num of queries: 101.4 +For target model GUE/4/cat.csv: original accuracy: 90.500%, adv accuracy: 0.000%, avg changed rate: 1.536%, num of queries: 101.4 diff --git a/TextFooler/output/FreeLB1/nt2/H3/results_log b/TextFooler/output/FreeLB1/nt2/H3/results_log index 52fddede..6eaef84f 100644 --- a/TextFooler/output/FreeLB1/nt2/H3/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 1.421%, num of queries: 480.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 54.400%, adv accuracy: 0.100%, avg changed rate: 2.666%, num of queries: 803.6 +For target model GUE/H3/cat.csv: original accuracy: 86.400%, adv accuracy: 0.000%, avg changed rate: 1.421%, num of queries: 480.8 +For target model GUE/H3/cat.csv: original accuracy: 54.400%, adv accuracy: 0.100%, avg changed rate: 2.666%, num of queries: 803.6 diff --git a/TextFooler/output/FreeLB1/nt2/H3K14ac/results_log b/TextFooler/output/FreeLB1/nt2/H3K14ac/results_log index ca51d3ee..d79699de 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K14ac/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 12.800%, adv accuracy: 0.000%, avg changed rate: 0.308%, num of queries: 157.1 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 73.500%, adv accuracy: 0.000%, avg changed rate: 1.063%, num of queries: 389.0 +For target model GUE/H3K14ac/cat.csv: original accuracy: 12.800%, adv accuracy: 0.000%, avg changed rate: 0.308%, num of queries: 157.1 +For target model GUE/H3K14ac/cat.csv: original accuracy: 73.500%, adv accuracy: 0.000%, avg changed rate: 1.063%, num of queries: 389.0 diff --git a/TextFooler/output/FreeLB1/nt2/H3K36me3/results_log b/TextFooler/output/FreeLB1/nt2/H3K36me3/results_log index 689e38b8..28fec394 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K36me3/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 70.000%, adv accuracy: 0.000%, avg changed rate: 0.335%, num of queries: 166.1 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 90.700%, adv accuracy: 0.000%, avg changed rate: 0.530%, num of queries: 250.9 +For target model GUE/H3K36me3/cat.csv: original accuracy: 70.000%, adv accuracy: 0.000%, avg changed rate: 0.335%, num of queries: 166.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 90.700%, adv accuracy: 0.000%, avg changed rate: 0.530%, num of queries: 250.9 diff --git a/TextFooler/output/FreeLB1/nt2/H3K4me1/results_log b/TextFooler/output/FreeLB1/nt2/H3K4me1/results_log index 867f146e..1b15de94 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K4me1/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 72.900%, adv accuracy: 0.000%, avg changed rate: 0.363%, num of queries: 171.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 86.500%, adv accuracy: 0.000%, avg changed rate: 0.536%, num of queries: 216.8 +For target model GUE/H3K4me1/cat.csv: original accuracy: 72.900%, adv accuracy: 0.000%, avg changed rate: 0.363%, num of queries: 171.5 +For target model GUE/H3K4me1/cat.csv: original accuracy: 86.500%, adv accuracy: 0.000%, avg changed rate: 0.536%, num of queries: 216.8 diff --git a/TextFooler/output/FreeLB1/nt2/H3K4me2/results_log b/TextFooler/output/FreeLB1/nt2/H3K4me2/results_log index 10d22791..1329d800 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K4me2/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K4me2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 30.600%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 141.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 84.800%, adv accuracy: 0.000%, avg changed rate: 0.649%, num of queries: 273.2 +For target model GUE/H3K4me2/cat.csv: original accuracy: 30.600%, adv accuracy: 0.000%, avg changed rate: 0.239%, num of queries: 141.2 +For target model GUE/H3K4me2/cat.csv: original accuracy: 84.800%, adv accuracy: 0.000%, avg changed rate: 0.649%, num of queries: 273.2 diff --git a/TextFooler/output/FreeLB1/nt2/H3K4me3/results_log b/TextFooler/output/FreeLB1/nt2/H3K4me3/results_log index 0f494aa4..9b75e919 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K4me3/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K4me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 36.800%, adv accuracy: 0.000%, avg changed rate: 0.247%, num of queries: 149.6 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 84.900%, adv accuracy: 0.000%, avg changed rate: 0.505%, num of queries: 223.8 +For target model GUE/H3K4me3/cat.csv: original accuracy: 36.800%, adv accuracy: 0.000%, avg changed rate: 0.247%, num of queries: 149.6 +For target model GUE/H3K4me3/cat.csv: original accuracy: 84.900%, adv accuracy: 0.000%, avg changed rate: 0.505%, num of queries: 223.8 diff --git a/TextFooler/output/FreeLB1/nt2/H3K79me3/results_log b/TextFooler/output/FreeLB1/nt2/H3K79me3/results_log index 01228201..5dc5b808 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K79me3/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 60.300%, adv accuracy: 0.000%, avg changed rate: 0.248%, num of queries: 162.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 88.900%, adv accuracy: 0.000%, avg changed rate: 0.573%, num of queries: 240.7 +For target model GUE/H3K79me3/cat.csv: original accuracy: 60.300%, adv accuracy: 0.000%, avg changed rate: 0.248%, num of queries: 162.8 +For target model GUE/H3K79me3/cat.csv: original accuracy: 88.900%, adv accuracy: 0.000%, avg changed rate: 0.573%, num of queries: 240.7 diff --git a/TextFooler/output/FreeLB1/nt2/H3K9ac/results_log b/TextFooler/output/FreeLB1/nt2/H3K9ac/results_log index d49d45d0..3c0b2add 100644 --- a/TextFooler/output/FreeLB1/nt2/H3K9ac/results_log +++ b/TextFooler/output/FreeLB1/nt2/H3K9ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 11.600%, adv accuracy: 0.000%, avg changed rate: 0.266%, num of queries: 147.6 -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 91.200%, adv accuracy: 0.000%, avg changed rate: 0.606%, num of queries: 249.4 +For target model GUE/H3K9ac/cat.csv: original accuracy: 11.600%, adv accuracy: 0.000%, avg changed rate: 0.266%, num of queries: 147.6 +For target model GUE/H3K9ac/cat.csv: original accuracy: 91.200%, adv accuracy: 0.000%, avg changed rate: 0.606%, num of queries: 249.4 diff --git a/TextFooler/output/FreeLB1/nt2/H4/results_log b/TextFooler/output/FreeLB1/nt2/H4/results_log index 0dedf41f..fbc03dc1 100644 --- a/TextFooler/output/FreeLB1/nt2/H4/results_log +++ b/TextFooler/output/FreeLB1/nt2/H4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 0.755%, num of queries: 318.9 -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 95.500%, adv accuracy: 0.000%, avg changed rate: 0.883%, num of queries: 299.2 +For target model GUE/H4/cat.csv: original accuracy: 93.100%, adv accuracy: 0.000%, avg changed rate: 0.755%, num of queries: 318.9 +For target model GUE/H4/cat.csv: original accuracy: 95.500%, adv accuracy: 0.000%, avg changed rate: 0.883%, num of queries: 299.2 diff --git a/TextFooler/output/FreeLB1/nt2/H4ac/results_log b/TextFooler/output/FreeLB1/nt2/H4ac/results_log index ba0dc5fd..3c7326f3 100644 --- a/TextFooler/output/FreeLB1/nt2/H4ac/results_log +++ b/TextFooler/output/FreeLB1/nt2/H4ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 35.700%, adv accuracy: 0.000%, avg changed rate: 0.245%, num of queries: 143.0 -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 79.600%, adv accuracy: 0.000%, avg changed rate: 0.578%, num of queries: 238.2 +For target model GUE/H4ac/cat.csv: original accuracy: 35.700%, adv accuracy: 0.000%, avg changed rate: 0.245%, num of queries: 143.0 +For target model GUE/H4ac/cat.csv: original accuracy: 79.600%, adv accuracy: 0.000%, avg changed rate: 0.578%, num of queries: 238.2 diff --git a/TextFooler/output/FreeLB1/nt2/prom_300_all/results_log b/TextFooler/output/FreeLB1/nt2/prom_300_all/results_log index 87011f79..99a712c2 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_300_all/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_300_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 39.600%, adv accuracy: 0.000%, avg changed rate: 0.456%, num of queries: 123.8 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 98.800%, adv accuracy: 0.300%, avg changed rate: 1.911%, num of queries: 355.5 +For target model GUE/prom_300_all/cat.csv: original accuracy: 39.600%, adv accuracy: 0.000%, avg changed rate: 0.456%, num of queries: 123.8 +For target model GUE/prom_300_all/cat.csv: original accuracy: 98.800%, adv accuracy: 0.300%, avg changed rate: 1.911%, num of queries: 355.5 diff --git a/TextFooler/output/FreeLB1/nt2/prom_300_notata/results_log b/TextFooler/output/FreeLB1/nt2/prom_300_notata/results_log index 893dce8b..1a9e1b83 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_300_notata/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_300_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 97.000%, adv accuracy: 27.900%, avg changed rate: 1.523%, num of queries: 878.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 99.100%, adv accuracy: 0.000%, avg changed rate: 1.356%, num of queries: 266.3 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 97.000%, adv accuracy: 27.900%, avg changed rate: 1.523%, num of queries: 878.3 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 99.100%, adv accuracy: 0.000%, avg changed rate: 1.356%, num of queries: 266.3 diff --git a/TextFooler/output/FreeLB1/nt2/prom_300_tata/results_log b/TextFooler/output/FreeLB1/nt2/prom_300_tata/results_log index cd6874b7..5a4a8557 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_300_tata/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_300_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 51.600%, adv accuracy: 0.000%, avg changed rate: 0.512%, num of queries: 125.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 97.100%, adv accuracy: 0.000%, avg changed rate: 1.368%, num of queries: 250.5 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 51.600%, adv accuracy: 0.000%, avg changed rate: 0.512%, num of queries: 125.3 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 97.100%, adv accuracy: 0.000%, avg changed rate: 1.368%, num of queries: 250.5 diff --git a/TextFooler/output/FreeLB1/nt2/prom_core_all/results_log b/TextFooler/output/FreeLB1/nt2/prom_core_all/results_log index 7020f5bf..8f82671b 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_core_all/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_core_all/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 67.100%, adv accuracy: 0.000%, avg changed rate: 1.554%, num of queries: 68.6 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 92.700%, adv accuracy: 0.000%, avg changed rate: 2.184%, num of queries: 87.3 +For target model GUE/prom_core_all/cat.csv: original accuracy: 67.100%, adv accuracy: 0.000%, avg changed rate: 1.554%, num of queries: 68.6 +For target model GUE/prom_core_all/cat.csv: original accuracy: 92.700%, adv accuracy: 0.000%, avg changed rate: 2.184%, num of queries: 87.3 diff --git a/TextFooler/output/FreeLB1/nt2/prom_core_notata/results_log b/TextFooler/output/FreeLB1/nt2/prom_core_notata/results_log index 67435112..e5ec4d99 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_core_notata/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_core_notata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 27.100%, adv accuracy: 0.000%, avg changed rate: 1.460%, num of queries: 62.7 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 93.200%, adv accuracy: 0.000%, avg changed rate: 2.347%, num of queries: 93.3 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 27.100%, adv accuracy: 0.000%, avg changed rate: 1.460%, num of queries: 62.7 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 93.200%, adv accuracy: 0.000%, avg changed rate: 2.347%, num of queries: 93.3 diff --git a/TextFooler/output/FreeLB1/nt2/prom_core_tata/results_log b/TextFooler/output/FreeLB1/nt2/prom_core_tata/results_log index 5b25db14..8229def9 100644 --- a/TextFooler/output/FreeLB1/nt2/prom_core_tata/results_log +++ b/TextFooler/output/FreeLB1/nt2/prom_core_tata/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 43.700%, adv accuracy: 0.000%, avg changed rate: 1.497%, num of queries: 64.3 -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 2.065%, num of queries: 82.6 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 43.700%, adv accuracy: 0.000%, avg changed rate: 1.497%, num of queries: 64.3 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 97.700%, adv accuracy: 0.000%, avg changed rate: 2.065%, num of queries: 82.6 diff --git a/TextFooler/output/FreeLB1/nt2/tf0/results_log b/TextFooler/output/FreeLB1/nt2/tf0/results_log index 617b0c94..4c80864b 100644 --- a/TextFooler/output/FreeLB1/nt2/tf0/results_log +++ b/TextFooler/output/FreeLB1/nt2/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 7.900%, adv accuracy: 0.000%, avg changed rate: 1.053%, num of queries: 79.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 85.500%, adv accuracy: 0.000%, avg changed rate: 2.231%, num of queries: 132.1 +For target model GUE/tf0/cat.csv: original accuracy: 7.900%, adv accuracy: 0.000%, avg changed rate: 1.053%, num of queries: 79.0 +For target model GUE/tf0/cat.csv: original accuracy: 85.500%, adv accuracy: 0.000%, avg changed rate: 2.231%, num of queries: 132.1 diff --git a/TextFooler/output/FreeLB1/nt2/tf1/results_log b/TextFooler/output/FreeLB1/nt2/tf1/results_log index deb5465b..65db1a76 100644 --- a/TextFooler/output/FreeLB1/nt2/tf1/results_log +++ b/TextFooler/output/FreeLB1/nt2/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 20.600%, adv accuracy: 0.000%, avg changed rate: 1.009%, num of queries: 73.8 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 86.700%, adv accuracy: 0.000%, avg changed rate: 2.012%, num of queries: 122.1 +For target model GUE/tf1/cat.csv: original accuracy: 20.600%, adv accuracy: 0.000%, avg changed rate: 1.009%, num of queries: 73.8 +For target model GUE/tf1/cat.csv: original accuracy: 86.700%, adv accuracy: 0.000%, avg changed rate: 2.012%, num of queries: 122.1 diff --git a/TextFooler/output/FreeLB1/nt2/tf2/results_log b/TextFooler/output/FreeLB1/nt2/tf2/results_log index dd882149..4276d31f 100644 --- a/TextFooler/output/FreeLB1/nt2/tf2/results_log +++ b/TextFooler/output/FreeLB1/nt2/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 52.100%, adv accuracy: 0.000%, avg changed rate: 1.760%, num of queries: 120.1 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 94.000%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 134.5 +For target model GUE/tf2/cat.csv: original accuracy: 52.100%, adv accuracy: 0.000%, avg changed rate: 1.760%, num of queries: 120.1 +For target model GUE/tf2/cat.csv: original accuracy: 94.000%, adv accuracy: 0.000%, avg changed rate: 1.882%, num of queries: 134.5 diff --git a/TextFooler/output/FreeLB1/nt2/tf3/results_log b/TextFooler/output/FreeLB1/nt2/tf3/results_log index 750fb0f1..e35e0d0e 100644 --- a/TextFooler/output/FreeLB1/nt2/tf3/results_log +++ b/TextFooler/output/FreeLB1/nt2/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 89.300%, adv accuracy: 0.000%, avg changed rate: 1.628%, num of queries: 107.6 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 92.200%, adv accuracy: 0.000%, avg changed rate: 1.833%, num of queries: 119.8 +For target model GUE/tf3/cat.csv: original accuracy: 89.300%, adv accuracy: 0.000%, avg changed rate: 1.628%, num of queries: 107.6 +For target model GUE/tf3/cat.csv: original accuracy: 92.200%, adv accuracy: 0.000%, avg changed rate: 1.833%, num of queries: 119.8 diff --git a/TextFooler/output/FreeLB1/nt2/tf4/results_log b/TextFooler/output/FreeLB1/nt2/tf4/results_log index c795eb65..f5bf156a 100644 --- a/TextFooler/output/FreeLB1/nt2/tf4/results_log +++ b/TextFooler/output/FreeLB1/nt2/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 51.300%, adv accuracy: 0.000%, avg changed rate: 1.137%, num of queries: 95.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 97.500%, adv accuracy: 0.200%, avg changed rate: 2.601%, num of queries: 169.0 +For target model GUE/tf4/cat.csv: original accuracy: 51.300%, adv accuracy: 0.000%, avg changed rate: 1.137%, num of queries: 95.0 +For target model GUE/tf4/cat.csv: original accuracy: 97.500%, adv accuracy: 0.200%, avg changed rate: 2.601%, num of queries: 169.0 diff --git a/TextFooler/output/dnabert/0/results_log b/TextFooler/output/dnabert/0/results_log index eddb6184..ba9a4bdc 100644 --- a/TextFooler/output/dnabert/0/results_log +++ b/TextFooler/output/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 94.400%, adv accuracy: 5.500%, avg changed rate: 3.230%, num of queries: 111.9 \ No newline at end of file +For target model GUE/0/cat.csv: original accuracy: 94.400%, adv accuracy: 5.500%, avg changed rate: 3.230%, num of queries: 111.9 \ No newline at end of file diff --git a/TextFooler/output/dnabert/1/results_log b/TextFooler/output/dnabert/1/results_log index 88487930..d6142ded 100644 --- a/TextFooler/output/dnabert/1/results_log +++ b/TextFooler/output/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 93.300%, adv accuracy: 5.100%, avg changed rate: 4.332%, num of queries: 130.4 +For target model GUE/1/cat.csv: original accuracy: 93.300%, adv accuracy: 5.100%, avg changed rate: 4.332%, num of queries: 130.4 diff --git a/TextFooler/output/dnabert/2/results_log b/TextFooler/output/dnabert/2/results_log index dc14b454..a5e483c5 100644 --- a/TextFooler/output/dnabert/2/results_log +++ b/TextFooler/output/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 93.900%, adv accuracy: 2.600%, avg changed rate: 4.656%, num of queries: 142.8 +For target model GUE/2/cat.csv: original accuracy: 93.900%, adv accuracy: 2.600%, avg changed rate: 4.656%, num of queries: 142.8 diff --git a/TextFooler/output/dnabert/3/results_log b/TextFooler/output/dnabert/3/results_log index 943897a5..18165c8c 100644 --- a/TextFooler/output/dnabert/3/results_log +++ b/TextFooler/output/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 94.200%, adv accuracy: 7.200%, avg changed rate: 4.872%, num of queries: 149.4 +For target model GUE/3/cat.csv: original accuracy: 94.200%, adv accuracy: 7.200%, avg changed rate: 4.872%, num of queries: 149.4 diff --git a/TextFooler/output/dnabert/4/results_log b/TextFooler/output/dnabert/4/results_log index 5b78345c..bbe84b84 100644 --- a/TextFooler/output/dnabert/4/results_log +++ b/TextFooler/output/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 84.800%, adv accuracy: 4.900%, avg changed rate: 2.954%, num of queries: 113.3 +For target model GUE/4/cat.csv: original accuracy: 84.800%, adv accuracy: 4.900%, avg changed rate: 2.954%, num of queries: 113.3 diff --git a/TextFooler/output/dnabert/H3/results_log b/TextFooler/output/dnabert/H3/results_log index 7ce586c7..7eeb0acc 100644 --- a/TextFooler/output/dnabert/H3/results_log +++ b/TextFooler/output/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 89.900%, adv accuracy: 8.600%, avg changed rate: 2.851%, num of queries: 529.4 +For target model GUE/H3/cat.csv: original accuracy: 89.900%, adv accuracy: 8.600%, avg changed rate: 2.851%, num of queries: 529.4 diff --git a/TextFooler/output/dnabert/H3K14ac/results_log b/TextFooler/output/dnabert/H3K14ac/results_log index 30a71d44..878e69bc 100644 --- a/TextFooler/output/dnabert/H3K14ac/results_log +++ b/TextFooler/output/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.209%, num of queries: 335.0 +For target model GUE/H3K14ac/cat.csv: original accuracy: 78.500%, adv accuracy: 0.000%, avg changed rate: 2.209%, num of queries: 335.0 diff --git a/TextFooler/output/dnabert/H3K36me3/results_log b/TextFooler/output/dnabert/H3K36me3/results_log index 382ac1ab..29effccd 100644 --- a/TextFooler/output/dnabert/H3K36me3/results_log +++ b/TextFooler/output/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 80.700%, adv accuracy: 0.500%, avg changed rate: 2.080%, num of queries: 327.5 +For target model GUE/H3K36me3/cat.csv: original accuracy: 80.700%, adv accuracy: 0.500%, avg changed rate: 2.080%, num of queries: 327.5 diff --git a/TextFooler/output/dnabert/H3K4me1/results_log b/TextFooler/output/dnabert/H3K4me1/results_log index 3e6bfca3..1fde940a 100644 --- a/TextFooler/output/dnabert/H3K4me1/results_log +++ b/TextFooler/output/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 82.000%, adv accuracy: 0.100%, avg changed rate: 1.585%, num of queries: 270.1 +For target model GUE/H3K4me1/cat.csv: original accuracy: 82.000%, adv accuracy: 0.100%, avg changed rate: 1.585%, num of queries: 270.1 diff --git a/TextFooler/output/dnabert/H3K4me2/results_log b/TextFooler/output/dnabert/H3K4me2/results_log index 5cd031da..492cb95a 100644 --- a/TextFooler/output/dnabert/H3K4me2/results_log +++ b/TextFooler/output/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 71.400%, adv accuracy: 0.100%, avg changed rate: 2.169%, num of queries: 327.0 +For target model GUE/H3K4me2/cat.csv: original accuracy: 71.400%, adv accuracy: 0.100%, avg changed rate: 2.169%, num of queries: 327.0 diff --git a/TextFooler/output/dnabert/H3K4me3/results_log b/TextFooler/output/dnabert/H3K4me3/results_log index a87afdbf..799fdb85 100644 --- a/TextFooler/output/dnabert/H3K4me3/results_log +++ b/TextFooler/output/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 77.500%, adv accuracy: 10.500%, avg changed rate: 1.318%, num of queries: 442.7 +For target model GUE/H3K4me3/cat.csv: original accuracy: 77.500%, adv accuracy: 10.500%, avg changed rate: 1.318%, num of queries: 442.7 diff --git a/TextFooler/output/dnabert/H3K79me3/results_log b/TextFooler/output/dnabert/H3K79me3/results_log index 8c351a85..31e801ac 100644 --- a/TextFooler/output/dnabert/H3K79me3/results_log +++ b/TextFooler/output/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 85.000%, adv accuracy: 3.200%, avg changed rate: 2.600%, num of queries: 425.1 +For target model GUE/H3K79me3/cat.csv: original accuracy: 85.000%, adv accuracy: 3.200%, avg changed rate: 2.600%, num of queries: 425.1 diff --git a/TextFooler/output/dnabert/H3K9ac/results_log b/TextFooler/output/dnabert/H3K9ac/results_log index e6ace361..e66bf66e 100644 --- a/TextFooler/output/dnabert/H3K9ac/results_log +++ b/TextFooler/output/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 87.400%, adv accuracy: 0.700%, avg changed rate: 2.082%, num of queries: 326.4 +For target model GUE/H3K9ac/cat.csv: original accuracy: 87.400%, adv accuracy: 0.700%, avg changed rate: 2.082%, num of queries: 326.4 diff --git a/TextFooler/output/dnabert/H4/results_log b/TextFooler/output/dnabert/H4/results_log index ad324d56..52f89b9f 100644 --- a/TextFooler/output/dnabert/H4/results_log +++ b/TextFooler/output/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 91.800%, adv accuracy: 3.700%, avg changed rate: 3.976%, num of queries: 567.4 +For target model GUE/H4/cat.csv: original accuracy: 91.800%, adv accuracy: 3.700%, avg changed rate: 3.976%, num of queries: 567.4 diff --git a/TextFooler/output/dnabert/H4ac/results_log b/TextFooler/output/dnabert/H4ac/results_log index cdf493ef..51127c88 100644 --- a/TextFooler/output/dnabert/H4ac/results_log +++ b/TextFooler/output/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 81.100%, adv accuracy: 0.300%, avg changed rate: 1.578%, num of queries: 280.1 +For target model GUE/H4ac/cat.csv: original accuracy: 81.100%, adv accuracy: 0.300%, avg changed rate: 1.578%, num of queries: 280.1 diff --git a/TextFooler/output/dnabert/prom_300_all/results_log b/TextFooler/output/dnabert/prom_300_all/results_log index 29f95074..c35caad4 100644 --- a/TextFooler/output/dnabert/prom_300_all/results_log +++ b/TextFooler/output/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 97.100%, adv accuracy: 27.400%, avg changed rate: 2.383%, num of queries: 477.5 +For target model GUE/prom_300_all/cat.csv: original accuracy: 97.100%, adv accuracy: 27.400%, avg changed rate: 2.383%, num of queries: 477.5 diff --git a/TextFooler/output/dnabert/prom_300_notata/results_log b/TextFooler/output/dnabert/prom_300_notata/results_log index 9284cebc..74a3e0c7 100644 --- a/TextFooler/output/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 98.000%, adv accuracy: 70.300%, avg changed rate: 1.847%, num of queries: 834.3 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 98.000%, adv accuracy: 70.300%, avg changed rate: 1.847%, num of queries: 834.3 diff --git a/TextFooler/output/dnabert/prom_300_tata/results_log b/TextFooler/output/dnabert/prom_300_tata/results_log index 791b93f2..bd6cd6bb 100644 --- a/TextFooler/output/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 90.800%, adv accuracy: 2.700%, avg changed rate: 3.461%, num of queries: 309.0 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 90.800%, adv accuracy: 2.700%, avg changed rate: 3.461%, num of queries: 309.0 diff --git a/TextFooler/output/dnabert/prom_core_all/results_log b/TextFooler/output/dnabert/prom_core_all/results_log index 3d98bdbd..32c18f96 100644 --- a/TextFooler/output/dnabert/prom_core_all/results_log +++ b/TextFooler/output/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 88.200%, adv accuracy: 2.300%, avg changed rate: 4.746%, num of queries: 96.5 +For target model GUE/prom_core_all/cat.csv: original accuracy: 88.200%, adv accuracy: 2.300%, avg changed rate: 4.746%, num of queries: 96.5 diff --git a/TextFooler/output/dnabert/prom_core_notata/results_log b/TextFooler/output/dnabert/prom_core_notata/results_log index 8a1fcdcd..e4eb8120 100644 --- a/TextFooler/output/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 85.500%, adv accuracy: 2.500%, avg changed rate: 4.699%, num of queries: 98.4 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 85.500%, adv accuracy: 2.500%, avg changed rate: 4.699%, num of queries: 98.4 diff --git a/TextFooler/output/dnabert/prom_core_tata/results_log b/TextFooler/output/dnabert/prom_core_tata/results_log index 05c7571d..7b2603cd 100644 --- a/TextFooler/output/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 88.200%, adv accuracy: 7.100%, avg changed rate: 3.986%, num of queries: 88.6 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 88.200%, adv accuracy: 7.100%, avg changed rate: 3.986%, num of queries: 88.6 diff --git a/TextFooler/output/dnabert/tf0/results_log b/TextFooler/output/dnabert/tf0/results_log index 435ab6bf..66f326ce 100644 --- a/TextFooler/output/dnabert/tf0/results_log +++ b/TextFooler/output/dnabert/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 86.900%, adv accuracy: 3.100%, avg changed rate: 4.778%, num of queries: 146.9 +For target model GUE/tf0/cat.csv: original accuracy: 86.900%, adv accuracy: 3.100%, avg changed rate: 4.778%, num of queries: 146.9 diff --git a/TextFooler/output/dnabert/tf1/results_log b/TextFooler/output/dnabert/tf1/results_log index 152a6251..2d720031 100644 --- a/TextFooler/output/dnabert/tf1/results_log +++ b/TextFooler/output/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 80.300%, adv accuracy: 1.600%, avg changed rate: 4.900%, num of queries: 140.5 +For target model GUE/tf1/cat.csv: original accuracy: 80.300%, adv accuracy: 1.600%, avg changed rate: 4.900%, num of queries: 140.5 diff --git a/TextFooler/output/dnabert/tf2/results_log b/TextFooler/output/dnabert/tf2/results_log index 70e30dd7..580dca85 100644 --- a/TextFooler/output/dnabert/tf2/results_log +++ b/TextFooler/output/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 82.500%, adv accuracy: 0.500%, avg changed rate: 4.084%, num of queries: 118.7 +For target model GUE/tf2/cat.csv: original accuracy: 82.500%, adv accuracy: 0.500%, avg changed rate: 4.084%, num of queries: 118.7 diff --git a/TextFooler/output/dnabert/tf3/results_log b/TextFooler/output/dnabert/tf3/results_log index a648594c..750e0c5b 100644 --- a/TextFooler/output/dnabert/tf3/results_log +++ b/TextFooler/output/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 80.100%, adv accuracy: 7.000%, avg changed rate: 4.195%, num of queries: 154.4 +For target model GUE/tf3/cat.csv: original accuracy: 80.100%, adv accuracy: 7.000%, avg changed rate: 4.195%, num of queries: 154.4 diff --git a/TextFooler/output/dnabert/tf4/results_log b/TextFooler/output/dnabert/tf4/results_log index 1a71806c..ef634c88 100644 --- a/TextFooler/output/dnabert/tf4/results_log +++ b/TextFooler/output/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 94.600%, adv accuracy: 1.100%, avg changed rate: 4.744%, num of queries: 139.3 +For target model GUE/tf4/cat.csv: original accuracy: 94.600%, adv accuracy: 1.100%, avg changed rate: 4.744%, num of queries: 139.3 diff --git a/TextFooler/output/hyena/0/results_log b/TextFooler/output/hyena/0/results_log index b134dabf..8c8c14d7 100644 --- a/TextFooler/output/hyena/0/results_log +++ b/TextFooler/output/hyena/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 53.700%, avg changed rate: 15.347%, num of queries: 152.2 +For target model GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 53.700%, avg changed rate: 15.347%, num of queries: 152.2 diff --git a/TextFooler/output/hyena/1/results_log b/TextFooler/output/hyena/1/results_log index e2240728..b2cbcca0 100644 --- a/TextFooler/output/hyena/1/results_log +++ b/TextFooler/output/hyena/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 47.000%, avg changed rate: nan%, num of queries: 151.2 +For target model GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 47.000%, avg changed rate: nan%, num of queries: 151.2 diff --git a/TextFooler/output/hyena/2/results_log b/TextFooler/output/hyena/2/results_log index cf66f6f7..f0b5b142 100644 --- a/TextFooler/output/hyena/2/results_log +++ b/TextFooler/output/hyena/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 149.8 +For target model GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 149.8 diff --git a/TextFooler/output/hyena/3/results_log b/TextFooler/output/hyena/3/results_log index 70b95d85..43548691 100644 --- a/TextFooler/output/hyena/3/results_log +++ b/TextFooler/output/hyena/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 153.4 +For target model GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 153.4 diff --git a/TextFooler/output/hyena/4/results_log b/TextFooler/output/hyena/4/results_log index 2cdcd554..ce85bbcb 100644 --- a/TextFooler/output/hyena/4/results_log +++ b/TextFooler/output/hyena/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.7 +For target model GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 152.7 diff --git a/TextFooler/output/hyena/H3/results_log b/TextFooler/output/hyena/H3/results_log index cab2f3aa..01ed70b1 100644 --- a/TextFooler/output/hyena/H3/results_log +++ b/TextFooler/output/hyena/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 749.1 +For target model GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 749.1 diff --git a/TextFooler/output/hyena/H3K14ac/results_log b/TextFooler/output/hyena/H3K14ac/results_log index cdd1791b..fd7b7302 100644 --- a/TextFooler/output/hyena/H3K14ac/results_log +++ b/TextFooler/output/hyena/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 750.1 +For target model GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 750.1 diff --git a/TextFooler/output/hyena/H3K36me3/results_log b/TextFooler/output/hyena/H3K36me3/results_log index 69dce776..979f4dac 100644 --- a/TextFooler/output/hyena/H3K36me3/results_log +++ b/TextFooler/output/hyena/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 55.400%, adv accuracy: 55.400%, avg changed rate: nan%, num of queries: 750.6 +For target model GUE/H3K36me3/cat.csv: original accuracy: 55.400%, adv accuracy: 55.400%, avg changed rate: nan%, num of queries: 750.6 diff --git a/TextFooler/output/hyena/H3K4me1/results_log b/TextFooler/output/hyena/H3K4me1/results_log index 5df4ee6e..d525e4f0 100644 --- a/TextFooler/output/hyena/H3K4me1/results_log +++ b/TextFooler/output/hyena/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 44.400%, adv accuracy: 43.200%, avg changed rate: 23.483%, num of queries: 752.3 +For target model GUE/H3K4me1/cat.csv: original accuracy: 44.400%, adv accuracy: 43.200%, avg changed rate: 23.483%, num of queries: 752.3 diff --git a/TextFooler/output/hyena/H3K4me2/results_log b/TextFooler/output/hyena/H3K4me2/results_log index b28644a2..68a1e173 100644 --- a/TextFooler/output/hyena/H3K4me2/results_log +++ b/TextFooler/output/hyena/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 59.700%, adv accuracy: 59.700%, avg changed rate: nan%, num of queries: 749.9 +For target model GUE/H3K4me2/cat.csv: original accuracy: 59.700%, adv accuracy: 59.700%, avg changed rate: nan%, num of queries: 749.9 diff --git a/TextFooler/output/hyena/H3K4me3/results_log b/TextFooler/output/hyena/H3K4me3/results_log index 0f1cacde..3d6d6efe 100644 --- a/TextFooler/output/hyena/H3K4me3/results_log +++ b/TextFooler/output/hyena/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 52.800%, adv accuracy: 52.200%, avg changed rate: 24.267%, num of queries: 750.2 +For target model GUE/H3K4me3/cat.csv: original accuracy: 52.800%, adv accuracy: 52.200%, avg changed rate: 24.267%, num of queries: 750.2 diff --git a/TextFooler/output/hyena/H3K79me3/results_log b/TextFooler/output/hyena/H3K79me3/results_log index 41de9e8d..2382d37a 100644 --- a/TextFooler/output/hyena/H3K79me3/results_log +++ b/TextFooler/output/hyena/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 47.500%, adv accuracy: 30.500%, avg changed rate: 8.722%, num of queries: 692.6 +For target model GUE/H3K79me3/cat.csv: original accuracy: 47.500%, adv accuracy: 30.500%, avg changed rate: 8.722%, num of queries: 692.6 diff --git a/TextFooler/output/hyena/H3K9ac/results_log b/TextFooler/output/hyena/H3K9ac/results_log index e972f31b..e592f7e5 100644 --- a/TextFooler/output/hyena/H3K9ac/results_log +++ b/TextFooler/output/hyena/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 53.500%, adv accuracy: 31.200%, avg changed rate: 14.790%, num of queries: 689.2 +For target model GUE/H3K9ac/cat.csv: original accuracy: 53.500%, adv accuracy: 31.200%, avg changed rate: 14.790%, num of queries: 689.2 diff --git a/TextFooler/output/hyena/H4/results_log b/TextFooler/output/hyena/H4/results_log index 7378c704..f60b8dac 100644 --- a/TextFooler/output/hyena/H4/results_log +++ b/TextFooler/output/hyena/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 45.000%, adv accuracy: 45.000%, avg changed rate: nan%, num of queries: 749.2 +For target model GUE/H4/cat.csv: original accuracy: 45.000%, adv accuracy: 45.000%, avg changed rate: nan%, num of queries: 749.2 diff --git a/TextFooler/output/hyena/H4ac/results_log b/TextFooler/output/hyena/H4ac/results_log index a1d21013..1b3451d4 100644 --- a/TextFooler/output/hyena/H4ac/results_log +++ b/TextFooler/output/hyena/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 54.000%, adv accuracy: 53.900%, avg changed rate: 1.000%, num of queries: 749.8 +For target model GUE/H4ac/cat.csv: original accuracy: 54.000%, adv accuracy: 53.900%, avg changed rate: 1.000%, num of queries: 749.8 diff --git a/TextFooler/output/hyena/prom_300_all/results_log b/TextFooler/output/hyena/prom_300_all/results_log index 05a447b2..bffb0381 100644 --- a/TextFooler/output/hyena/prom_300_all/results_log +++ b/TextFooler/output/hyena/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 55.500%, adv accuracy: 29.700%, avg changed rate: 10.205%, num of queries: 401.4 +For target model GUE/prom_300_all/cat.csv: original accuracy: 55.500%, adv accuracy: 29.700%, avg changed rate: 10.205%, num of queries: 401.4 diff --git a/TextFooler/output/hyena/prom_300_notata/results_log b/TextFooler/output/hyena/prom_300_notata/results_log index 5f399b37..ca33d5bd 100644 --- a/TextFooler/output/hyena/prom_300_notata/results_log +++ b/TextFooler/output/hyena/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 51.600%, avg changed rate: 4.000%, num of queries: 450.4 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 51.600%, avg changed rate: 4.000%, num of queries: 450.4 diff --git a/TextFooler/output/hyena/prom_300_tata/results_log b/TextFooler/output/hyena/prom_300_tata/results_log index ae736159..527fa870 100644 --- a/TextFooler/output/hyena/prom_300_tata/results_log +++ b/TextFooler/output/hyena/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 49.900%, adv accuracy: 38.500%, avg changed rate: 8.170%, num of queries: 427.5 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 49.900%, adv accuracy: 38.500%, avg changed rate: 8.170%, num of queries: 427.5 diff --git a/TextFooler/output/hyena/prom_core_all/results_log b/TextFooler/output/hyena/prom_core_all/results_log index 9ba2fa5f..5b8e2ed0 100644 --- a/TextFooler/output/hyena/prom_core_all/results_log +++ b/TextFooler/output/hyena/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 105.7 +For target model GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 105.7 diff --git a/TextFooler/output/hyena/prom_core_notata/results_log b/TextFooler/output/hyena/prom_core_notata/results_log index d116c584..f9e43d5d 100644 --- a/TextFooler/output/hyena/prom_core_notata/results_log +++ b/TextFooler/output/hyena/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 50.900%, adv accuracy: 50.900%, avg changed rate: nan%, num of queries: 105.9 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 50.900%, adv accuracy: 50.900%, avg changed rate: nan%, num of queries: 105.9 diff --git a/TextFooler/output/hyena/prom_core_tata/results_log b/TextFooler/output/hyena/prom_core_tata/results_log index 75d8e1ce..6edc50f8 100644 --- a/TextFooler/output/hyena/prom_core_tata/results_log +++ b/TextFooler/output/hyena/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 51.400%, adv accuracy: 51.400%, avg changed rate: nan%, num of queries: 104.7 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 51.400%, adv accuracy: 51.400%, avg changed rate: nan%, num of queries: 104.7 diff --git a/TextFooler/output/hyena/tf0/results_log b/TextFooler/output/hyena/tf0/results_log index be383c8a..fa25f97d 100644 --- a/TextFooler/output/hyena/tf0/results_log +++ b/TextFooler/output/hyena/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 153.0 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 153.0 diff --git a/TextFooler/output/hyena/tf1/results_log b/TextFooler/output/hyena/tf1/results_log index 8804c23e..792c152c 100644 --- a/TextFooler/output/hyena/tf1/results_log +++ b/TextFooler/output/hyena/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 152.9 +For target model GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 152.9 diff --git a/TextFooler/output/hyena/tf2/results_log b/TextFooler/output/hyena/tf2/results_log index b4599c57..bf5810cd 100644 --- a/TextFooler/output/hyena/tf2/results_log +++ b/TextFooler/output/hyena/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 152.9 +For target model GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 152.9 diff --git a/TextFooler/output/hyena/tf3/results_log b/TextFooler/output/hyena/tf3/results_log index 78983319..bfa9aebb 100644 --- a/TextFooler/output/hyena/tf3/results_log +++ b/TextFooler/output/hyena/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 152.7 +For target model GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 50.400%, avg changed rate: nan%, num of queries: 152.7 diff --git a/TextFooler/output/hyena/tf4/results_log b/TextFooler/output/hyena/tf4/results_log index 18a29055..f7b66d52 100644 --- a/TextFooler/output/hyena/tf4/results_log +++ b/TextFooler/output/hyena/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 152.6 +For target model GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 152.6 diff --git a/TextFooler/output/invert.py b/TextFooler/output/invert.py index 0fb7c3ba..1219f59c 100644 --- a/TextFooler/output/invert.py +++ b/TextFooler/output/invert.py @@ -45,7 +45,7 @@ def process_folders(input_folder): print(f"Empty CSV generated (no valid data): {input_file} → {output_file}") # 设置输入目录 -input_dir = "/projects/p32013/DNABERT-meta/TextFooler/output/hyena" +input_dir = "TextFooler/output/hyena" # 运行处理 process_folders(input_dir) diff --git a/TextFooler/output/nt1/0/results_log b/TextFooler/output/nt1/0/results_log index 4753a9ff..fbd77c99 100644 --- a/TextFooler/output/nt1/0/results_log +++ b/TextFooler/output/nt1/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 54.100%, avg changed rate: nan%, num of queries: 37.8 +For target model GUE/0/cat.csv: original accuracy: 54.100%, adv accuracy: 54.100%, avg changed rate: nan%, num of queries: 37.8 diff --git a/TextFooler/output/nt1/1/results_log b/TextFooler/output/nt1/1/results_log index d4d3a14a..211ae51d 100644 --- a/TextFooler/output/nt1/1/results_log +++ b/TextFooler/output/nt1/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 73.000%, adv accuracy: 63.900%, avg changed rate: 2.959%, num of queries: 35.7 +For target model GUE/1/cat.csv: original accuracy: 73.000%, adv accuracy: 63.900%, avg changed rate: 2.959%, num of queries: 35.7 diff --git a/TextFooler/output/nt1/2/results_log b/TextFooler/output/nt1/2/results_log index f871e532..d2c6e98f 100644 --- a/TextFooler/output/nt1/2/results_log +++ b/TextFooler/output/nt1/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 38.8 +For target model GUE/2/cat.csv: original accuracy: 49.400%, adv accuracy: 49.400%, avg changed rate: nan%, num of queries: 38.8 diff --git a/TextFooler/output/nt1/3/results_log b/TextFooler/output/nt1/3/results_log index 94ad82af..520c531a 100644 --- a/TextFooler/output/nt1/3/results_log +++ b/TextFooler/output/nt1/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 37.9 +For target model GUE/3/cat.csv: original accuracy: 50.100%, adv accuracy: 50.100%, avg changed rate: nan%, num of queries: 37.9 diff --git a/TextFooler/output/nt1/4/results_log b/TextFooler/output/nt1/4/results_log index 56bd64d6..9ff28ffb 100644 --- a/TextFooler/output/nt1/4/results_log +++ b/TextFooler/output/nt1/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 38.1 +For target model GUE/4/cat.csv: original accuracy: 49.000%, adv accuracy: 49.000%, avg changed rate: nan%, num of queries: 38.1 diff --git a/TextFooler/output/nt1/H3/results_log b/TextFooler/output/nt1/H3/results_log index 078c8a35..3490c9ba 100644 --- a/TextFooler/output/nt1/H3/results_log +++ b/TextFooler/output/nt1/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 68.400%, adv accuracy: 23.100%, avg changed rate: 1.782%, num of queries: 114.9 +For target model GUE/H3/cat.csv: original accuracy: 68.400%, adv accuracy: 23.100%, avg changed rate: 1.782%, num of queries: 114.9 diff --git a/TextFooler/output/nt1/H3K14ac/results_log b/TextFooler/output/nt1/H3K14ac/results_log index e4dd0258..33087c95 100644 --- a/TextFooler/output/nt1/H3K14ac/results_log +++ b/TextFooler/output/nt1/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 148.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 60.200%, avg changed rate: nan%, num of queries: 148.4 diff --git a/TextFooler/output/nt1/H3K36me3/results_log b/TextFooler/output/nt1/H3K36me3/results_log index b5aa48e3..73cde1f0 100644 --- a/TextFooler/output/nt1/H3K36me3/results_log +++ b/TextFooler/output/nt1/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 58.900%, adv accuracy: 28.100%, avg changed rate: 2.412%, num of queries: 123.9 +For target model GUE/H3K36me3/cat.csv: original accuracy: 58.900%, adv accuracy: 28.100%, avg changed rate: 2.412%, num of queries: 123.9 diff --git a/TextFooler/output/nt1/H3K4me1/results_log b/TextFooler/output/nt1/H3K4me1/results_log index 50104f46..fb36be11 100644 --- a/TextFooler/output/nt1/H3K4me1/results_log +++ b/TextFooler/output/nt1/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 58.900%, adv accuracy: 48.700%, avg changed rate: 1.755%, num of queries: 139.5 +For target model GUE/H3K4me1/cat.csv: original accuracy: 58.900%, adv accuracy: 48.700%, avg changed rate: 1.755%, num of queries: 139.5 diff --git a/TextFooler/output/nt1/H3K4me2/results_log b/TextFooler/output/nt1/H3K4me2/results_log index b40bef0b..a0b18185 100644 --- a/TextFooler/output/nt1/H3K4me2/results_log +++ b/TextFooler/output/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 59.700%, adv accuracy: 59.700%, avg changed rate: nan%, num of queries: 148.6 +For target model GUE/H3K4me2/cat.csv: original accuracy: 59.700%, adv accuracy: 59.700%, avg changed rate: nan%, num of queries: 148.6 diff --git a/TextFooler/output/nt1/H3K4me3/results_log b/TextFooler/output/nt1/H3K4me3/results_log index d9cde9bd..6d6e592f 100644 --- a/TextFooler/output/nt1/H3K4me3/results_log +++ b/TextFooler/output/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 52.800%, adv accuracy: 52.800%, avg changed rate: nan%, num of queries: 148.3 +For target model GUE/H3K4me3/cat.csv: original accuracy: 52.800%, adv accuracy: 52.800%, avg changed rate: nan%, num of queries: 148.3 diff --git a/TextFooler/output/nt1/H3K79me3/results_log b/TextFooler/output/nt1/H3K79me3/results_log index 33750f36..0fd4ef8f 100644 --- a/TextFooler/output/nt1/H3K79me3/results_log +++ b/TextFooler/output/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 47.100%, adv accuracy: 47.000%, avg changed rate: 4.800%, num of queries: 148.2 +For target model GUE/H3K79me3/cat.csv: original accuracy: 47.100%, adv accuracy: 47.000%, avg changed rate: 4.800%, num of queries: 148.2 diff --git a/TextFooler/output/nt1/H3K9ac/results_log b/TextFooler/output/nt1/H3K9ac/results_log index ecfb79c6..28dea0d3 100644 --- a/TextFooler/output/nt1/H3K9ac/results_log +++ b/TextFooler/output/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 148.5 +For target model GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 148.5 diff --git a/TextFooler/output/nt1/H4/results_log b/TextFooler/output/nt1/H4/results_log index 87bf9f5a..2b520274 100644 --- a/TextFooler/output/nt1/H4/results_log +++ b/TextFooler/output/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 54.600%, adv accuracy: 43.300%, avg changed rate: 1.085%, num of queries: 136.9 +For target model GUE/H4/cat.csv: original accuracy: 54.600%, adv accuracy: 43.300%, avg changed rate: 1.085%, num of queries: 136.9 diff --git a/TextFooler/output/nt1/H4ac/results_log b/TextFooler/output/nt1/H4ac/results_log index 81fd9c15..9e051015 100644 --- a/TextFooler/output/nt1/H4ac/results_log +++ b/TextFooler/output/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 55.200%, adv accuracy: 50.100%, avg changed rate: 2.110%, num of queries: 143.9 +For target model GUE/H4ac/cat.csv: original accuracy: 55.200%, adv accuracy: 50.100%, avg changed rate: 2.110%, num of queries: 143.9 diff --git a/TextFooler/output/nt1/prom_300_all/results_log b/TextFooler/output/nt1/prom_300_all/results_log index 8bf8f390..f1a1a2a0 100644 --- a/TextFooler/output/nt1/prom_300_all/results_log +++ b/TextFooler/output/nt1/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 52.700%, adv accuracy: 52.600%, avg changed rate: 0.333%, num of queries: 90.3 +For target model GUE/prom_300_all/cat.csv: original accuracy: 52.700%, adv accuracy: 52.600%, avg changed rate: 0.333%, num of queries: 90.3 diff --git a/TextFooler/output/nt1/prom_300_notata/results_log b/TextFooler/output/nt1/prom_300_notata/results_log index eac85d56..f56e856e 100644 --- a/TextFooler/output/nt1/prom_300_notata/results_log +++ b/TextFooler/output/nt1/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 90.7 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 51.700%, avg changed rate: nan%, num of queries: 90.7 diff --git a/TextFooler/output/nt1/prom_300_tata/results_log b/TextFooler/output/nt1/prom_300_tata/results_log index e16655d0..6775caf2 100644 --- a/TextFooler/output/nt1/prom_300_tata/results_log +++ b/TextFooler/output/nt1/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 49.900%, adv accuracy: 49.300%, avg changed rate: 1.667%, num of queries: 89.2 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 49.900%, adv accuracy: 49.300%, avg changed rate: 1.667%, num of queries: 89.2 diff --git a/TextFooler/output/nt1/prom_core_all/results_log b/TextFooler/output/nt1/prom_core_all/results_log index c6101758..5f1f50f1 100644 --- a/TextFooler/output/nt1/prom_core_all/results_log +++ b/TextFooler/output/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 27.4 +For target model GUE/prom_core_all/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 27.4 diff --git a/TextFooler/output/nt1/prom_core_notata/results_log b/TextFooler/output/nt1/prom_core_notata/results_log index f1769aff..52a41700 100644 --- a/TextFooler/output/nt1/prom_core_notata/results_log +++ b/TextFooler/output/nt1/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 27.5 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 49.100%, adv accuracy: 49.100%, avg changed rate: nan%, num of queries: 27.5 diff --git a/TextFooler/output/nt1/prom_core_tata/results_log b/TextFooler/output/nt1/prom_core_tata/results_log index 72e7634b..36f4b9c1 100644 --- a/TextFooler/output/nt1/prom_core_tata/results_log +++ b/TextFooler/output/nt1/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 51.400%, adv accuracy: 51.400%, avg changed rate: nan%, num of queries: 27.3 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 51.400%, adv accuracy: 51.400%, avg changed rate: nan%, num of queries: 27.3 diff --git a/TextFooler/output/nt1/tf0/results_log b/TextFooler/output/nt1/tf0/results_log index c73ef9c1..22ecbd26 100644 --- a/TextFooler/output/nt1/tf0/results_log +++ b/TextFooler/output/nt1/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 38.6 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 51.300%, avg changed rate: nan%, num of queries: 38.6 diff --git a/TextFooler/output/nt1/tf1/results_log b/TextFooler/output/nt1/tf1/results_log index 55db9aec..257348a4 100644 --- a/TextFooler/output/nt1/tf1/results_log +++ b/TextFooler/output/nt1/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 38.3 +For target model GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 38.3 diff --git a/TextFooler/output/nt1/tf2/results_log b/TextFooler/output/nt1/tf2/results_log index 9a97c46a..21666e12 100644 --- a/TextFooler/output/nt1/tf2/results_log +++ b/TextFooler/output/nt1/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 37.8 +For target model GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 46.600%, avg changed rate: nan%, num of queries: 37.8 diff --git a/TextFooler/output/nt1/tf3/results_log b/TextFooler/output/nt1/tf3/results_log index eac875bc..7a3b587b 100644 --- a/TextFooler/output/nt1/tf3/results_log +++ b/TextFooler/output/nt1/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 46.000%, avg changed rate: 4.725%, num of queries: 37.0 +For target model GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 46.000%, avg changed rate: 4.725%, num of queries: 37.0 diff --git a/TextFooler/output/nt1/tf4/results_log b/TextFooler/output/nt1/tf4/results_log index 78c00746..7dccc2da 100644 --- a/TextFooler/output/nt1/tf4/results_log +++ b/TextFooler/output/nt1/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 50.800%, adv accuracy: 37.900%, avg changed rate: 4.275%, num of queries: 35.0 +For target model GUE/tf4/cat.csv: original accuracy: 50.800%, adv accuracy: 37.900%, avg changed rate: 4.275%, num of queries: 35.0 diff --git a/TextFooler/output/nt2/0/results_log b/TextFooler/output/nt2/0/results_log index 03ee471c..3d2a2665 100644 --- a/TextFooler/output/nt2/0/results_log +++ b/TextFooler/output/nt2/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 46.100%, adv accuracy: 0.100%, avg changed rate: 4.798%, num of queries: 246.7 +For target model GUE/0/cat.csv: original accuracy: 46.100%, adv accuracy: 0.100%, avg changed rate: 4.798%, num of queries: 246.7 diff --git a/TextFooler/output/nt2/1/results_log b/TextFooler/output/nt2/1/results_log index c4e7918d..7c8dc356 100644 --- a/TextFooler/output/nt2/1/results_log +++ b/TextFooler/output/nt2/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 54.300%, adv accuracy: 0.100%, avg changed rate: 4.671%, num of queries: 265.9 +For target model GUE/1/cat.csv: original accuracy: 54.300%, adv accuracy: 0.100%, avg changed rate: 4.671%, num of queries: 265.9 diff --git a/TextFooler/output/nt2/2/results_log b/TextFooler/output/nt2/2/results_log index 2725cd01..6d4afa98 100644 --- a/TextFooler/output/nt2/2/results_log +++ b/TextFooler/output/nt2/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 56.400%, adv accuracy: 2.400%, avg changed rate: 4.650%, num of queries: 272.4 +For target model GUE/2/cat.csv: original accuracy: 56.400%, adv accuracy: 2.400%, avg changed rate: 4.650%, num of queries: 272.4 diff --git a/TextFooler/output/nt2/3/results_log b/TextFooler/output/nt2/3/results_log index 72faa9e9..71783dbd 100644 --- a/TextFooler/output/nt2/3/results_log +++ b/TextFooler/output/nt2/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 54.400%, adv accuracy: 0.000%, avg changed rate: 1.747%, num of queries: 103.0 +For target model GUE/3/cat.csv: original accuracy: 54.400%, adv accuracy: 0.000%, avg changed rate: 1.747%, num of queries: 103.0 diff --git a/TextFooler/output/nt2/4/results_log b/TextFooler/output/nt2/4/results_log index ebcce58c..c01690ed 100644 --- a/TextFooler/output/nt2/4/results_log +++ b/TextFooler/output/nt2/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 1.100%, avg changed rate: 9.504%, num of queries: 489.4 +For target model GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 1.100%, avg changed rate: 9.504%, num of queries: 489.4 diff --git a/TextFooler/output/nt2/H3/results_log b/TextFooler/output/nt2/H3/results_log index b26b015c..7b646dd5 100644 --- a/TextFooler/output/nt2/H3/results_log +++ b/TextFooler/output/nt2/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 56.400%, adv accuracy: 0.000%, avg changed rate: 3.323%, num of queries: 849.4 +For target model GUE/H3/cat.csv: original accuracy: 56.400%, adv accuracy: 0.000%, avg changed rate: 3.323%, num of queries: 849.4 diff --git a/TextFooler/output/nt2/H3K14ac/results_log b/TextFooler/output/nt2/H3K14ac/results_log index 76cc865f..709127c7 100644 --- a/TextFooler/output/nt2/H3K14ac/results_log +++ b/TextFooler/output/nt2/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 74.900%, adv accuracy: 0.000%, avg changed rate: 1.236%, num of queries: 378.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 74.900%, adv accuracy: 0.000%, avg changed rate: 1.236%, num of queries: 378.4 diff --git a/TextFooler/output/nt2/H3K36me3/results_log b/TextFooler/output/nt2/H3K36me3/results_log index 04021e39..f25b1cb2 100644 --- a/TextFooler/output/nt2/H3K36me3/results_log +++ b/TextFooler/output/nt2/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 67.900%, adv accuracy: 0.000%, avg changed rate: 0.650%, num of queries: 236.3 +For target model GUE/H3K36me3/cat.csv: original accuracy: 67.900%, adv accuracy: 0.000%, avg changed rate: 0.650%, num of queries: 236.3 diff --git a/TextFooler/output/nt2/H3K4me1/results_log b/TextFooler/output/nt2/H3K4me1/results_log index 089dc835..e7d1b30a 100644 --- a/TextFooler/output/nt2/H3K4me1/results_log +++ b/TextFooler/output/nt2/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 63.300%, adv accuracy: 0.000%, avg changed rate: 0.930%, num of queries: 301.3 +For target model GUE/H3K4me1/cat.csv: original accuracy: 63.300%, adv accuracy: 0.000%, avg changed rate: 0.930%, num of queries: 301.3 diff --git a/TextFooler/output/nt2/H3K4me2/results_log b/TextFooler/output/nt2/H3K4me2/results_log index 2a2c758c..c440e1bf 100644 --- a/TextFooler/output/nt2/H3K4me2/results_log +++ b/TextFooler/output/nt2/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 45.100%, adv accuracy: 0.000%, avg changed rate: 1.467%, num of queries: 427.3 +For target model GUE/H3K4me2/cat.csv: original accuracy: 45.100%, adv accuracy: 0.000%, avg changed rate: 1.467%, num of queries: 427.3 diff --git a/TextFooler/output/nt2/H3K4me3/results_log b/TextFooler/output/nt2/H3K4me3/results_log index 8b79dfad..60d28162 100644 --- a/TextFooler/output/nt2/H3K4me3/results_log +++ b/TextFooler/output/nt2/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 59.800%, adv accuracy: 0.000%, avg changed rate: 0.559%, num of queries: 214.9 +For target model GUE/H3K4me3/cat.csv: original accuracy: 59.800%, adv accuracy: 0.000%, avg changed rate: 0.559%, num of queries: 214.9 diff --git a/TextFooler/output/nt2/H3K79me3/results_log b/TextFooler/output/nt2/H3K79me3/results_log index e2094c32..681e6515 100644 --- a/TextFooler/output/nt2/H3K79me3/results_log +++ b/TextFooler/output/nt2/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 77.200%, adv accuracy: 0.000%, avg changed rate: 0.817%, num of queries: 275.7 +For target model GUE/H3K79me3/cat.csv: original accuracy: 77.200%, adv accuracy: 0.000%, avg changed rate: 0.817%, num of queries: 275.7 diff --git a/TextFooler/output/nt2/H3K9ac/results_log b/TextFooler/output/nt2/H3K9ac/results_log index 9b8196f7..34b8a792 100644 --- a/TextFooler/output/nt2/H3K9ac/results_log +++ b/TextFooler/output/nt2/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 53.600%, adv accuracy: 0.000%, avg changed rate: 1.861%, num of queries: 522.5 +For target model GUE/H3K9ac/cat.csv: original accuracy: 53.600%, adv accuracy: 0.000%, avg changed rate: 1.861%, num of queries: 522.5 diff --git a/TextFooler/output/nt2/H4/results_log b/TextFooler/output/nt2/H4/results_log index f4098d40..74892da0 100644 --- a/TextFooler/output/nt2/H4/results_log +++ b/TextFooler/output/nt2/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 83.000%, adv accuracy: 0.000%, avg changed rate: 1.667%, num of queries: 472.4 +For target model GUE/H4/cat.csv: original accuracy: 83.000%, adv accuracy: 0.000%, avg changed rate: 1.667%, num of queries: 472.4 diff --git a/TextFooler/output/nt2/H4ac/results_log b/TextFooler/output/nt2/H4ac/results_log index b7528ec2..ebc798b5 100644 --- a/TextFooler/output/nt2/H4ac/results_log +++ b/TextFooler/output/nt2/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 69.300%, adv accuracy: 0.000%, avg changed rate: 0.724%, num of queries: 253.2 +For target model GUE/H4ac/cat.csv: original accuracy: 69.300%, adv accuracy: 0.000%, avg changed rate: 0.724%, num of queries: 253.2 diff --git a/TextFooler/output/nt2/prom_300_all/results_log b/TextFooler/output/nt2/prom_300_all/results_log index a808c8ae..432f08b3 100644 --- a/TextFooler/output/nt2/prom_300_all/results_log +++ b/TextFooler/output/nt2/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 54.700%, adv accuracy: 0.000%, avg changed rate: 4.286%, num of queries: 664.5 +For target model GUE/prom_300_all/cat.csv: original accuracy: 54.700%, adv accuracy: 0.000%, avg changed rate: 4.286%, num of queries: 664.5 diff --git a/TextFooler/output/nt2/prom_300_notata/results_log b/TextFooler/output/nt2/prom_300_notata/results_log index 88861a0f..3e7e468d 100644 --- a/TextFooler/output/nt2/prom_300_notata/results_log +++ b/TextFooler/output/nt2/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 5.900%, avg changed rate: 10.945%, num of queries: 1726.8 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 51.700%, adv accuracy: 5.900%, avg changed rate: 10.945%, num of queries: 1726.8 diff --git a/TextFooler/output/nt2/prom_300_tata/results_log b/TextFooler/output/nt2/prom_300_tata/results_log index 77f9aae4..cfba1b78 100644 --- a/TextFooler/output/nt2/prom_300_tata/results_log +++ b/TextFooler/output/nt2/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 76.000%, adv accuracy: 0.000%, avg changed rate: 0.939%, num of queries: 180.6 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 76.000%, adv accuracy: 0.000%, avg changed rate: 0.939%, num of queries: 180.6 diff --git a/TextFooler/output/nt2/prom_core_all/results_log b/TextFooler/output/nt2/prom_core_all/results_log index 12999b59..d59a31d9 100644 --- a/TextFooler/output/nt2/prom_core_all/results_log +++ b/TextFooler/output/nt2/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 51.300%, adv accuracy: 0.100%, avg changed rate: 6.733%, num of queries: 235.3 +For target model GUE/prom_core_all/cat.csv: original accuracy: 51.300%, adv accuracy: 0.100%, avg changed rate: 6.733%, num of queries: 235.3 diff --git a/TextFooler/output/nt2/prom_core_notata/results_log b/TextFooler/output/nt2/prom_core_notata/results_log index 3431e5ed..de77cde9 100644 --- a/TextFooler/output/nt2/prom_core_notata/results_log +++ b/TextFooler/output/nt2/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 49.200%, adv accuracy: 0.000%, avg changed rate: 7.805%, num of queries: 268.4 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 49.200%, adv accuracy: 0.000%, avg changed rate: 7.805%, num of queries: 268.4 diff --git a/TextFooler/output/nt2/prom_core_tata/results_log b/TextFooler/output/nt2/prom_core_tata/results_log index 7a130528..59024f33 100644 --- a/TextFooler/output/nt2/prom_core_tata/results_log +++ b/TextFooler/output/nt2/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 51.700%, adv accuracy: 30.900%, avg changed rate: 13.455%, num of queries: 602.8 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 51.700%, adv accuracy: 30.900%, avg changed rate: 13.455%, num of queries: 602.8 diff --git a/TextFooler/output/nt2/tf0/results_log b/TextFooler/output/nt2/tf0/results_log index 6859bc03..f39e52d3 100644 --- a/TextFooler/output/nt2/tf0/results_log +++ b/TextFooler/output/nt2/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 52.200%, adv accuracy: 0.000%, avg changed rate: 5.451%, num of queries: 285.0 +For target model GUE/tf0/cat.csv: original accuracy: 52.200%, adv accuracy: 0.000%, avg changed rate: 5.451%, num of queries: 285.0 diff --git a/TextFooler/output/nt2/tf1/results_log b/TextFooler/output/nt2/tf1/results_log index 0b045a0d..fa2d62ae 100644 --- a/TextFooler/output/nt2/tf1/results_log +++ b/TextFooler/output/nt2/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.200%, adv accuracy: 0.000%, avg changed rate: 7.378%, num of queries: 376.2 +For target model GUE/tf1/cat.csv: original accuracy: 48.200%, adv accuracy: 0.000%, avg changed rate: 7.378%, num of queries: 376.2 diff --git a/TextFooler/output/nt2/tf2/results_log b/TextFooler/output/nt2/tf2/results_log index d591127b..dcbc3abb 100644 --- a/TextFooler/output/nt2/tf2/results_log +++ b/TextFooler/output/nt2/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 5.200%, avg changed rate: 13.524%, num of queries: 696.5 +For target model GUE/tf2/cat.csv: original accuracy: 46.600%, adv accuracy: 5.200%, avg changed rate: 13.524%, num of queries: 696.5 diff --git a/TextFooler/output/nt2/tf3/results_log b/TextFooler/output/nt2/tf3/results_log index cdeebe01..4edba973 100644 --- a/TextFooler/output/nt2/tf3/results_log +++ b/TextFooler/output/nt2/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 0.100%, avg changed rate: 7.470%, num of queries: 379.0 +For target model GUE/tf3/cat.csv: original accuracy: 50.400%, adv accuracy: 0.100%, avg changed rate: 7.470%, num of queries: 379.0 diff --git a/TextFooler/output/nt2/tf4/results_log b/TextFooler/output/nt2/tf4/results_log index 1c0c8f06..70c18ba1 100644 --- a/TextFooler/output/nt2/tf4/results_log +++ b/TextFooler/output/nt2/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 66.400%, adv accuracy: 0.000%, avg changed rate: 1.785%, num of queries: 107.5 +For target model GUE/tf4/cat.csv: original accuracy: 66.400%, adv accuracy: 0.000%, avg changed rate: 1.785%, num of queries: 107.5 diff --git a/TextFooler/output/og/0/results_log b/TextFooler/output/og/0/results_log index b28c7bc3..b48be59f 100644 --- a/TextFooler/output/og/0/results_log +++ b/TextFooler/output/og/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 80.200%, adv accuracy: 0.000%, avg changed rate: 2.563%, num of queries: 151.5 +For target model GUE/0/cat.csv: original accuracy: 80.200%, adv accuracy: 0.000%, avg changed rate: 2.563%, num of queries: 151.5 diff --git a/TextFooler/output/og/1/results_log b/TextFooler/output/og/1/results_log index 06eb9cff..db64225b 100644 --- a/TextFooler/output/og/1/results_log +++ b/TextFooler/output/og/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 88.600%, adv accuracy: 0.100%, avg changed rate: 3.786%, num of queries: 214.0 +For target model GUE/1/cat.csv: original accuracy: 88.600%, adv accuracy: 0.100%, avg changed rate: 3.786%, num of queries: 214.0 diff --git a/TextFooler/output/og/2/results_log b/TextFooler/output/og/2/results_log index 5823d009..4c2da2b3 100644 --- a/TextFooler/output/og/2/results_log +++ b/TextFooler/output/og/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 98.000%, adv accuracy: 0.000%, avg changed rate: 3.627%, num of queries: 205.8 +For target model GUE/2/cat.csv: original accuracy: 98.000%, adv accuracy: 0.000%, avg changed rate: 3.627%, num of queries: 205.8 diff --git a/TextFooler/output/og/3/results_log b/TextFooler/output/og/3/results_log index fcb62bf5..3eef2b83 100644 --- a/TextFooler/output/og/3/results_log +++ b/TextFooler/output/og/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 97.200%, adv accuracy: 0.100%, avg changed rate: 3.308%, num of queries: 193.6 +For target model GUE/3/cat.csv: original accuracy: 97.200%, adv accuracy: 0.100%, avg changed rate: 3.308%, num of queries: 193.6 diff --git a/TextFooler/output/og/4/results_log b/TextFooler/output/og/4/results_log index a1fbeb75..e228c975 100644 --- a/TextFooler/output/og/4/results_log +++ b/TextFooler/output/og/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 74.000%, adv accuracy: 0.000%, avg changed rate: 2.506%, num of queries: 148.5 +For target model GUE/4/cat.csv: original accuracy: 74.000%, adv accuracy: 0.000%, avg changed rate: 2.506%, num of queries: 148.5 diff --git a/TextFooler/output/og/H3/results_log b/TextFooler/output/og/H3/results_log index bc3cf504..10cbaa30 100644 --- a/TextFooler/output/og/H3/results_log +++ b/TextFooler/output/og/H3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 89.600%, adv accuracy: 0.200%, avg changed rate: 2.179%, num of queries: 658.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 88.500%, adv accuracy: 0.400%, avg changed rate: 1.965%, num of queries: 615.8 +For target model GUE/H3/cat.csv: original accuracy: 89.600%, adv accuracy: 0.200%, avg changed rate: 2.179%, num of queries: 658.7 +For target model GUE/H3/cat.csv: original accuracy: 88.500%, adv accuracy: 0.400%, avg changed rate: 1.965%, num of queries: 615.8 diff --git a/TextFooler/output/og/H3K14ac/results_log b/TextFooler/output/og/H3K14ac/results_log index 1b01f6cd..91192222 100644 --- a/TextFooler/output/og/H3K14ac/results_log +++ b/TextFooler/output/og/H3K14ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 1.368%, num of queries: 446.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 0.772%, num of queries: 297.2 +For target model GUE/H3K14ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 1.368%, num of queries: 446.2 +For target model GUE/H3K14ac/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 0.772%, num of queries: 297.2 diff --git a/TextFooler/output/og/H3K36me3/results_log b/TextFooler/output/og/H3K36me3/results_log index 28f85005..e606daff 100644 --- a/TextFooler/output/og/H3K36me3/results_log +++ b/TextFooler/output/og/H3K36me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 88.400%, adv accuracy: 0.000%, avg changed rate: 0.784%, num of queries: 300.2 -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 84.200%, adv accuracy: 0.000%, avg changed rate: 1.107%, num of queries: 381.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 88.400%, adv accuracy: 0.000%, avg changed rate: 0.784%, num of queries: 300.2 +For target model GUE/H3K36me3/cat.csv: original accuracy: 84.200%, adv accuracy: 0.000%, avg changed rate: 1.107%, num of queries: 381.1 diff --git a/TextFooler/output/og/H3K4me1/results_log b/TextFooler/output/og/H3K4me1/results_log index 991e5966..e125111c 100644 --- a/TextFooler/output/og/H3K4me1/results_log +++ b/TextFooler/output/og/H3K4me1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 0.973%, num of queries: 347.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 77.600%, adv accuracy: 0.000%, avg changed rate: 1.432%, num of queries: 462.5 +For target model GUE/H3K4me1/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 0.973%, num of queries: 347.7 +For target model GUE/H3K4me1/cat.csv: original accuracy: 77.600%, adv accuracy: 0.000%, avg changed rate: 1.432%, num of queries: 462.5 diff --git a/TextFooler/output/og/H3K4me2/results_log b/TextFooler/output/og/H3K4me2/results_log index 98c9aba0..db371b18 100644 --- a/TextFooler/output/og/H3K4me2/results_log +++ b/TextFooler/output/og/H3K4me2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 74.000%, adv accuracy: 0.000%, avg changed rate: 1.370%, num of queries: 446.5 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 83.300%, adv accuracy: 0.000%, avg changed rate: 0.827%, num of queries: 310.8 +For target model GUE/H3K4me2/cat.csv: original accuracy: 74.000%, adv accuracy: 0.000%, avg changed rate: 1.370%, num of queries: 446.5 +For target model GUE/H3K4me2/cat.csv: original accuracy: 83.300%, adv accuracy: 0.000%, avg changed rate: 0.827%, num of queries: 310.8 diff --git a/TextFooler/output/og/H3K4me3/results_log b/TextFooler/output/og/H3K4me3/results_log index cdf0cad7..43a286d6 100644 --- a/TextFooler/output/og/H3K4me3/results_log +++ b/TextFooler/output/og/H3K4me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 72.100%, adv accuracy: 0.000%, avg changed rate: 0.902%, num of queries: 329.8 -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 73.600%, adv accuracy: 0.000%, avg changed rate: 0.809%, num of queries: 306.6 +For target model GUE/H3K4me3/cat.csv: original accuracy: 72.100%, adv accuracy: 0.000%, avg changed rate: 0.902%, num of queries: 329.8 +For target model GUE/H3K4me3/cat.csv: original accuracy: 73.600%, adv accuracy: 0.000%, avg changed rate: 0.809%, num of queries: 306.6 diff --git a/TextFooler/output/og/H3K79me3/results_log b/TextFooler/output/og/H3K79me3/results_log index 7b501ce9..25e0b4ed 100644 --- a/TextFooler/output/og/H3K79me3/results_log +++ b/TextFooler/output/og/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 85.500%, adv accuracy: 0.000%, avg changed rate: 1.191%, num of queries: 402.3 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 87.000%, adv accuracy: 0.000%, avg changed rate: 1.480%, num of queries: 475.4 +For target model GUE/H3K79me3/cat.csv: original accuracy: 85.500%, adv accuracy: 0.000%, avg changed rate: 1.191%, num of queries: 402.3 +For target model GUE/H3K79me3/cat.csv: original accuracy: 87.000%, adv accuracy: 0.000%, avg changed rate: 1.480%, num of queries: 475.4 diff --git a/TextFooler/output/og/H3K9ac/results_log b/TextFooler/output/og/H3K9ac/results_log index 0693fcae..1efe36e9 100644 --- a/TextFooler/output/og/H3K9ac/results_log +++ b/TextFooler/output/og/H3K9ac/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 82.300%, adv accuracy: 0.000%, avg changed rate: 1.038%, num of queries: 363.7 -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 84.300%, adv accuracy: 0.000%, avg changed rate: 1.509%, num of queries: 481.8 +For target model GUE/H3K9ac/cat.csv: original accuracy: 82.300%, adv accuracy: 0.000%, avg changed rate: 1.038%, num of queries: 363.7 +For target model GUE/H3K9ac/cat.csv: original accuracy: 84.300%, adv accuracy: 0.000%, avg changed rate: 1.509%, num of queries: 481.8 diff --git a/TextFooler/output/og/H4/results_log b/TextFooler/output/og/H4/results_log index 118ab9a3..479b4699 100644 --- a/TextFooler/output/og/H4/results_log +++ b/TextFooler/output/og/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 91.800%, adv accuracy: 10.200%, avg changed rate: 3.181%, num of queries: 1382.1 +For target model GUE/H4/cat.csv: original accuracy: 91.800%, adv accuracy: 10.200%, avg changed rate: 3.181%, num of queries: 1382.1 diff --git a/TextFooler/output/og/H4ac/results_log b/TextFooler/output/og/H4ac/results_log index 26d8c75f..652dd7dc 100644 --- a/TextFooler/output/og/H4ac/results_log +++ b/TextFooler/output/og/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 0.707%, num of queries: 281.0 +For target model GUE/H4ac/cat.csv: original accuracy: 86.600%, adv accuracy: 0.000%, avg changed rate: 0.707%, num of queries: 281.0 diff --git a/TextFooler/output/og/prom_300_all/results_log b/TextFooler/output/og/prom_300_all/results_log index 310a99c9..8ad80faa 100644 --- a/TextFooler/output/og/prom_300_all/results_log +++ b/TextFooler/output/og/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 77.400%, adv accuracy: 0.100%, avg changed rate: 3.649%, num of queries: 616.3 +For target model GUE/prom_300_all/cat.csv: original accuracy: 77.400%, adv accuracy: 0.100%, avg changed rate: 3.649%, num of queries: 616.3 diff --git a/TextFooler/output/og/prom_300_notata/results_log b/TextFooler/output/og/prom_300_notata/results_log index 7bfbfad7..8f2d2b0d 100644 --- a/TextFooler/output/og/prom_300_notata/results_log +++ b/TextFooler/output/og/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.552%, num of queries: 295.5 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 95.400%, adv accuracy: 0.000%, avg changed rate: 1.552%, num of queries: 295.5 diff --git a/TextFooler/output/og/prom_300_tata/results_log b/TextFooler/output/og/prom_300_tata/results_log index 29c7f2f3..a0688c80 100644 --- a/TextFooler/output/og/prom_300_tata/results_log +++ b/TextFooler/output/og/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 2.030%, num of queries: 366.9 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 79.100%, adv accuracy: 0.000%, avg changed rate: 2.030%, num of queries: 366.9 diff --git a/TextFooler/output/og/prom_core_all/results_log b/TextFooler/output/og/prom_core_all/results_log index 61469288..0b2270cd 100644 --- a/TextFooler/output/og/prom_core_all/results_log +++ b/TextFooler/output/og/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 3.516%, num of queries: 139.4 +For target model GUE/prom_core_all/cat.csv: original accuracy: 85.400%, adv accuracy: 0.000%, avg changed rate: 3.516%, num of queries: 139.4 diff --git a/TextFooler/output/og/prom_core_notata/results_log b/TextFooler/output/og/prom_core_notata/results_log index fd70dd5a..6eb0763e 100644 --- a/TextFooler/output/og/prom_core_notata/results_log +++ b/TextFooler/output/og/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 78.300%, adv accuracy: 0.000%, avg changed rate: 3.373%, num of queries: 133.9 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 78.300%, adv accuracy: 0.000%, avg changed rate: 3.373%, num of queries: 133.9 diff --git a/TextFooler/output/og/prom_core_tata/results_log b/TextFooler/output/og/prom_core_tata/results_log index 859b0ed9..79de1d18 100644 --- a/TextFooler/output/og/prom_core_tata/results_log +++ b/TextFooler/output/og/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 90.100%, adv accuracy: 0.000%, avg changed rate: 3.902%, num of queries: 153.9 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 90.100%, adv accuracy: 0.000%, avg changed rate: 3.902%, num of queries: 153.9 diff --git a/TextFooler/output/og/tf0/results_log b/TextFooler/output/og/tf0/results_log index d82da35e..1a4fce7b 100644 --- a/TextFooler/output/og/tf0/results_log +++ b/TextFooler/output/og/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 71.700%, adv accuracy: 0.000%, avg changed rate: 5.069%, num of queries: 278.0 +For target model GUE/tf0/cat.csv: original accuracy: 71.700%, adv accuracy: 0.000%, avg changed rate: 5.069%, num of queries: 278.0 diff --git a/TextFooler/output/og/tf1/results_log b/TextFooler/output/og/tf1/results_log index 8a387486..34d94ac5 100644 --- a/TextFooler/output/og/tf1/results_log +++ b/TextFooler/output/og/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 3.461%, num of queries: 197.0 +For target model GUE/tf1/cat.csv: original accuracy: 79.700%, adv accuracy: 0.000%, avg changed rate: 3.461%, num of queries: 197.0 diff --git a/TextFooler/output/og/tf2/results_log b/TextFooler/output/og/tf2/results_log index 6c61a649..516c642e 100644 --- a/TextFooler/output/og/tf2/results_log +++ b/TextFooler/output/og/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 83.600%, adv accuracy: 0.100%, avg changed rate: 2.469%, num of queries: 147.6 +For target model GUE/tf2/cat.csv: original accuracy: 83.600%, adv accuracy: 0.100%, avg changed rate: 2.469%, num of queries: 147.6 diff --git a/TextFooler/output/og/tf3/results_log b/TextFooler/output/og/tf3/results_log index 9cb9ef9a..42d7c9f8 100644 --- a/TextFooler/output/og/tf3/results_log +++ b/TextFooler/output/og/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 68.600%, adv accuracy: 0.100%, avg changed rate: 2.858%, num of queries: 171.6 +For target model GUE/tf3/cat.csv: original accuracy: 68.600%, adv accuracy: 0.100%, avg changed rate: 2.858%, num of queries: 171.6 diff --git a/TextFooler/output/og/tf4/results_log b/TextFooler/output/og/tf4/results_log index 4f9de1bf..d8f4e35e 100644 --- a/TextFooler/output/og/tf4/results_log +++ b/TextFooler/output/og/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 88.600%, adv accuracy: 0.000%, avg changed rate: 2.831%, num of queries: 166.0 +For target model GUE/tf4/cat.csv: original accuracy: 88.600%, adv accuracy: 0.000%, avg changed rate: 2.831%, num of queries: 166.0 diff --git a/TextFooler/output/quantize/dnabert/0/results_log b/TextFooler/output/quantize/dnabert/0/results_log index d1936d9f..cd9be9e5 100644 --- a/TextFooler/output/quantize/dnabert/0/results_log +++ b/TextFooler/output/quantize/dnabert/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 45.800%, adv accuracy: 35.000%, avg changed rate: 3.089%, num of queries: 269.6 +For target model GUE/0/cat.csv: original accuracy: 45.800%, adv accuracy: 35.000%, avg changed rate: 3.089%, num of queries: 269.6 diff --git a/TextFooler/output/quantize/dnabert/1/results_log b/TextFooler/output/quantize/dnabert/1/results_log index 01f2f911..ef806cd5 100644 --- a/TextFooler/output/quantize/dnabert/1/results_log +++ b/TextFooler/output/quantize/dnabert/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 46.800%, avg changed rate: 15.347%, num of queries: 978.0 +For target model GUE/1/cat.csv: original accuracy: 47.000%, adv accuracy: 46.800%, avg changed rate: 15.347%, num of queries: 978.0 diff --git a/TextFooler/output/quantize/dnabert/2/results_log b/TextFooler/output/quantize/dnabert/2/results_log index 295982c0..a84b94ad 100644 --- a/TextFooler/output/quantize/dnabert/2/results_log +++ b/TextFooler/output/quantize/dnabert/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 57.100%, adv accuracy: 28.400%, avg changed rate: 1.432%, num of queries: 103.9 +For target model GUE/2/cat.csv: original accuracy: 57.100%, adv accuracy: 28.400%, avg changed rate: 1.432%, num of queries: 103.9 diff --git a/TextFooler/output/quantize/dnabert/3/results_log b/TextFooler/output/quantize/dnabert/3/results_log index 8ccd7ef7..17b0baee 100644 --- a/TextFooler/output/quantize/dnabert/3/results_log +++ b/TextFooler/output/quantize/dnabert/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 51.300%, adv accuracy: 37.500%, avg changed rate: 3.752%, num of queries: 249.1 +For target model GUE/3/cat.csv: original accuracy: 51.300%, adv accuracy: 37.500%, avg changed rate: 3.752%, num of queries: 249.1 diff --git a/TextFooler/output/quantize/dnabert/4/results_log b/TextFooler/output/quantize/dnabert/4/results_log index 162b68c3..b9206a18 100644 --- a/TextFooler/output/quantize/dnabert/4/results_log +++ b/TextFooler/output/quantize/dnabert/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 1123.8 +For target model GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 51.000%, avg changed rate: nan%, num of queries: 1123.8 diff --git a/TextFooler/output/quantize/dnabert/H3/results_log b/TextFooler/output/quantize/dnabert/H3/results_log index 5b2843c7..ab308637 100644 --- a/TextFooler/output/quantize/dnabert/H3/results_log +++ b/TextFooler/output/quantize/dnabert/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.400%, avg changed rate: 7.800%, num of queries: 4747.2 +For target model GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.400%, avg changed rate: 7.800%, num of queries: 4747.2 diff --git a/TextFooler/output/quantize/dnabert/H3K14ac/results_log b/TextFooler/output/quantize/dnabert/H3K14ac/results_log index cc5dc920..5810b5e4 100644 --- a/TextFooler/output/quantize/dnabert/H3K14ac/results_log +++ b/TextFooler/output/quantize/dnabert/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 59.400%, adv accuracy: 53.600%, avg changed rate: 0.486%, num of queries: 973.7 +For target model GUE/H3K14ac/cat.csv: original accuracy: 59.400%, adv accuracy: 53.600%, avg changed rate: 0.486%, num of queries: 973.7 diff --git a/TextFooler/output/quantize/dnabert/H3K36me3/results_log b/TextFooler/output/quantize/dnabert/H3K36me3/results_log index ba83829f..dfdbe5aa 100644 --- a/TextFooler/output/quantize/dnabert/H3K36me3/results_log +++ b/TextFooler/output/quantize/dnabert/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 48.100%, adv accuracy: 36.500%, avg changed rate: 0.229%, num of queries: 291.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 48.100%, adv accuracy: 36.500%, avg changed rate: 0.229%, num of queries: 291.1 diff --git a/TextFooler/output/quantize/dnabert/H3K4me1/results_log b/TextFooler/output/quantize/dnabert/H3K4me1/results_log index b5aacb21..c2a98df3 100644 --- a/TextFooler/output/quantize/dnabert/H3K4me1/results_log +++ b/TextFooler/output/quantize/dnabert/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 45.300%, adv accuracy: 42.800%, avg changed rate: 0.360%, num of queries: 859.6 +For target model GUE/H3K4me1/cat.csv: original accuracy: 45.300%, adv accuracy: 42.800%, avg changed rate: 0.360%, num of queries: 859.6 diff --git a/TextFooler/output/quantize/dnabert/H3K4me2/results_log b/TextFooler/output/quantize/dnabert/H3K4me2/results_log index 2b9b3f42..6c60669b 100644 --- a/TextFooler/output/quantize/dnabert/H3K4me2/results_log +++ b/TextFooler/output/quantize/dnabert/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 61.900%, adv accuracy: 46.100%, avg changed rate: 0.200%, num of queries: 202.1 +For target model GUE/H3K4me2/cat.csv: original accuracy: 61.900%, adv accuracy: 46.100%, avg changed rate: 0.200%, num of queries: 202.1 diff --git a/TextFooler/output/quantize/dnabert/H3K4me3/results_log b/TextFooler/output/quantize/dnabert/H3K4me3/results_log index 7bcfdeb6..5f0c5967 100644 --- a/TextFooler/output/quantize/dnabert/H3K4me3/results_log +++ b/TextFooler/output/quantize/dnabert/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 53.100%, adv accuracy: 46.600%, avg changed rate: 0.366%, num of queries: 401.4 +For target model GUE/H3K4me3/cat.csv: original accuracy: 53.100%, adv accuracy: 46.600%, avg changed rate: 0.366%, num of queries: 401.4 diff --git a/TextFooler/output/quantize/dnabert/H3K79me3/results_log b/TextFooler/output/quantize/dnabert/H3K79me3/results_log index 67ddb7e3..2e458c15 100644 --- a/TextFooler/output/quantize/dnabert/H3K79me3/results_log +++ b/TextFooler/output/quantize/dnabert/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 53.500%, adv accuracy: 51.200%, avg changed rate: 0.948%, num of queries: 931.3 +For target model GUE/H3K79me3/cat.csv: original accuracy: 53.500%, adv accuracy: 51.200%, avg changed rate: 0.948%, num of queries: 931.3 diff --git a/TextFooler/output/quantize/dnabert/H3K9ac/results_log b/TextFooler/output/quantize/dnabert/H3K9ac/results_log index 5e0c5de1..43b6655e 100644 --- a/TextFooler/output/quantize/dnabert/H3K9ac/results_log +++ b/TextFooler/output/quantize/dnabert/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 5154.1 +For target model GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 5154.1 diff --git a/TextFooler/output/quantize/dnabert/H4/results_log b/TextFooler/output/quantize/dnabert/H4/results_log index 028b90ce..3717df80 100644 --- a/TextFooler/output/quantize/dnabert/H4/results_log +++ b/TextFooler/output/quantize/dnabert/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 45.300%, adv accuracy: 40.100%, avg changed rate: 0.254%, num of queries: 352.9 +For target model GUE/H4/cat.csv: original accuracy: 45.300%, adv accuracy: 40.100%, avg changed rate: 0.254%, num of queries: 352.9 diff --git a/TextFooler/output/quantize/dnabert/H4ac/results_log b/TextFooler/output/quantize/dnabert/H4ac/results_log index 16e621b1..81777465 100644 --- a/TextFooler/output/quantize/dnabert/H4ac/results_log +++ b/TextFooler/output/quantize/dnabert/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 53.900%, adv accuracy: 53.200%, avg changed rate: 4.800%, num of queries: 1880.3 +For target model GUE/H4ac/cat.csv: original accuracy: 53.900%, adv accuracy: 53.200%, avg changed rate: 4.800%, num of queries: 1880.3 diff --git a/TextFooler/output/quantize/dnabert/prom_300_all/results_log b/TextFooler/output/quantize/dnabert/prom_300_all/results_log index 8545de8f..1e2bac24 100644 --- a/TextFooler/output/quantize/dnabert/prom_300_all/results_log +++ b/TextFooler/output/quantize/dnabert/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 66.000%, adv accuracy: 47.800%, avg changed rate: 0.410%, num of queries: 187.7 +For target model GUE/prom_300_all/cat.csv: original accuracy: 66.000%, adv accuracy: 47.800%, avg changed rate: 0.410%, num of queries: 187.7 diff --git a/TextFooler/output/quantize/dnabert/prom_300_notata/results_log b/TextFooler/output/quantize/dnabert/prom_300_notata/results_log index e5320838..d7647ba2 100644 --- a/TextFooler/output/quantize/dnabert/prom_300_notata/results_log +++ b/TextFooler/output/quantize/dnabert/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 69.800%, adv accuracy: 57.900%, avg changed rate: 0.683%, num of queries: 547.1 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 69.800%, adv accuracy: 57.900%, avg changed rate: 0.683%, num of queries: 547.1 diff --git a/TextFooler/output/quantize/dnabert/prom_300_tata/results_log b/TextFooler/output/quantize/dnabert/prom_300_tata/results_log index 70a39fdd..6ef85e26 100644 --- a/TextFooler/output/quantize/dnabert/prom_300_tata/results_log +++ b/TextFooler/output/quantize/dnabert/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 54.800%, adv accuracy: 38.200%, avg changed rate: 0.392%, num of queries: 222.4 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 54.800%, adv accuracy: 38.200%, avg changed rate: 0.392%, num of queries: 222.4 diff --git a/TextFooler/output/quantize/dnabert/prom_core_all/results_log b/TextFooler/output/quantize/dnabert/prom_core_all/results_log index 76a9f973..f41cf9e8 100644 --- a/TextFooler/output/quantize/dnabert/prom_core_all/results_log +++ b/TextFooler/output/quantize/dnabert/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 64.500%, adv accuracy: 23.300%, avg changed rate: 4.504%, num of queries: 182.5 +For target model GUE/prom_core_all/cat.csv: original accuracy: 64.500%, adv accuracy: 23.300%, avg changed rate: 4.504%, num of queries: 182.5 diff --git a/TextFooler/output/quantize/dnabert/prom_core_notata/results_log b/TextFooler/output/quantize/dnabert/prom_core_notata/results_log index 8c06deba..a593fe9c 100644 --- a/TextFooler/output/quantize/dnabert/prom_core_notata/results_log +++ b/TextFooler/output/quantize/dnabert/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 75.700%, adv accuracy: 24.300%, avg changed rate: 3.730%, num of queries: 150.3 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 75.700%, adv accuracy: 24.300%, avg changed rate: 3.730%, num of queries: 150.3 diff --git a/TextFooler/output/quantize/dnabert/prom_core_tata/results_log b/TextFooler/output/quantize/dnabert/prom_core_tata/results_log index 699b5359..9c86ed03 100644 --- a/TextFooler/output/quantize/dnabert/prom_core_tata/results_log +++ b/TextFooler/output/quantize/dnabert/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 54.300%, adv accuracy: 21.000%, avg changed rate: 1.553%, num of queries: 87.3 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 54.300%, adv accuracy: 21.000%, avg changed rate: 1.553%, num of queries: 87.3 diff --git a/TextFooler/output/quantize/dnabert/tf0/results_log b/TextFooler/output/quantize/dnabert/tf0/results_log index b27b0680..cf4d3680 100644 --- a/TextFooler/output/quantize/dnabert/tf0/results_log +++ b/TextFooler/output/quantize/dnabert/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 50.700%, avg changed rate: 15.512%, num of queries: 1045.4 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 48.700%, avg changed rate: 15.804%, num of queries: 1040.3 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 50.700%, avg changed rate: 15.512%, num of queries: 1045.4 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 48.700%, avg changed rate: 15.804%, num of queries: 1040.3 diff --git a/TextFooler/output/quantize/dnabert/tf1/results_log b/TextFooler/output/quantize/dnabert/tf1/results_log index 747fe6cb..511ca422 100644 --- a/TextFooler/output/quantize/dnabert/tf1/results_log +++ b/TextFooler/output/quantize/dnabert/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 1078.2 +For target model GUE/tf1/cat.csv: original accuracy: 48.000%, adv accuracy: 48.000%, avg changed rate: nan%, num of queries: 1078.2 diff --git a/TextFooler/output/quantize/dnabert/tf2/results_log b/TextFooler/output/quantize/dnabert/tf2/results_log index 056ba435..938d7565 100644 --- a/TextFooler/output/quantize/dnabert/tf2/results_log +++ b/TextFooler/output/quantize/dnabert/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.900%, adv accuracy: 40.300%, avg changed rate: 8.356%, num of queries: 852.3 +For target model GUE/tf2/cat.csv: original accuracy: 46.900%, adv accuracy: 40.300%, avg changed rate: 8.356%, num of queries: 852.3 diff --git a/TextFooler/output/quantize/dnabert/tf3/results_log b/TextFooler/output/quantize/dnabert/tf3/results_log index 9bbd1563..207ced77 100644 --- a/TextFooler/output/quantize/dnabert/tf3/results_log +++ b/TextFooler/output/quantize/dnabert/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 55.300%, adv accuracy: 34.100%, avg changed rate: 5.390%, num of queries: 370.7 +For target model GUE/tf3/cat.csv: original accuracy: 55.300%, adv accuracy: 34.100%, avg changed rate: 5.390%, num of queries: 370.7 diff --git a/TextFooler/output/quantize/dnabert/tf4/results_log b/TextFooler/output/quantize/dnabert/tf4/results_log index 49b3a6cc..25e75309 100644 --- a/TextFooler/output/quantize/dnabert/tf4/results_log +++ b/TextFooler/output/quantize/dnabert/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.000%, avg changed rate: 8.911%, num of queries: 1065.8 +For target model GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 49.000%, avg changed rate: 8.911%, num of queries: 1065.8 diff --git a/TextFooler/output/quantize/dnabert_softmax/0/results_log b/TextFooler/output/quantize/dnabert_softmax/0/results_log index e86caf9a..39bacaa7 100644 --- a/TextFooler/output/quantize/dnabert_softmax/0/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 47.400%, adv accuracy: 28.700%, avg changed rate: 3.394%, num of queries: 281.7 +For target model GUE/0/cat.csv: original accuracy: 47.400%, adv accuracy: 28.700%, avg changed rate: 3.394%, num of queries: 281.7 diff --git a/TextFooler/output/quantize/dnabert_softmax/1/results_log b/TextFooler/output/quantize/dnabert_softmax/1/results_log index a338ebf4..60379370 100644 --- a/TextFooler/output/quantize/dnabert_softmax/1/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 47.300%, adv accuracy: 43.400%, avg changed rate: 6.474%, num of queries: 858.6 +For target model GUE/1/cat.csv: original accuracy: 47.300%, adv accuracy: 43.400%, avg changed rate: 6.474%, num of queries: 858.6 diff --git a/TextFooler/output/quantize/dnabert_softmax/2/results_log b/TextFooler/output/quantize/dnabert_softmax/2/results_log index 3c1bad40..de8de123 100644 --- a/TextFooler/output/quantize/dnabert_softmax/2/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 61.300%, adv accuracy: 25.900%, avg changed rate: 1.091%, num of queries: 87.8 +For target model GUE/2/cat.csv: original accuracy: 61.300%, adv accuracy: 25.900%, avg changed rate: 1.091%, num of queries: 87.8 diff --git a/TextFooler/output/quantize/dnabert_softmax/3/results_log b/TextFooler/output/quantize/dnabert_softmax/3/results_log index 07f583ae..aaa90dd5 100644 --- a/TextFooler/output/quantize/dnabert_softmax/3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 52.500%, adv accuracy: 31.200%, avg changed rate: 1.348%, num of queries: 103.3 +For target model GUE/3/cat.csv: original accuracy: 52.500%, adv accuracy: 31.200%, avg changed rate: 1.348%, num of queries: 103.3 diff --git a/TextFooler/output/quantize/dnabert_softmax/4/results_log b/TextFooler/output/quantize/dnabert_softmax/4/results_log index 9e9d8bfe..f15c4edb 100644 --- a/TextFooler/output/quantize/dnabert_softmax/4/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 43.100%, avg changed rate: 8.121%, num of queries: 782.9 +For target model GUE/4/cat.csv: original accuracy: 51.000%, adv accuracy: 43.100%, avg changed rate: 8.121%, num of queries: 782.9 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3/results_log b/TextFooler/output/quantize/dnabert_softmax/H3/results_log index f4fa8a01..94ecad11 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 4960.3 +For target model GUE/H3/cat.csv: original accuracy: 51.500%, adv accuracy: 51.500%, avg changed rate: nan%, num of queries: 4960.3 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K14ac/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K14ac/results_log index 97913418..fb673acb 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K14ac/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 57.900%, avg changed rate: 0.609%, num of queries: 993.9 +For target model GUE/H3K14ac/cat.csv: original accuracy: 60.200%, adv accuracy: 57.900%, avg changed rate: 0.609%, num of queries: 993.9 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K36me3/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K36me3/results_log index 186ee572..5ea48ee1 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K36me3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 46.600%, adv accuracy: 39.300%, avg changed rate: 0.249%, num of queries: 322.1 +For target model GUE/H3K36me3/cat.csv: original accuracy: 46.600%, adv accuracy: 39.300%, avg changed rate: 0.249%, num of queries: 322.1 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K4me1/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K4me1/results_log index 64344f78..e25e6c11 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K4me1/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 44.300%, adv accuracy: 43.400%, avg changed rate: 2.978%, num of queries: 1405.6 +For target model GUE/H3K4me1/cat.csv: original accuracy: 44.300%, adv accuracy: 43.400%, avg changed rate: 2.978%, num of queries: 1405.6 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K4me2/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K4me2/results_log index 74e90c91..b432db02 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K4me2/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 58.300%, adv accuracy: 39.700%, avg changed rate: 0.202%, num of queries: 179.7 +For target model GUE/H3K4me2/cat.csv: original accuracy: 58.300%, adv accuracy: 39.700%, avg changed rate: 0.202%, num of queries: 179.7 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K4me3/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K4me3/results_log index 091969db..8c22cea4 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K4me3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 53.100%, adv accuracy: 50.900%, avg changed rate: 0.418%, num of queries: 904.7 +For target model GUE/H3K4me3/cat.csv: original accuracy: 53.100%, adv accuracy: 50.900%, avg changed rate: 0.418%, num of queries: 904.7 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K79me3/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K79me3/results_log index 3eb181b3..ac4436d4 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K79me3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K79me3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 53.000%, adv accuracy: 50.900%, avg changed rate: 1.333%, num of queries: 507.0 -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 53.700%, adv accuracy: 51.900%, avg changed rate: 0.322%, num of queries: 528.9 +For target model GUE/H3K79me3/cat.csv: original accuracy: 53.000%, adv accuracy: 50.900%, avg changed rate: 1.333%, num of queries: 507.0 +For target model GUE/H3K79me3/cat.csv: original accuracy: 53.700%, adv accuracy: 51.900%, avg changed rate: 0.322%, num of queries: 528.9 diff --git a/TextFooler/output/quantize/dnabert_softmax/H3K9ac/results_log b/TextFooler/output/quantize/dnabert_softmax/H3K9ac/results_log index 216e171a..9c961d7a 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H3K9ac/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 5161.0 +For target model GUE/H3K9ac/cat.csv: original accuracy: 54.600%, adv accuracy: 54.600%, avg changed rate: nan%, num of queries: 5161.0 diff --git a/TextFooler/output/quantize/dnabert_softmax/H4/results_log b/TextFooler/output/quantize/dnabert_softmax/H4/results_log index 4f221167..0084b073 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H4/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 45.400%, adv accuracy: 43.500%, avg changed rate: 0.547%, num of queries: 599.9 -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 45.100%, adv accuracy: 43.100%, avg changed rate: 0.880%, num of queries: 597.0 +For target model GUE/H4/cat.csv: original accuracy: 45.400%, adv accuracy: 43.500%, avg changed rate: 0.547%, num of queries: 599.9 +For target model GUE/H4/cat.csv: original accuracy: 45.100%, adv accuracy: 43.100%, avg changed rate: 0.880%, num of queries: 597.0 diff --git a/TextFooler/output/quantize/dnabert_softmax/H4ac/results_log b/TextFooler/output/quantize/dnabert_softmax/H4ac/results_log index d4805ebf..7e787b1a 100644 --- a/TextFooler/output/quantize/dnabert_softmax/H4ac/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 54.200%, adv accuracy: 53.400%, avg changed rate: 4.575%, num of queries: 1897.6 +For target model GUE/H4ac/cat.csv: original accuracy: 54.200%, adv accuracy: 53.400%, avg changed rate: 4.575%, num of queries: 1897.6 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_300_all/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_300_all/results_log index 7aa3c8ef..e7df5f0a 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_300_all/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 66.300%, adv accuracy: 47.600%, avg changed rate: 0.383%, num of queries: 182.0 +For target model GUE/prom_300_all/cat.csv: original accuracy: 66.300%, adv accuracy: 47.600%, avg changed rate: 0.383%, num of queries: 182.0 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_300_notata/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_300_notata/results_log index 1246d75e..bf48f715 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_300_notata/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 81.100%, adv accuracy: 62.900%, avg changed rate: 0.419%, num of queries: 173.7 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 81.100%, adv accuracy: 62.900%, avg changed rate: 0.419%, num of queries: 173.7 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_300_tata/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_300_tata/results_log index 9bd82c09..5ce18268 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_300_tata/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 57.200%, adv accuracy: 40.300%, avg changed rate: 0.347%, num of queries: 145.7 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 57.200%, adv accuracy: 40.300%, avg changed rate: 0.347%, num of queries: 145.7 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_core_all/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_core_all/results_log index 13dd5908..eba12eed 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_core_all/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 79.700%, adv accuracy: 30.000%, avg changed rate: 2.989%, num of queries: 132.8 +For target model GUE/prom_core_all/cat.csv: original accuracy: 79.700%, adv accuracy: 30.000%, avg changed rate: 2.989%, num of queries: 132.8 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_core_notata/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_core_notata/results_log index 9ed9478f..91d1dc4d 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_core_notata/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 81.800%, adv accuracy: 31.800%, avg changed rate: 3.177%, num of queries: 131.8 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 81.800%, adv accuracy: 31.800%, avg changed rate: 3.177%, num of queries: 131.8 diff --git a/TextFooler/output/quantize/dnabert_softmax/prom_core_tata/results_log b/TextFooler/output/quantize/dnabert_softmax/prom_core_tata/results_log index ed7d020a..d1edecc5 100644 --- a/TextFooler/output/quantize/dnabert_softmax/prom_core_tata/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 53.000%, adv accuracy: 27.100%, avg changed rate: 1.467%, num of queries: 100.9 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 53.000%, adv accuracy: 27.100%, avg changed rate: 1.467%, num of queries: 100.9 diff --git a/TextFooler/output/quantize/dnabert_softmax/tf0/results_log b/TextFooler/output/quantize/dnabert_softmax/tf0/results_log index da5c6594..8657d787 100644 --- a/TextFooler/output/quantize/dnabert_softmax/tf0/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/tf0/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 44.400%, avg changed rate: 10.389%, num of queries: 892.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 40.800%, avg changed rate: 9.618%, num of queries: 743.4 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 44.400%, avg changed rate: 10.389%, num of queries: 892.0 +For target model GUE/tf0/cat.csv: original accuracy: 51.300%, adv accuracy: 40.800%, avg changed rate: 9.618%, num of queries: 743.4 diff --git a/TextFooler/output/quantize/dnabert_softmax/tf1/results_log b/TextFooler/output/quantize/dnabert_softmax/tf1/results_log index 0a22ef2f..1a7d8a12 100644 --- a/TextFooler/output/quantize/dnabert_softmax/tf1/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/tf1/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.100%, adv accuracy: 45.400%, avg changed rate: 6.014%, num of queries: 934.2 -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 48.200%, adv accuracy: 45.700%, avg changed rate: 6.257%, num of queries: 917.8 +For target model GUE/tf1/cat.csv: original accuracy: 48.100%, adv accuracy: 45.400%, avg changed rate: 6.014%, num of queries: 934.2 +For target model GUE/tf1/cat.csv: original accuracy: 48.200%, adv accuracy: 45.700%, avg changed rate: 6.257%, num of queries: 917.8 diff --git a/TextFooler/output/quantize/dnabert_softmax/tf2/results_log b/TextFooler/output/quantize/dnabert_softmax/tf2/results_log index 05e8879f..5a76d96d 100644 --- a/TextFooler/output/quantize/dnabert_softmax/tf2/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/tf2/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 47.000%, adv accuracy: 41.600%, avg changed rate: 10.469%, num of queries: 940.3 -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 46.700%, adv accuracy: 42.600%, avg changed rate: 9.877%, num of queries: 928.4 +For target model GUE/tf2/cat.csv: original accuracy: 47.000%, adv accuracy: 41.600%, avg changed rate: 10.469%, num of queries: 940.3 +For target model GUE/tf2/cat.csv: original accuracy: 46.700%, adv accuracy: 42.600%, avg changed rate: 9.877%, num of queries: 928.4 diff --git a/TextFooler/output/quantize/dnabert_softmax/tf3/results_log b/TextFooler/output/quantize/dnabert_softmax/tf3/results_log index 912cd8c1..b23ffc84 100644 --- a/TextFooler/output/quantize/dnabert_softmax/tf3/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/tf3/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 52.500%, adv accuracy: 32.200%, avg changed rate: 7.687%, num of queries: 473.4 -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 51.700%, adv accuracy: 32.900%, avg changed rate: 8.237%, num of queries: 506.5 +For target model GUE/tf3/cat.csv: original accuracy: 52.500%, adv accuracy: 32.200%, avg changed rate: 7.687%, num of queries: 473.4 +For target model GUE/tf3/cat.csv: original accuracy: 51.700%, adv accuracy: 32.900%, avg changed rate: 8.237%, num of queries: 506.5 diff --git a/TextFooler/output/quantize/dnabert_softmax/tf4/results_log b/TextFooler/output/quantize/dnabert_softmax/tf4/results_log index f74dc7c4..db542d68 100644 --- a/TextFooler/output/quantize/dnabert_softmax/tf4/results_log +++ b/TextFooler/output/quantize/dnabert_softmax/tf4/results_log @@ -1,2 +1,2 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 46.900%, avg changed rate: 7.876%, num of queries: 1016.0 -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 47.700%, avg changed rate: 5.799%, num of queries: 1005.2 +For target model GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 46.900%, avg changed rate: 7.876%, num of queries: 1016.0 +For target model GUE/tf4/cat.csv: original accuracy: 49.100%, adv accuracy: 47.700%, avg changed rate: 5.799%, num of queries: 1005.2 diff --git a/TextFooler/output/quantize/nt1/0/results_log b/TextFooler/output/quantize/nt1/0/results_log index e4adc954..5dfdeb22 100644 --- a/TextFooler/output/quantize/nt1/0/results_log +++ b/TextFooler/output/quantize/nt1/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 88.300%, adv accuracy: 18.400%, avg changed rate: 3.647%, num of queries: 29.3 +For target model GUE/0/cat.csv: original accuracy: 88.300%, adv accuracy: 18.400%, avg changed rate: 3.647%, num of queries: 29.3 diff --git a/TextFooler/output/quantize/nt1/1/results_log b/TextFooler/output/quantize/nt1/1/results_log index e097e613..fdc5bd11 100644 --- a/TextFooler/output/quantize/nt1/1/results_log +++ b/TextFooler/output/quantize/nt1/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 92.000%, adv accuracy: 54.800%, avg changed rate: 3.984%, num of queries: 32.6 +For target model GUE/1/cat.csv: original accuracy: 92.000%, adv accuracy: 54.800%, avg changed rate: 3.984%, num of queries: 32.6 diff --git a/TextFooler/output/quantize/nt1/2/results_log b/TextFooler/output/quantize/nt1/2/results_log index afffc263..343c2464 100644 --- a/TextFooler/output/quantize/nt1/2/results_log +++ b/TextFooler/output/quantize/nt1/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 94.700%, adv accuracy: 26.600%, avg changed rate: 4.884%, num of queries: 30.8 +For target model GUE/2/cat.csv: original accuracy: 94.700%, adv accuracy: 26.600%, avg changed rate: 4.884%, num of queries: 30.8 diff --git a/TextFooler/output/quantize/nt1/3/results_log b/TextFooler/output/quantize/nt1/3/results_log index adb95c64..20441f59 100644 --- a/TextFooler/output/quantize/nt1/3/results_log +++ b/TextFooler/output/quantize/nt1/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 83.300%, adv accuracy: 16.400%, avg changed rate: 3.315%, num of queries: 28.6 +For target model GUE/3/cat.csv: original accuracy: 83.300%, adv accuracy: 16.400%, avg changed rate: 3.315%, num of queries: 28.6 diff --git a/TextFooler/output/quantize/nt1/4/results_log b/TextFooler/output/quantize/nt1/4/results_log index fcd80b23..5dc35424 100644 --- a/TextFooler/output/quantize/nt1/4/results_log +++ b/TextFooler/output/quantize/nt1/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 90.900%, adv accuracy: 23.500%, avg changed rate: 3.740%, num of queries: 29.7 +For target model GUE/4/cat.csv: original accuracy: 90.900%, adv accuracy: 23.500%, avg changed rate: 3.740%, num of queries: 29.7 diff --git a/TextFooler/output/quantize/nt1/H3/results_log b/TextFooler/output/quantize/nt1/H3/results_log index bf19b9f0..8c828d5e 100644 --- a/TextFooler/output/quantize/nt1/H3/results_log +++ b/TextFooler/output/quantize/nt1/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 96.900%, adv accuracy: 28.600%, avg changed rate: 2.490%, num of queries: 116.4 +For target model GUE/H3/cat.csv: original accuracy: 96.900%, adv accuracy: 28.600%, avg changed rate: 2.490%, num of queries: 116.4 diff --git a/TextFooler/output/quantize/nt1/H3K14ac/results_log b/TextFooler/output/quantize/nt1/H3K14ac/results_log index ca3317a6..0c20b1d4 100644 --- a/TextFooler/output/quantize/nt1/H3K14ac/results_log +++ b/TextFooler/output/quantize/nt1/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 79.500%, adv accuracy: 16.400%, avg changed rate: 1.892%, num of queries: 108.4 +For target model GUE/H3K14ac/cat.csv: original accuracy: 79.500%, adv accuracy: 16.400%, avg changed rate: 1.892%, num of queries: 108.4 diff --git a/TextFooler/output/quantize/nt1/H3K36me3/results_log b/TextFooler/output/quantize/nt1/H3K36me3/results_log index 8d84a8f7..a2b1701c 100644 --- a/TextFooler/output/quantize/nt1/H3K36me3/results_log +++ b/TextFooler/output/quantize/nt1/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 82.200%, adv accuracy: 18.300%, avg changed rate: 2.107%, num of queries: 110.3 +For target model GUE/H3K36me3/cat.csv: original accuracy: 82.200%, adv accuracy: 18.300%, avg changed rate: 2.107%, num of queries: 110.3 diff --git a/TextFooler/output/quantize/nt1/H3K4me1/results_log b/TextFooler/output/quantize/nt1/H3K4me1/results_log index 4ba126cb..d2fdccf8 100644 --- a/TextFooler/output/quantize/nt1/H3K4me1/results_log +++ b/TextFooler/output/quantize/nt1/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 77.100%, adv accuracy: 17.700%, avg changed rate: 1.950%, num of queries: 109.8 +For target model GUE/H3K4me1/cat.csv: original accuracy: 77.100%, adv accuracy: 17.700%, avg changed rate: 1.950%, num of queries: 109.8 diff --git a/TextFooler/output/quantize/nt1/H3K4me2/results_log b/TextFooler/output/quantize/nt1/H3K4me2/results_log index 26155098..8bc630a8 100644 --- a/TextFooler/output/quantize/nt1/H3K4me2/results_log +++ b/TextFooler/output/quantize/nt1/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 77.600%, adv accuracy: 22.900%, avg changed rate: 1.650%, num of queries: 112.2 +For target model GUE/H3K4me2/cat.csv: original accuracy: 77.600%, adv accuracy: 22.900%, avg changed rate: 1.650%, num of queries: 112.2 diff --git a/TextFooler/output/quantize/nt1/H3K4me3/results_log b/TextFooler/output/quantize/nt1/H3K4me3/results_log index e85e0cac..a133e96a 100644 --- a/TextFooler/output/quantize/nt1/H3K4me3/results_log +++ b/TextFooler/output/quantize/nt1/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 73.100%, adv accuracy: 9.400%, avg changed rate: 1.672%, num of queries: 103.2 +For target model GUE/H3K4me3/cat.csv: original accuracy: 73.100%, adv accuracy: 9.400%, avg changed rate: 1.672%, num of queries: 103.2 diff --git a/TextFooler/output/quantize/nt1/H3K79me3/results_log b/TextFooler/output/quantize/nt1/H3K79me3/results_log index 8fbb77c8..0892e59a 100644 --- a/TextFooler/output/quantize/nt1/H3K79me3/results_log +++ b/TextFooler/output/quantize/nt1/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 88.400%, adv accuracy: 25.200%, avg changed rate: 2.228%, num of queries: 111.5 +For target model GUE/H3K79me3/cat.csv: original accuracy: 88.400%, adv accuracy: 25.200%, avg changed rate: 2.228%, num of queries: 111.5 diff --git a/TextFooler/output/quantize/nt1/H3K9ac/results_log b/TextFooler/output/quantize/nt1/H3K9ac/results_log index d1dee08c..17dac98e 100644 --- a/TextFooler/output/quantize/nt1/H3K9ac/results_log +++ b/TextFooler/output/quantize/nt1/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 84.500%, adv accuracy: 22.500%, avg changed rate: 1.966%, num of queries: 109.9 +For target model GUE/H3K9ac/cat.csv: original accuracy: 84.500%, adv accuracy: 22.500%, avg changed rate: 1.966%, num of queries: 109.9 diff --git a/TextFooler/output/quantize/nt1/H4/results_log b/TextFooler/output/quantize/nt1/H4/results_log index 619ee66e..a8899a34 100644 --- a/TextFooler/output/quantize/nt1/H4/results_log +++ b/TextFooler/output/quantize/nt1/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 95.900%, adv accuracy: 41.700%, avg changed rate: 2.913%, num of queries: 121.5 +For target model GUE/H4/cat.csv: original accuracy: 95.900%, adv accuracy: 41.700%, avg changed rate: 2.913%, num of queries: 121.5 diff --git a/TextFooler/output/quantize/nt1/H4ac/results_log b/TextFooler/output/quantize/nt1/H4ac/results_log index a5ba1c52..c2205287 100644 --- a/TextFooler/output/quantize/nt1/H4ac/results_log +++ b/TextFooler/output/quantize/nt1/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 78.700%, adv accuracy: 21.900%, avg changed rate: 1.729%, num of queries: 107.5 +For target model GUE/H4ac/cat.csv: original accuracy: 78.700%, adv accuracy: 21.900%, avg changed rate: 1.729%, num of queries: 107.5 diff --git a/TextFooler/output/quantize/nt1/prom_300_all/results_log b/TextFooler/output/quantize/nt1/prom_300_all/results_log index 130443ad..4eeecef3 100644 --- a/TextFooler/output/quantize/nt1/prom_300_all/results_log +++ b/TextFooler/output/quantize/nt1/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 95.900%, adv accuracy: 38.800%, avg changed rate: 2.610%, num of queries: 72.4 +For target model GUE/prom_300_all/cat.csv: original accuracy: 95.900%, adv accuracy: 38.800%, avg changed rate: 2.610%, num of queries: 72.4 diff --git a/TextFooler/output/quantize/nt1/prom_300_notata/results_log b/TextFooler/output/quantize/nt1/prom_300_notata/results_log index 9138f57a..01ec641b 100644 --- a/TextFooler/output/quantize/nt1/prom_300_notata/results_log +++ b/TextFooler/output/quantize/nt1/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 96.900%, adv accuracy: 44.000%, avg changed rate: 2.786%, num of queries: 74.1 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 96.900%, adv accuracy: 44.000%, avg changed rate: 2.786%, num of queries: 74.1 diff --git a/TextFooler/output/quantize/nt1/prom_300_tata/results_log b/TextFooler/output/quantize/nt1/prom_300_tata/results_log index ffe34861..6637429c 100644 --- a/TextFooler/output/quantize/nt1/prom_300_tata/results_log +++ b/TextFooler/output/quantize/nt1/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 93.200%, adv accuracy: 39.000%, avg changed rate: 2.783%, num of queries: 72.4 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 93.200%, adv accuracy: 39.000%, avg changed rate: 2.783%, num of queries: 72.4 diff --git a/TextFooler/output/quantize/nt1/prom_core_all/results_log b/TextFooler/output/quantize/nt1/prom_core_all/results_log index faf5ed85..67333eb2 100644 --- a/TextFooler/output/quantize/nt1/prom_core_all/results_log +++ b/TextFooler/output/quantize/nt1/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 82.200%, adv accuracy: 27.800%, avg changed rate: 4.648%, num of queries: 22.6 +For target model GUE/prom_core_all/cat.csv: original accuracy: 82.200%, adv accuracy: 27.800%, avg changed rate: 4.648%, num of queries: 22.6 diff --git a/TextFooler/output/quantize/nt1/prom_core_notata/results_log b/TextFooler/output/quantize/nt1/prom_core_notata/results_log index 56c58df5..be894f35 100644 --- a/TextFooler/output/quantize/nt1/prom_core_notata/results_log +++ b/TextFooler/output/quantize/nt1/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 87.400%, adv accuracy: 31.700%, avg changed rate: 4.245%, num of queries: 22.5 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 87.400%, adv accuracy: 31.700%, avg changed rate: 4.245%, num of queries: 22.5 diff --git a/TextFooler/output/quantize/nt1/prom_core_tata/results_log b/TextFooler/output/quantize/nt1/prom_core_tata/results_log index 3724d7a9..f59bae8c 100644 --- a/TextFooler/output/quantize/nt1/prom_core_tata/results_log +++ b/TextFooler/output/quantize/nt1/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 93.900%, adv accuracy: 53.700%, avg changed rate: 4.712%, num of queries: 24.0 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 93.900%, adv accuracy: 53.700%, avg changed rate: 4.712%, num of queries: 24.0 diff --git a/TextFooler/output/quantize/nt1/tf0/results_log b/TextFooler/output/quantize/nt1/tf0/results_log index c4b4ba78..0bd8fa3e 100644 --- a/TextFooler/output/quantize/nt1/tf0/results_log +++ b/TextFooler/output/quantize/nt1/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 85.000%, adv accuracy: 36.200%, avg changed rate: 3.816%, num of queries: 31.8 +For target model GUE/tf0/cat.csv: original accuracy: 85.000%, adv accuracy: 36.200%, avg changed rate: 3.816%, num of queries: 31.8 diff --git a/TextFooler/output/quantize/nt1/tf1/results_log b/TextFooler/output/quantize/nt1/tf1/results_log index ba5e7cde..54708643 100644 --- a/TextFooler/output/quantize/nt1/tf1/results_log +++ b/TextFooler/output/quantize/nt1/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 85.700%, adv accuracy: 41.200%, avg changed rate: 3.231%, num of queries: 32.0 +For target model GUE/tf1/cat.csv: original accuracy: 85.700%, adv accuracy: 41.200%, avg changed rate: 3.231%, num of queries: 32.0 diff --git a/TextFooler/output/quantize/nt1/tf2/results_log b/TextFooler/output/quantize/nt1/tf2/results_log index cec25736..88a48607 100644 --- a/TextFooler/output/quantize/nt1/tf2/results_log +++ b/TextFooler/output/quantize/nt1/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 92.600%, adv accuracy: 30.300%, avg changed rate: 3.732%, num of queries: 30.4 +For target model GUE/tf2/cat.csv: original accuracy: 92.600%, adv accuracy: 30.300%, avg changed rate: 3.732%, num of queries: 30.4 diff --git a/TextFooler/output/quantize/nt1/tf3/results_log b/TextFooler/output/quantize/nt1/tf3/results_log index 99376f41..cba23d19 100644 --- a/TextFooler/output/quantize/nt1/tf3/results_log +++ b/TextFooler/output/quantize/nt1/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 84.000%, adv accuracy: 21.800%, avg changed rate: 3.698%, num of queries: 29.4 +For target model GUE/tf3/cat.csv: original accuracy: 84.000%, adv accuracy: 21.800%, avg changed rate: 3.698%, num of queries: 29.4 diff --git a/TextFooler/output/quantize/nt1/tf4/results_log b/TextFooler/output/quantize/nt1/tf4/results_log index 299b1398..aa7e83c0 100644 --- a/TextFooler/output/quantize/nt1/tf4/results_log +++ b/TextFooler/output/quantize/nt1/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 95.000%, adv accuracy: 44.400%, avg changed rate: 4.068%, num of queries: 32.0 +For target model GUE/tf4/cat.csv: original accuracy: 95.000%, adv accuracy: 44.400%, avg changed rate: 4.068%, num of queries: 32.0 diff --git a/TextFooler/output/quantize/nt1_softmax/0/results_log b/TextFooler/output/quantize/nt1_softmax/0/results_log index a994f413..a780155d 100644 --- a/TextFooler/output/quantize/nt1_softmax/0/results_log +++ b/TextFooler/output/quantize/nt1_softmax/0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/0/cat.csv: original accuracy: 77.800%, adv accuracy: 12.600%, avg changed rate: 3.461%, num of queries: 28.6 +For target model GUE/0/cat.csv: original accuracy: 77.800%, adv accuracy: 12.600%, avg changed rate: 3.461%, num of queries: 28.6 diff --git a/TextFooler/output/quantize/nt1_softmax/1/results_log b/TextFooler/output/quantize/nt1_softmax/1/results_log index 61d43ae5..14fd7fc1 100644 --- a/TextFooler/output/quantize/nt1_softmax/1/results_log +++ b/TextFooler/output/quantize/nt1_softmax/1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/1/cat.csv: original accuracy: 90.700%, adv accuracy: 49.800%, avg changed rate: 3.895%, num of queries: 32.0 +For target model GUE/1/cat.csv: original accuracy: 90.700%, adv accuracy: 49.800%, avg changed rate: 3.895%, num of queries: 32.0 diff --git a/TextFooler/output/quantize/nt1_softmax/2/results_log b/TextFooler/output/quantize/nt1_softmax/2/results_log index 6657b105..0f804a9d 100644 --- a/TextFooler/output/quantize/nt1_softmax/2/results_log +++ b/TextFooler/output/quantize/nt1_softmax/2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/2/cat.csv: original accuracy: 82.800%, adv accuracy: 26.800%, avg changed rate: 4.954%, num of queries: 31.6 +For target model GUE/2/cat.csv: original accuracy: 82.800%, adv accuracy: 26.800%, avg changed rate: 4.954%, num of queries: 31.6 diff --git a/TextFooler/output/quantize/nt1_softmax/3/results_log b/TextFooler/output/quantize/nt1_softmax/3/results_log index 97c60f78..069d88ae 100644 --- a/TextFooler/output/quantize/nt1_softmax/3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/3/cat.csv: original accuracy: 63.500%, adv accuracy: 17.300%, avg changed rate: 3.776%, num of queries: 29.5 +For target model GUE/3/cat.csv: original accuracy: 63.500%, adv accuracy: 17.300%, avg changed rate: 3.776%, num of queries: 29.5 diff --git a/TextFooler/output/quantize/nt1_softmax/4/results_log b/TextFooler/output/quantize/nt1_softmax/4/results_log index efe8a7a1..f7ac2d7f 100644 --- a/TextFooler/output/quantize/nt1_softmax/4/results_log +++ b/TextFooler/output/quantize/nt1_softmax/4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/4/cat.csv: original accuracy: 85.300%, adv accuracy: 20.200%, avg changed rate: 3.384%, num of queries: 29.0 +For target model GUE/4/cat.csv: original accuracy: 85.300%, adv accuracy: 20.200%, avg changed rate: 3.384%, num of queries: 29.0 diff --git a/TextFooler/output/quantize/nt1_softmax/H3/results_log b/TextFooler/output/quantize/nt1_softmax/H3/results_log index 6f7c0e0e..92b1cdfe 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3/cat.csv: original accuracy: 94.100%, adv accuracy: 24.500%, avg changed rate: 2.617%, num of queries: 115.1 +For target model GUE/H3/cat.csv: original accuracy: 94.100%, adv accuracy: 24.500%, avg changed rate: 2.617%, num of queries: 115.1 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K14ac/results_log b/TextFooler/output/quantize/nt1_softmax/H3K14ac/results_log index 7ee80de1..b5d22d1b 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K14ac/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K14ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K14ac/cat.csv: original accuracy: 81.600%, adv accuracy: 21.500%, avg changed rate: 1.650%, num of queries: 110.1 +For target model GUE/H3K14ac/cat.csv: original accuracy: 81.600%, adv accuracy: 21.500%, avg changed rate: 1.650%, num of queries: 110.1 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K36me3/results_log b/TextFooler/output/quantize/nt1_softmax/H3K36me3/results_log index c9b515f2..8d29319a 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K36me3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K36me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K36me3/cat.csv: original accuracy: 81.900%, adv accuracy: 18.400%, avg changed rate: 2.066%, num of queries: 110.6 +For target model GUE/H3K36me3/cat.csv: original accuracy: 81.900%, adv accuracy: 18.400%, avg changed rate: 2.066%, num of queries: 110.6 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K4me1/results_log b/TextFooler/output/quantize/nt1_softmax/H3K4me1/results_log index 7c116ab4..66228c76 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K4me1/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K4me1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me1/cat.csv: original accuracy: 74.200%, adv accuracy: 21.600%, avg changed rate: 1.855%, num of queries: 112.0 +For target model GUE/H3K4me1/cat.csv: original accuracy: 74.200%, adv accuracy: 21.600%, avg changed rate: 1.855%, num of queries: 112.0 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K4me2/results_log b/TextFooler/output/quantize/nt1_softmax/H3K4me2/results_log index 2768afd5..aef3a313 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K4me2/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K4me2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me2/cat.csv: original accuracy: 76.500%, adv accuracy: 22.700%, avg changed rate: 1.553%, num of queries: 111.7 +For target model GUE/H3K4me2/cat.csv: original accuracy: 76.500%, adv accuracy: 22.700%, avg changed rate: 1.553%, num of queries: 111.7 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K4me3/results_log b/TextFooler/output/quantize/nt1_softmax/H3K4me3/results_log index e73a1e5d..c5b5c82c 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K4me3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K4me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K4me3/cat.csv: original accuracy: 71.800%, adv accuracy: 9.900%, avg changed rate: 1.765%, num of queries: 104.3 +For target model GUE/H3K4me3/cat.csv: original accuracy: 71.800%, adv accuracy: 9.900%, avg changed rate: 1.765%, num of queries: 104.3 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K79me3/results_log b/TextFooler/output/quantize/nt1_softmax/H3K79me3/results_log index 2dc699bb..59445291 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K79me3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K79me3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K79me3/cat.csv: original accuracy: 86.800%, adv accuracy: 27.000%, avg changed rate: 2.131%, num of queries: 112.4 +For target model GUE/H3K79me3/cat.csv: original accuracy: 86.800%, adv accuracy: 27.000%, avg changed rate: 2.131%, num of queries: 112.4 diff --git a/TextFooler/output/quantize/nt1_softmax/H3K9ac/results_log b/TextFooler/output/quantize/nt1_softmax/H3K9ac/results_log index d1a363eb..da5ca494 100644 --- a/TextFooler/output/quantize/nt1_softmax/H3K9ac/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H3K9ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H3K9ac/cat.csv: original accuracy: 85.500%, adv accuracy: 28.000%, avg changed rate: 1.537%, num of queries: 110.1 +For target model GUE/H3K9ac/cat.csv: original accuracy: 85.500%, adv accuracy: 28.000%, avg changed rate: 1.537%, num of queries: 110.1 diff --git a/TextFooler/output/quantize/nt1_softmax/H4/results_log b/TextFooler/output/quantize/nt1_softmax/H4/results_log index e6032992..accb7780 100644 --- a/TextFooler/output/quantize/nt1_softmax/H4/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4/cat.csv: original accuracy: 93.800%, adv accuracy: 42.100%, avg changed rate: 2.666%, num of queries: 121.6 +For target model GUE/H4/cat.csv: original accuracy: 93.800%, adv accuracy: 42.100%, avg changed rate: 2.666%, num of queries: 121.6 diff --git a/TextFooler/output/quantize/nt1_softmax/H4ac/results_log b/TextFooler/output/quantize/nt1_softmax/H4ac/results_log index 1fca82d9..7fc0cad4 100644 --- a/TextFooler/output/quantize/nt1_softmax/H4ac/results_log +++ b/TextFooler/output/quantize/nt1_softmax/H4ac/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/H4ac/cat.csv: original accuracy: 78.300%, adv accuracy: 22.000%, avg changed rate: 1.631%, num of queries: 108.4 +For target model GUE/H4ac/cat.csv: original accuracy: 78.300%, adv accuracy: 22.000%, avg changed rate: 1.631%, num of queries: 108.4 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_300_all/results_log b/TextFooler/output/quantize/nt1_softmax/prom_300_all/results_log index c75b82cf..2d71ed6e 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_300_all/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_300_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_all/cat.csv: original accuracy: 95.000%, adv accuracy: 30.000%, avg changed rate: 3.161%, num of queries: 71.2 +For target model GUE/prom_300_all/cat.csv: original accuracy: 95.000%, adv accuracy: 30.000%, avg changed rate: 3.161%, num of queries: 71.2 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_300_notata/results_log b/TextFooler/output/quantize/nt1_softmax/prom_300_notata/results_log index 8f98f8bf..e61afcdb 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_300_notata/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_300_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_notata/cat.csv: original accuracy: 97.000%, adv accuracy: 35.500%, avg changed rate: 3.280%, num of queries: 72.9 +For target model GUE/prom_300_notata/cat.csv: original accuracy: 97.000%, adv accuracy: 35.500%, avg changed rate: 3.280%, num of queries: 72.9 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_300_tata/results_log b/TextFooler/output/quantize/nt1_softmax/prom_300_tata/results_log index be65e3a2..3661eef2 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_300_tata/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_300_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_300_tata/cat.csv: original accuracy: 90.800%, adv accuracy: 38.000%, avg changed rate: 2.646%, num of queries: 71.8 +For target model GUE/prom_300_tata/cat.csv: original accuracy: 90.800%, adv accuracy: 38.000%, avg changed rate: 2.646%, num of queries: 71.8 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_core_all/results_log b/TextFooler/output/quantize/nt1_softmax/prom_core_all/results_log index bfcadd68..252c8eb9 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_core_all/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_core_all/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_all/cat.csv: original accuracy: 71.400%, adv accuracy: 28.900%, avg changed rate: 5.082%, num of queries: 23.3 +For target model GUE/prom_core_all/cat.csv: original accuracy: 71.400%, adv accuracy: 28.900%, avg changed rate: 5.082%, num of queries: 23.3 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_core_notata/results_log b/TextFooler/output/quantize/nt1_softmax/prom_core_notata/results_log index 8d83d973..836ea19e 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_core_notata/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_core_notata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_notata/cat.csv: original accuracy: 85.700%, adv accuracy: 27.300%, avg changed rate: 4.689%, num of queries: 22.4 +For target model GUE/prom_core_notata/cat.csv: original accuracy: 85.700%, adv accuracy: 27.300%, avg changed rate: 4.689%, num of queries: 22.4 diff --git a/TextFooler/output/quantize/nt1_softmax/prom_core_tata/results_log b/TextFooler/output/quantize/nt1_softmax/prom_core_tata/results_log index 5eb9824a..4b986dc0 100644 --- a/TextFooler/output/quantize/nt1_softmax/prom_core_tata/results_log +++ b/TextFooler/output/quantize/nt1_softmax/prom_core_tata/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/prom_core_tata/cat.csv: original accuracy: 90.500%, adv accuracy: 46.100%, avg changed rate: 4.611%, num of queries: 23.5 +For target model GUE/prom_core_tata/cat.csv: original accuracy: 90.500%, adv accuracy: 46.100%, avg changed rate: 4.611%, num of queries: 23.5 diff --git a/TextFooler/output/quantize/nt1_softmax/tf0/results_log b/TextFooler/output/quantize/nt1_softmax/tf0/results_log index 3e93b816..18951c2a 100644 --- a/TextFooler/output/quantize/nt1_softmax/tf0/results_log +++ b/TextFooler/output/quantize/nt1_softmax/tf0/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf0/cat.csv: original accuracy: 82.200%, adv accuracy: 25.300%, avg changed rate: 3.967%, num of queries: 30.6 +For target model GUE/tf0/cat.csv: original accuracy: 82.200%, adv accuracy: 25.300%, avg changed rate: 3.967%, num of queries: 30.6 diff --git a/TextFooler/output/quantize/nt1_softmax/tf1/results_log b/TextFooler/output/quantize/nt1_softmax/tf1/results_log index 2cd19359..1cdeba95 100644 --- a/TextFooler/output/quantize/nt1_softmax/tf1/results_log +++ b/TextFooler/output/quantize/nt1_softmax/tf1/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf1/cat.csv: original accuracy: 82.900%, adv accuracy: 28.600%, avg changed rate: 3.700%, num of queries: 30.8 +For target model GUE/tf1/cat.csv: original accuracy: 82.900%, adv accuracy: 28.600%, avg changed rate: 3.700%, num of queries: 30.8 diff --git a/TextFooler/output/quantize/nt1_softmax/tf2/results_log b/TextFooler/output/quantize/nt1_softmax/tf2/results_log index 5f310b88..e7c35c3a 100644 --- a/TextFooler/output/quantize/nt1_softmax/tf2/results_log +++ b/TextFooler/output/quantize/nt1_softmax/tf2/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf2/cat.csv: original accuracy: 84.200%, adv accuracy: 23.600%, avg changed rate: 3.616%, num of queries: 29.6 +For target model GUE/tf2/cat.csv: original accuracy: 84.200%, adv accuracy: 23.600%, avg changed rate: 3.616%, num of queries: 29.6 diff --git a/TextFooler/output/quantize/nt1_softmax/tf3/results_log b/TextFooler/output/quantize/nt1_softmax/tf3/results_log index 48b80c31..46cee0fd 100644 --- a/TextFooler/output/quantize/nt1_softmax/tf3/results_log +++ b/TextFooler/output/quantize/nt1_softmax/tf3/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf3/cat.csv: original accuracy: 78.400%, adv accuracy: 17.500%, avg changed rate: 3.606%, num of queries: 29.0 +For target model GUE/tf3/cat.csv: original accuracy: 78.400%, adv accuracy: 17.500%, avg changed rate: 3.606%, num of queries: 29.0 diff --git a/TextFooler/output/quantize/nt1_softmax/tf4/results_log b/TextFooler/output/quantize/nt1_softmax/tf4/results_log index 34132976..5921566c 100644 --- a/TextFooler/output/quantize/nt1_softmax/tf4/results_log +++ b/TextFooler/output/quantize/nt1_softmax/tf4/results_log @@ -1 +1 @@ -For target model /projects/p32013/DNABERT-meta/GUE/tf4/cat.csv: original accuracy: 94.100%, adv accuracy: 28.800%, avg changed rate: 4.118%, num of queries: 30.2 +For target model GUE/tf4/cat.csv: original accuracy: 94.100%, adv accuracy: 28.800%, avg changed rate: 4.118%, num of queries: 30.2 diff --git a/TextFooler/run_attack_classification.py b/TextFooler/run_attack_classification.py index 28dff6f7..dd9042f0 100644 --- a/TextFooler/run_attack_classification.py +++ b/TextFooler/run_attack_classification.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/FreeLB/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/FreeLB/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -78,7 +78,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/FreeLB/{model}/{model}_{dataset_dir}" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/FreeLB/{model}/{model}_{dataset_dir}" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification1.py b/TextFooler/run_attack_classification1.py index 22fc13d6..d557de8f 100644 --- a/TextFooler/run_attack_classification1.py +++ b/TextFooler/run_attack_classification1.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model nt ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/FreeLB/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/FreeLB/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'nt2' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -78,7 +78,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/FreeLB/{model}/{model}_{dataset_dir}" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/FreeLB/{model}/{model}_{dataset_dir}" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_adfar.py b/TextFooler/run_attack_classification_adfar.py index a8e29d8e..94bce799 100644 --- a/TextFooler/run_attack_classification_adfar.py +++ b/TextFooler/run_attack_classification_adfar.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ - '--nclasses 2 --tokenizer_path /scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ + '--nclasses 2 --tokenizer_path /scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -82,7 +82,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/4times_adv_double_0-7" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/4times_adv_double_0-7" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_adfar1.py b/TextFooler/run_attack_classification_adfar1.py index 81bca620..277b938a 100644 --- a/TextFooler/run_attack_classification_adfar1.py +++ b/TextFooler/run_attack_classification_adfar1.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model nt ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ - '--nclasses 2 --tokenizer_path /scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ + '--nclasses 2 --tokenizer_path /scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'nt2' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -84,7 +84,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/4times_adv_double_0-7" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/4times_adv_double_0-7" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_adfar2.py b/TextFooler/run_attack_classification_adfar2.py index aa671b97..9a61db4d 100644 --- a/TextFooler/run_attack_classification_adfar2.py +++ b/TextFooler/run_attack_classification_adfar2.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model hyena ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/ADFAR/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ - '--nclasses 2 --tokenizer_path /scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ + '--nclasses 2 --tokenizer_path /scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/origin' \ # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'hyena' dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -82,7 +82,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/{model}/4times_adv_double_0-7" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/ADFAR/GUE/GUE/{model}/{dataset_dir}/{model}/4times_adv_double_0-7" # Check if the dataset file exists if os.path.exists(dataset_path): # Format the command with the current dataset and target model path diff --git a/TextFooler/run_attack_classification_all.py b/TextFooler/run_attack_classification_all.py index 51ca0ec0..a4994abc 100644 --- a/TextFooler/run_attack_classification_all.py +++ b/TextFooler/run_attack_classification_all.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model nt ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/All/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/All/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'nt2' dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -80,7 +80,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/all" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/all" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_all2.py b/TextFooler/run_attack_classification_all2.py index 66f7fc47..c3ef2c4d 100644 --- a/TextFooler/run_attack_classification_all2.py +++ b/TextFooler/run_attack_classification_all2.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/All/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/All/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", "H3K9ac", "H4", "H4ac",] @@ -78,7 +78,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/all" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/all" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_at.py b/TextFooler/run_attack_classification_at.py index fbcd88a7..845246f2 100644 --- a/TextFooler/run_attack_classification_at.py +++ b/TextFooler/run_attack_classification_at.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/AT/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/AT/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -83,7 +83,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler/checkpoint-200" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler/checkpoint-200" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_at1.py b/TextFooler/run_attack_classification_at1.py index 0f96dfac..2c14ac05 100644 --- a/TextFooler/run_attack_classification_at1.py +++ b/TextFooler/run_attack_classification_at1.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model hyena ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/AT/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/AT/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'hyena' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -82,7 +82,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_at2.py b/TextFooler/run_attack_classification_at2.py index 53110e5b..eedaa720 100644 --- a/TextFooler/run_attack_classification_at2.py +++ b/TextFooler/run_attack_classification_at2.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model og ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/AT/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/AT/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'og' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -80,7 +80,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_at3.py b/TextFooler/run_attack_classification_at3.py index 741ba7d0..dcc91863 100644 --- a/TextFooler/run_attack_classification_at3.py +++ b/TextFooler/run_attack_classification_at3.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,15 +58,15 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model hyena ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/AT/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/AT/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'hyena' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -81,7 +81,7 @@ # Loop over each dataset directory for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'five_percent/cat.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/textfooler" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_quantize.py b/TextFooler/run_attack_classification_quantize.py index 81ba0ef2..d3fba8d9 100644 --- a/TextFooler/run_attack_classification_quantize.py +++ b/TextFooler/run_attack_classification_quantize.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2 --quantize' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,16 +58,16 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/quantize/{model}/{dataset_dir} ' \ + '--output_dir TextFooler/output/quantize/{model}/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2 --quantize ' \ '--train_file {train_path}' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -80,7 +80,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') train_path=os.path.join(base_dir, dataset_dir, 'train.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/origin" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/TextFooler/run_attack_classification_quantize2.py b/TextFooler/run_attack_classification_quantize2.py index d7200a55..187b9361 100644 --- a/TextFooler/run_attack_classification_quantize2.py +++ b/TextFooler/run_attack_classification_quantize2.py @@ -1,52 +1,52 @@ # import os # # for BERT target -# command = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/0/cat.csv ' \ +# command = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/0/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_0 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_0 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2 --quantize' -# command1 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/1/cat.csv ' \ +# command1 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/1/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_1 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_1 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command2 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/2/cat.csv ' \ +# command2 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/2/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_2 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_2 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command3 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/3/cat.csv ' \ +# command3 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/3/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_3 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_3 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' -# command4 = 'python attack_classification.py --dataset_path /projects/p32013/DNABERT-meta/BERT-Attack/GUE/mouse/4/cat.csv ' \ +# command4 = 'python attack_classification.py --dataset_path BERT-Attack/GUE/mouse/4/cat.csv ' \ # '--target_model bert ' \ -# '--target_model_path /scratch/hlv8980/GERM_ICML/output_zhihan_vanilla_Full_double/zhihan_vanilla_dnabert2_Full_double_4 ' \ +# '--target_model_path /scratch/anonymous/dnabert2_4 ' \ # '--max_seq_length 256 --batch_size 32 ' \ -# '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ -# '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ -# '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ +# '--counter_fitting_embeddings_path TextFooler/embeddings/subword_dnabert2_embeddings.txt ' \ +# '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting.npy ' \ +# '--USE_cache_path TextFooler/tf_cache ' \ # '--nclasses 2' # os.system(command) @@ -58,16 +58,16 @@ command_template = 'python attack_classification_general.py --dataset_path {dataset_path} ' \ '--target_model bert ' \ '--target_model_path {target_model_path} ' \ - '--output_dir /projects/p32013/DNABERT-meta/TextFooler/output/quantize/{model}_softmax/{dataset_dir} ' \ + '--output_dir TextFooler/output/quantize/{model}_softmax/{dataset_dir} ' \ '--max_seq_length 256 --batch_size 128 ' \ - '--counter_fitting_embeddings_path /projects/p32013/DNABERT-meta/TextFooler/embeddings/subword_{model}_embeddings.txt ' \ - '--counter_fitting_cos_sim_path /projects/p32013/DNABERT-meta/TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ - '--USE_cache_path /projects/p32013/DNABERT-meta/TextFooler/tf_cache ' \ + '--counter_fitting_embeddings_path TextFooler/embeddings/subword_{model}_embeddings.txt ' \ + '--counter_fitting_cos_sim_path TextFooler/cos_sim_counter_fitting/cos_sim_counter_fitting_{model}.npy ' \ + '--USE_cache_path TextFooler/tf_cache ' \ '--nclasses 2 --quantize --attn_softmax softmax1 ' \ '--train_file {train_path}' # Set the base directory for the datasets -base_dir = '/projects/p32013/DNABERT-meta/GUE' +base_dir = 'GUE' model = 'dnabert' # dataset_dirs = ["H3", "H3K14ac", "H3K36me3", "H3K4me1", "H3K4me2", "H3K4me3", "H3K79me3", # "H3K9ac", "H4", "H4ac", "prom_core_all", "prom_core_notata", "prom_core_tata", @@ -80,7 +80,7 @@ for dataset_dir in dataset_dirs: dataset_path = os.path.join(base_dir, dataset_dir, 'cat.csv') train_path=os.path.join(base_dir, dataset_dir, 'train.csv') - target_model_path = f"/scratch/hlv8980/Attack_Benchmark/models/{model}/{dataset_dir}/origin" + target_model_path = f"/scratch/anonymous/Attack_Benchmark/models/{model}/{dataset_dir}/origin" # Check if the dataset file exists if os.path.exists(dataset_path): diff --git a/UAP/calculate.py b/UAP/calculate.py index dc5e9f56..1ea435e2 100644 --- a/UAP/calculate.py +++ b/UAP/calculate.py @@ -3,7 +3,7 @@ import pandas as pd # 设置主路径 -root_dir = "/projects/p32013/DNABERT-meta/UAP/results" +root_dir = "UAP/results" # 存储结果 asr_results = [] diff --git a/UAP/results/asr.py b/UAP/results/asr.py index 7bd562ff..d534e388 100644 --- a/UAP/results/asr.py +++ b/UAP/results/asr.py @@ -3,7 +3,7 @@ import csv # 设置你的results路径 -results_dir = "/projects/p32013/DNABERT-meta/UAP/results" +results_dir = "UAP/results" output_csv = "asr_results.csv" # 准备输出数据 diff --git a/UAP/run.sh b/UAP/run.sh index 9625cd7f..2cf864de 100644 --- a/UAP/run.sh +++ b/UAP/run.sh @@ -1,18 +1,18 @@ -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("prom_300_tata") model='bert' for task in "${tasks[@]}"; do - python search.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + python search.py --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ - --cache_dir /projects/p32013/DNABERT-meta/UAP/.cache + --cache_dir UAP/.cache echo "${task} finished" done diff --git a/UAP/run_H4.sh b/UAP/run_H4.sh index 82dfa03a..2596f010 100644 --- a/UAP/run_H4.sh +++ b/UAP/run_H4.sh @@ -1,7 +1,7 @@ #!/bin/bash -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("H3K79me3" "H3K9ac" "H4" "H4ac") @@ -23,7 +23,7 @@ for task in "${tasks[@]}"; do echo "==================================================" # 为每个任务创建单独的缓存目录 - task_cache_dir="/projects/p32013/DNABERT-meta/UAP/.cache/${task}" + task_cache_dir="UAP/.cache/${task}" mkdir -p ${task_cache_dir} # 设置任务特定的环境变量 @@ -32,14 +32,14 @@ for task in "${tasks[@]}"; do # 运行任务 python search_new.py \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} \ --num_label 2 \ --n_gpu 1 \ --max_seq_length 256 \ --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ --cache_dir ${task_cache_dir} diff --git a/UAP/run_batch.sh b/UAP/run_batch.sh index 18794c87..66e845b4 100644 --- a/UAP/run_batch.sh +++ b/UAP/run_batch.sh @@ -1,30 +1,30 @@ -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("H3K36me3" "H3K4me2" "H3K4me3") model='bert' for task in "${tasks[@]}"; do - python search.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + python search.py --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ - --cache_dir /projects/p32013/DNABERT-meta/UAP/.cache + --cache_dir UAP/.cache echo "${task} finished" done # for task in "${tasks[@]}"; do # ( -# python search.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ -# --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ +# python search.py --data_dir GUE/${task} \ +# --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ # --task_name ${task} --num_label 2 --n_gpu 1 \ # --max_seq_length 256 --batch_size 128 \ -# --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ +# --output_dir UAP/results/${task} \ # --model_type bert \ -# --cache_dir /projects/p32013/DNABERT-meta/UAP/.cache +# --cache_dir UAP/.cache # ) 2>&1 | tee "log_${task}.txt" # echo "${task} finished" diff --git a/UAP/run_new.sh b/UAP/run_new.sh index 295216ea..2bbbc575 100755 --- a/UAP/run_new.sh +++ b/UAP/run_new.sh @@ -1,18 +1,18 @@ -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("prom_300_all") model='bert' for task in "${tasks[@]}"; do - python search.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + python search.py --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ - --cache_dir /projects/p32013/DNABERT-meta/UAP/.cache + --cache_dir UAP/.cache echo "${task} finished" done diff --git a/UAP/run_number.sh b/UAP/run_number.sh index 9d6f4b65..0674389c 100644 --- a/UAP/run_number.sh +++ b/UAP/run_number.sh @@ -1,7 +1,7 @@ #!/bin/bash -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("0" "1" "2" "3") @@ -23,7 +23,7 @@ for task in "${tasks[@]}"; do echo "==================================================" # 为每个任务创建单独的缓存目录 - task_cache_dir="/projects/p32013/DNABERT-meta/UAP/.cache/${task}" + task_cache_dir="UAP/.cache/${task}" mkdir -p ${task_cache_dir} # 设置任务特定的环境变量 @@ -32,14 +32,14 @@ for task in "${tasks[@]}"; do # 运行任务 python search_new.py \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} \ --num_label 2 \ --n_gpu 1 \ --max_seq_length 256 \ --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ --cache_dir ${task_cache_dir} diff --git a/UAP/run_pro.sh b/UAP/run_pro.sh index 765df3bb..6c936c5f 100644 --- a/UAP/run_pro.sh +++ b/UAP/run_pro.sh @@ -1,7 +1,7 @@ #!/bin/bash -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata") @@ -23,7 +23,7 @@ for task in "${tasks[@]}"; do echo "==================================================" # 为每个任务创建单独的缓存目录 - task_cache_dir="/projects/p32013/DNABERT-meta/UAP/.cache/${task}" + task_cache_dir="UAP/.cache/${task}" mkdir -p ${task_cache_dir} # 设置任务特定的环境变量 @@ -32,14 +32,14 @@ for task in "${tasks[@]}"; do # 运行任务 python search_new.py \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} \ --num_label 2 \ --n_gpu 1 \ --max_seq_length 256 \ --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ --cache_dir ${task_cache_dir} diff --git a/UAP/run_prom_300_notata.sh b/UAP/run_prom_300_notata.sh index ac3c4f17..f52f9bc7 100644 --- a/UAP/run_prom_300_notata.sh +++ b/UAP/run_prom_300_notata.sh @@ -1,18 +1,18 @@ -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("prom_300_notata") model='bert' for task in "${tasks[@]}"; do - python search.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + python search.py --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ - --cache_dir /projects/p32013/DNABERT-meta/UAP/.cache + --cache_dir UAP/.cache echo "${task} finished" done diff --git a/UAP/run_tf.sh b/UAP/run_tf.sh index 5295e99e..fc5c200a 100644 --- a/UAP/run_tf.sh +++ b/UAP/run_tf.sh @@ -1,7 +1,7 @@ #!/bin/bash -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/UAP +export HF_HOME="/.cache/" +cd UAP # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("2") @@ -23,7 +23,7 @@ for task in "${tasks[@]}"; do echo "==================================================" # 为每个任务创建单独的缓存目录 - task_cache_dir="/projects/p32013/DNABERT-meta/UAP/.cache/${task}" + task_cache_dir="UAP/.cache/${task}" mkdir -p ${task_cache_dir} # 设置任务特定的环境变量 @@ -32,14 +32,14 @@ for task in "${tasks[@]}"; do # 运行任务 python search_new_2.py \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} \ --num_label 2 \ --n_gpu 1 \ --max_seq_length 256 \ --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/UAP/results/${task} \ + --output_dir UAP/results/${task} \ --model_type bert \ --cache_dir ${task_cache_dir} diff --git a/adv_results/dnabert/H3/results_log b/adv_results/dnabert/H3/results_log deleted file mode 100644 index e69de29b..00000000 diff --git a/auto-attack/calculate.py b/auto-attack/calculate.py index 7bb3b53e..3694da95 100644 --- a/auto-attack/calculate.py +++ b/auto-attack/calculate.py @@ -35,7 +35,7 @@ def process_json_folder(folder_path): # 示例运行 if __name__ == "__main__": - folder = "/projects/p32013/DNABERT-meta/auto-attack/results" # 替换为你的 JSON 文件夹路径 + folder = "auto-attack/results" # 替换为你的 JSON 文件夹路径 results = process_json_folder(folder) for r in results: diff --git a/auto-attack/results/0_attack_results.json b/auto-attack/results/0_attack_results.json index 637bde1a..3584622e 100644 --- a/auto-attack/results/0_attack_results.json +++ b/auto-attack/results/0_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "0", - "model_name": "magicslabnu/DNABERT-2-finetuned-0", + "model_name": "anonymous/DNABERT-2-finetuned-0", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/1_attack_results.json b/auto-attack/results/1_attack_results.json index 308c60ae..b0454c44 100644 --- a/auto-attack/results/1_attack_results.json +++ b/auto-attack/results/1_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "1", - "model_name": "magicslabnu/DNABERT-2-finetuned-1", + "model_name": "anonymous/DNABERT-2-finetuned-1", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/2_attack_results.json b/auto-attack/results/2_attack_results.json index a678e254..f21fdb12 100644 --- a/auto-attack/results/2_attack_results.json +++ b/auto-attack/results/2_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "2", - "model_name": "magicslabnu/DNABERT-2-finetuned-2", + "model_name": "anonymous/DNABERT-2-finetuned-2", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/3_attack_results.json b/auto-attack/results/3_attack_results.json index ba02aac4..68454316 100644 --- a/auto-attack/results/3_attack_results.json +++ b/auto-attack/results/3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "3", - "model_name": "magicslabnu/DNABERT-2-finetuned-3", + "model_name": "anonymous/DNABERT-2-finetuned-3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/4_attack_results.json b/auto-attack/results/4_attack_results.json index b440f9ec..4075e3ea 100644 --- a/auto-attack/results/4_attack_results.json +++ b/auto-attack/results/4_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "4", - "model_name": "magicslabnu/DNABERT-2-finetuned-4", + "model_name": "anonymous/DNABERT-2-finetuned-4", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K14ac_attack_results.json b/auto-attack/results/H3K14ac_attack_results.json index f376dcc1..8e92d6c7 100644 --- a/auto-attack/results/H3K14ac_attack_results.json +++ b/auto-attack/results/H3K14ac_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K14ac", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K14ac", + "model_name": "anonymous/DNABERT-2-finetuned-H3K14ac", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K36me3_attack_results.json b/auto-attack/results/H3K36me3_attack_results.json index cc71c52d..6f4b7431 100644 --- a/auto-attack/results/H3K36me3_attack_results.json +++ b/auto-attack/results/H3K36me3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K36me3", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K36me3", + "model_name": "anonymous/DNABERT-2-finetuned-H3K36me3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K4me1_attack_results.json b/auto-attack/results/H3K4me1_attack_results.json index adf84412..b0374e30 100644 --- a/auto-attack/results/H3K4me1_attack_results.json +++ b/auto-attack/results/H3K4me1_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K4me1", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K4me1", + "model_name": "anonymous/DNABERT-2-finetuned-H3K4me1", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K4me2_attack_results.json b/auto-attack/results/H3K4me2_attack_results.json index 95d6baab..aad4de6a 100644 --- a/auto-attack/results/H3K4me2_attack_results.json +++ b/auto-attack/results/H3K4me2_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K4me2", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K4me2", + "model_name": "anonymous/DNABERT-2-finetuned-H3K4me2", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K4me3_attack_results.json b/auto-attack/results/H3K4me3_attack_results.json index 9d22c0c1..43f03d83 100644 --- a/auto-attack/results/H3K4me3_attack_results.json +++ b/auto-attack/results/H3K4me3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K4me3", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K4me3", + "model_name": "anonymous/DNABERT-2-finetuned-H3K4me3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K79me3_attack_results.json b/auto-attack/results/H3K79me3_attack_results.json index 607cff51..c1300907 100644 --- a/auto-attack/results/H3K79me3_attack_results.json +++ b/auto-attack/results/H3K79me3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K79me3", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K79me3", + "model_name": "anonymous/DNABERT-2-finetuned-H3K79me3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3K9ac_attack_results.json b/auto-attack/results/H3K9ac_attack_results.json index d88a24bc..39404f53 100644 --- a/auto-attack/results/H3K9ac_attack_results.json +++ b/auto-attack/results/H3K9ac_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3K9ac", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3K9ac", + "model_name": "anonymous/DNABERT-2-finetuned-H3K9ac", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H3_attack_results.json b/auto-attack/results/H3_attack_results.json index e2f10ce4..87b4dbb3 100644 --- a/auto-attack/results/H3_attack_results.json +++ b/auto-attack/results/H3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H3", - "model_name": "magicslabnu/DNABERT-2-finetuned-H3", + "model_name": "anonymous/DNABERT-2-finetuned-H3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H4_attack_results.json b/auto-attack/results/H4_attack_results.json index 78e9f38d..fb0e8c7f 100644 --- a/auto-attack/results/H4_attack_results.json +++ b/auto-attack/results/H4_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H4", - "model_name": "magicslabnu/DNABERT-2-finetuned-H4", + "model_name": "anonymous/DNABERT-2-finetuned-H4", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/H4ac_attack_results.json b/auto-attack/results/H4ac_attack_results.json index ea9711c1..76887272 100644 --- a/auto-attack/results/H4ac_attack_results.json +++ b/auto-attack/results/H4ac_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "H4ac", - "model_name": "magicslabnu/DNABERT-2-finetuned-H4ac", + "model_name": "anonymous/DNABERT-2-finetuned-H4ac", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_300_all_attack_results.json b/auto-attack/results/prom_300_all_attack_results.json index 35eaf3a7..eba3da3a 100644 --- a/auto-attack/results/prom_300_all_attack_results.json +++ b/auto-attack/results/prom_300_all_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_300_all", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_300_all", + "model_name": "anonymous/DNABERT-2-finetuned-prom_300_all", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_300_notata_attack_results.json b/auto-attack/results/prom_300_notata_attack_results.json index 9ba2fb56..022fdc61 100644 --- a/auto-attack/results/prom_300_notata_attack_results.json +++ b/auto-attack/results/prom_300_notata_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_300_notata", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_300_notata", + "model_name": "anonymous/DNABERT-2-finetuned-prom_300_notata", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_300_tata_attack_results.json b/auto-attack/results/prom_300_tata_attack_results.json index 76c5981c..12d14ff5 100644 --- a/auto-attack/results/prom_300_tata_attack_results.json +++ b/auto-attack/results/prom_300_tata_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_300_tata", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_300_tata", + "model_name": "anonymous/DNABERT-2-finetuned-prom_300_tata", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_core_all_attack_results.json b/auto-attack/results/prom_core_all_attack_results.json index 52887d3d..82e36b2d 100644 --- a/auto-attack/results/prom_core_all_attack_results.json +++ b/auto-attack/results/prom_core_all_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_core_all", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_core_all", + "model_name": "anonymous/DNABERT-2-finetuned-prom_core_all", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_core_notata_attack_results.json b/auto-attack/results/prom_core_notata_attack_results.json index 07166d09..0b8ff6cf 100644 --- a/auto-attack/results/prom_core_notata_attack_results.json +++ b/auto-attack/results/prom_core_notata_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_core_notata", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_core_notata", + "model_name": "anonymous/DNABERT-2-finetuned-prom_core_notata", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/prom_core_tata_attack_results.json b/auto-attack/results/prom_core_tata_attack_results.json index 3cb9a762..b68ce31c 100644 --- a/auto-attack/results/prom_core_tata_attack_results.json +++ b/auto-attack/results/prom_core_tata_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "prom_core_tata", - "model_name": "magicslabnu/DNABERT-2-finetuned-prom_core_tata", + "model_name": "anonymous/DNABERT-2-finetuned-prom_core_tata", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/tf0_attack_results.json b/auto-attack/results/tf0_attack_results.json index 7ac6040e..da95d0f7 100644 --- a/auto-attack/results/tf0_attack_results.json +++ b/auto-attack/results/tf0_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "tf0", - "model_name": "magicslabnu/DNABERT-2-finetuned-tf0", + "model_name": "anonymous/DNABERT-2-finetuned-tf0", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/tf1_attack_results.json b/auto-attack/results/tf1_attack_results.json index 096818f5..9c02336f 100644 --- a/auto-attack/results/tf1_attack_results.json +++ b/auto-attack/results/tf1_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "tf1", - "model_name": "magicslabnu/DNABERT-2-finetuned-tf1", + "model_name": "anonymous/DNABERT-2-finetuned-tf1", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/tf2_attack_results.json b/auto-attack/results/tf2_attack_results.json index 1cc7709a..40cff6d1 100644 --- a/auto-attack/results/tf2_attack_results.json +++ b/auto-attack/results/tf2_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "tf2", - "model_name": "magicslabnu/DNABERT-2-finetuned-tf2", + "model_name": "anonymous/DNABERT-2-finetuned-tf2", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/tf3_attack_results.json b/auto-attack/results/tf3_attack_results.json index e3d9e30f..8d09f686 100644 --- a/auto-attack/results/tf3_attack_results.json +++ b/auto-attack/results/tf3_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "tf3", - "model_name": "magicslabnu/DNABERT-2-finetuned-tf3", + "model_name": "anonymous/DNABERT-2-finetuned-tf3", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/results/tf4_attack_results.json b/auto-attack/results/tf4_attack_results.json index d041a06b..b6b000ee 100644 --- a/auto-attack/results/tf4_attack_results.json +++ b/auto-attack/results/tf4_attack_results.json @@ -1,6 +1,6 @@ { "task_name": "tf4", - "model_name": "magicslabnu/DNABERT-2-finetuned-tf4", + "model_name": "anonymous/DNABERT-2-finetuned-tf4", "model_type": "bert", "epsilon": 10.0, "max_seq_length": 256, diff --git a/auto-attack/run.sh b/auto-attack/run.sh index 53c79fee..036c3d13 100644 --- a/auto-attack/run.sh +++ b/auto-attack/run.sh @@ -1,16 +1,16 @@ -export HF_HOME="/projects/p32013/.cache/" -cd /projects/p32013/DNABERT-meta/auto-attack +export HF_HOME="/.cache/" +cd auto-attack # tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") tasks=("1") model='bert' for task in "${tasks[@]}"; do - python auto_new.py --data_dir /projects/p32013/DNABERT-meta/GUE/${task} \ - --model_name_or_path magicslabnu/DNABERT-2-finetuned-${task} \ + python auto_new.py --data_dir GUE/${task} \ + --model_name_or_path anonymous/DNABERT-2-finetuned-${task} \ --task_name ${task} --num_label 2 --n_gpu 1 \ --max_seq_length 256 --batch_size 128 \ - --output_dir /projects/p32013/DNABERT-meta/auto-attack/results \ + --output_dir auto-attack/results \ --model_type bert echo "${task} finished" diff --git a/checkpoints/dnabert_H3/checkpoint-best/config.json b/checkpoints/dnabert_H3/checkpoint-best/config.json deleted file mode 100644 index 06f39051..00000000 --- a/checkpoints/dnabert_H3/checkpoint-best/config.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "alibi_starting_size": 512, - "architectures": [ - "DNABertForSequenceClassification" - ], - "attention_probs_dropout_prob": 0.0, - "auto_map": { - "AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig", - "AutoModel": "zhihan1996/DNABERT-2-117M--bert_layers.BertModel", - "AutoModelForMaskedLM": "zhihan1996/DNABERT-2-117M--bert_layers.BertForMaskedLM", - "AutoModelForSequenceClassification": "zhihan1996/DNABERT-2-117M--bert_layers.BertForSequenceClassification" - }, - "classifier_dropout": null, - "finetuning_task": "h3", - "gradient_checkpointing": false, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 512, - "model_type": "bert", - "num_attention_heads": 12, - "num_hidden_layers": 12, - "pad_token_id": 0, - "position_embedding_type": "absolute", - "problem_type": "single_label_classification", - "torch_dtype": "float32", - "transformers_version": "4.51.3", - "type_vocab_size": 2, - "use_cache": true, - "vocab_size": 4096 -} diff --git a/checkpoints/dnabert_H3/checkpoint-best/special_tokens_map.json b/checkpoints/dnabert_H3/checkpoint-best/special_tokens_map.json deleted file mode 100644 index 9bbecc17..00000000 --- a/checkpoints/dnabert_H3/checkpoint-best/special_tokens_map.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "cls_token": { - "content": "[CLS]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "[PAD]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "[SEP]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "[UNK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - } -} diff --git a/checkpoints/dnabert_H3/checkpoint-best/tokenizer.json b/checkpoints/dnabert_H3/checkpoint-best/tokenizer.json deleted file mode 100644 index 505b1ab2..00000000 --- a/checkpoints/dnabert_H3/checkpoint-best/tokenizer.json +++ /dev/null @@ -1,20604 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 256, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 256 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "[PAD]" - }, - "added_tokens": [ - { - "id": 0, - "content": "[UNK]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 1, - "content": "[CLS]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 2, - "content": "[SEP]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 3, - "content": "[PAD]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 4, - "content": "[MASK]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "Whitespace" - }, - "post_processor": { - "type": "TemplateProcessing", - "single": [ - { - "SpecialToken": { - "id": "[CLS]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "A", - "type_id": 0 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 0 - } - } - ], - "pair": [ - { - "SpecialToken": { - "id": "[CLS]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "A", - "type_id": 0 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "B", - "type_id": 1 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 1 - } - } - ], - "special_tokens": { - "[CLS]": { - "id": "[CLS]", - "ids": [ - 1 - ], - "tokens": [ - "[CLS]" - ] - }, - "[SEP]": { - "id": "[SEP]", - "ids": [ - 2 - ], - "tokens": [ - "[SEP]" - ] - } - } - }, - "decoder": null, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": "[UNK]", - "continuing_subword_prefix": null, - "end_of_word_suffix": null, - "fuse_unk": false, - "byte_fallback": false, - "ignore_merges": false, - "vocab": { - "[UNK]": 0, - "[CLS]": 1, - "[SEP]": 2, - "[PAD]": 3, - "[MASK]": 4, - "A": 5, - "C": 6, - "G": 7, - "T": 8, - "AA": 9, - "TT": 10, - "TG": 11, - "CA": 12, - "CC": 13, - "TA": 14, - "GG": 15, - "TC": 16, - "GA": 17, - "AAA": 18, - "GC": 19, - "TAA": 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a/checkpoints/dnabert_H3/checkpoint-best/tokenizer_config.json b/checkpoints/dnabert_H3/checkpoint-best/tokenizer_config.json deleted file mode 100644 index 5ac2d68c..00000000 --- a/checkpoints/dnabert_H3/checkpoint-best/tokenizer_config.json +++ /dev/null @@ -1,61 +0,0 @@ -{ - "added_tokens_decoder": { - "0": { - "content": "[UNK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "1": { - "content": "[CLS]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "2": { - "content": "[SEP]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "3": { - "content": "[PAD]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "4": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - } - }, - "clean_up_tokenization_spaces": false, - "cls_token": "[CLS]", - "do_lower_case": true, - "extra_special_tokens": {}, - "mask_token": "[MASK]", - "max_length": 256, - "model_max_length": 256, - "pad_to_multiple_of": null, - "pad_token": "[PAD]", - "pad_token_type_id": 0, - "padding_side": "right", - "sep_token": "[SEP]", - "stride": 0, - "tokenizer_class": "PreTrainedTokenizer", - "truncation_side": "right", - "truncation_strategy": "longest_first", - "unk_token": "[UNK]" -} diff --git a/checkpoints/dnabert_H3/checkpoint-last/config.json b/checkpoints/dnabert_H3/checkpoint-last/config.json deleted file mode 100644 index 06f39051..00000000 --- a/checkpoints/dnabert_H3/checkpoint-last/config.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "alibi_starting_size": 512, - "architectures": [ - "DNABertForSequenceClassification" - ], - "attention_probs_dropout_prob": 0.0, - "auto_map": { - "AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig", - "AutoModel": 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b/checkpoints/dnabert_H3/checkpoint-last/special_tokens_map.json deleted file mode 100644 index 9bbecc17..00000000 --- a/checkpoints/dnabert_H3/checkpoint-last/special_tokens_map.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "cls_token": { - "content": "[CLS]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "[PAD]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "[SEP]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "[UNK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - } -} diff --git a/checkpoints/dnabert_H3/checkpoint-last/tokenizer.json b/checkpoints/dnabert_H3/checkpoint-last/tokenizer.json deleted file mode 100644 index 505b1ab2..00000000 --- a/checkpoints/dnabert_H3/checkpoint-last/tokenizer.json +++ /dev/null @@ -1,20604 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 256, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 256 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "[PAD]" - }, - "added_tokens": [ - { - "id": 0, - "content": "[UNK]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 1, - "content": "[CLS]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 2, - "content": "[SEP]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 3, - "content": "[PAD]", - "single_word": false, - "lstrip": false, - "rstrip": false, - 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"single_word": false, - "special": true - }, - "4": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - } - }, - "clean_up_tokenization_spaces": false, - "cls_token": "[CLS]", - "do_lower_case": true, - "extra_special_tokens": {}, - "mask_token": "[MASK]", - "max_length": 256, - "model_max_length": 256, - "pad_to_multiple_of": null, - "pad_token": "[PAD]", - "pad_token_type_id": 0, - "padding_side": "right", - "sep_token": "[SEP]", - "stride": 0, - "tokenizer_class": "PreTrainedTokenizer", - "truncation_side": "right", - "truncation_strategy": "longest_first", - "unk_token": "[UNK]" -} diff --git a/dnabert/a.sh b/dnabert/a.sh deleted file mode 100644 index cba39d22..00000000 --- a/dnabert/a.sh +++ /dev/null @@ -1,513 +0,0 @@ -for data in real_go -do - CUDA_VISIBLE_DEVICES=1 python train.py \ - --model_name_or_path kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16 \ - --data_path /root/MOE_DNA/ICLR/classification/species/$data \ - --kmer -1 \ - --run_name debug_caduceus_$data \ - --model_max_length 2048 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 16 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-4 \ - --num_train_epochs 20 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_caduceus/$data \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 10 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False -done - -for data in real_reorder real_evo real_genslm real_go -do - CUDA_VISIBLE_DEVICES=4,5 torchrun --nproc_per_node=2 --master_port=12313 train.py \ - --model_name_or_path zhihan1996/DNABERT-2-117M \ - --data_path /root/MOE_DNA/ICLR/classification/pairwise/$data \ - --kmer -1 \ - --run_name debug_nt_$data \ - --model_max_length 512 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 16 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 20 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_nt \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100000 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False -done - -for data in go_real -do - CUDA_VISIBLE_DEVICES=1 python train.py \ - --model_name_or_path zhihan1996/DNABERT-2-117M \ - --data_path /root/MOE_DNA/ICLR/classification/species/$data \ - --kmer -1 \ - --run_name debug_dnabert2_$data \ - --model_max_length 512 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 16 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 20 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_dnabert2_1 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100000 \ - --overwrite_output_dir True \ - --greater_is_better True \ - --metric_for_best_model f1 \ - --log_level info \ - --find_unused_parameters False -done - - - -for data in go_real -do - CUDA_VISIBLE_DEVICES=3 python train.py \ - --model_name_or_path LongSafari/hyenadna-small-32k-seqlen-hf \ - --data_path /root/MOE_DNA/ICLR/classification/species_1_500/$data \ - --kmer -1 \ - --run_name ddddd$data \ - --model_max_length 2000 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 16 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 20 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debugddd \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100000 \ - --overwrite_output_dir True \ - --greater_is_better True \ - --metric_for_best_model f1 \ - --log_level info \ - --find_unused_parameters False -done - - - - -for data in real_reorder -do - CUDA_VISIBLE_DEVICES=0,1 torchrun --nproc_per_node=2 --master-port=12314 train.py \ - --model_name_or_path InstaDeepAI/nucleotide-transformer-v2-500m-multi-species \ - --data_path /root/MOE_DNA/ICLR/classification/species/$data \ - --kmer -1 \ - --run_name debug_nt_$data \ - --model_max_length 512 \ - --per_device_train_batch_size 2 \ - --per_device_eval_batch_size 16 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 20 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_nt_$data \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100000 \ - --overwrite_output_dir True \ - --greater_is_better True \ - --metric_for_best_model f1 \ - --log_level info \ - --find_unused_parameters False -done - - - -for data in real_rand_reorder -do - CUDA_VISIBLE_DEVICES=5 python train.py \ - --regression \ - --model_name_or_path zhihan1996/DNABERT-2-117M \ - --data_path /root/MOE_DNA/ICLR/regression/$data \ - --kmer -1 \ - --run_name debug_dnabert2_$data \ - --model_max_length 512 \ - --per_device_train_batch_size 32 \ - --per_device_eval_batch_size 256 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 2 \ - --fp16 \ - --save_steps 500 \ - --output_dir output/dnabert2_regression \ - --evaluation_strategy steps \ - --eval_steps 500 \ - --warmup_ratio 0.05 \ - --logging_steps 1 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False -done - - - -for data in ref_1/no_aug -do - CUDA_VISIBLE_DEVICES=2,3,4,5 torchrun --nproc_per_node=4 --master_port=12342 train.py \ - --model_name_or_path zhihan1996/DNABERT-2-117M \ - --data_path /root/MOE_DNA/ICLR/augmentation/$data \ - --kmer -1 \ - --run_name debug_dnabert2_$data \ - --model_max_length 512 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 32 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 40 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_aug_dnabert2 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False -done - - -for data in ref_1/aug -do - CUDA_VISIBLE_DEVICES=2,3,4,5 torchrun --nproc_per_node=4 --master_port=1234 train.py \ - --model_name_or_path zhihan1996/DNABERT-2-117M \ - --data_path /root/MOE_DNA/ICLR/augmentation/$data \ - --kmer -1 \ - --run_name debug_dnabert2_$data \ - --model_max_length 1024 \ - --per_device_train_batch_size 4 \ - --per_device_eval_batch_size 32 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 40 \ - --fp16 \ - --save_steps 200 \ - --output_dir output/debug_aug_dnabert2 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False -done - - -CUDA_VISIBLE_DEVICES=5 python generate_go.py \ - --temperature 0.7 \ - --presence_penalty 0.0 \ - --frequency_penalty 0.0 \ - --repetition_penalty 1.0 \ - --num_generation_from_each_prompt 1 \ - --min_length 700 \ - --max_length 1000 \ - --data_dir /root/MOE_DNA/ICLR/augmentation/ref_1/no_aug/train.csv - - -for temp in 0.5 0.7 1 - do - for presence_penalty in 0.0 0.5 - do - for frequency_penalty in 0.0 0.5 - do - for repetition_penalty in 1.0 1.5 - do - - CUDA_VISIBLE_DEVICES=4 python generate_go.py \ - --temperature $temp \ - --presence_penalty $presence_penalty \ - --frequency_penalty $frequency_penalty \ - --repetition_penalty $repetition_penalty \ - - done - done - done - done -done - - -CUDA_VISIBLE_DEVICES=5 python generate_go.py \ - --temperature 1.0 \ - --presence_penalty 0.0 \ - --frequency_penalty 0.0 \ - --repetition_penalty 1.0 \ - --data_dir /root/MOE_DNA/ICLR/augmentation/ref_1/no_aug/train.csv - -for temp in 0.3 0.5 1 - do - for presence_penalty in 0.0 0.5 - do - for frequency_penalty in 0.0 0.5 - do - for repetition_penalty in 1.0 1.5 - do - - CUDA_VISIBLE_DEVICES=4 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --temperature $temp \ - --presence_penalty $presence_penalty \ - --frequency_penalty $frequency_penalty \ - --repetition_penalty $repetition_penalty \ - - done - done - done - done -done - - - -for temp in 0.3 0.7 1 -do - for presence_penalty in 0.5 - do - for frequency_penalty in 0.5 - do - for repetition_penalty in 1.0 - do - - CUDA_VISIBLE_DEVICES=4 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --data_dir /root/MOE_DNA/ICLR/data/coding_non_coding.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/coding_non_coding \ - --max_output_bp 2000 \ - --temperature $temp \ - --presence_penalty $presence_penalty \ - --frequency_penalty $frequency_penalty \ - --repetition_penalty $repetition_penalty \ - - done - done - done -done - - - -export temp=0.3 -CUDA_VISIBLE_DEVICES=0 python run_evo.py --temperature $temp - - -export temp=0.5 -CUDA_VISIBLE_DEVICES=1 python run_evo.py --temperature $temp - -export temp=0.7 -CUDA_VISIBLE_DEVICES=2 python run_evo.py --temperature $temp - - -export temp=1 -CUDA_VISIBLE_DEVICES=5 python run_genslm.py --temperature $temp --model-name genslm_250M_patric - - -export temp=1 -CUDA_VISIBLE_DEVICES=0 python run_evo.py \ - --temperature $temp \ - --data_dir /root/MOE_DNA/ICLR/data/coding_non_coding.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/coding_non_coding - - - -for temp in 1 -do - for presence_penalty in 0.5 - do - for frequency_penalty in 0.5 - do - for repetition_penalty in 1.0 - do - - CUDA_VISIBLE_DEVICES=3 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size 4B \ - --data_dir /root/MOE_DNA/ICLR/data/cai/extracted_random_contigs.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/cai \ - --max_output_bp 2100 \ - --temperature $temp \ - --presence_penalty $presence_penalty \ - --frequency_penalty $frequency_penalty \ - --repetition_penalty $repetition_penalty \ - - done - done - done -done - - - -for temp in 1 -do - for presence_penalty in 0.5 - do - for frequency_penalty in 0.5 - do - for repetition_penalty in 1.0 - do - - CUDA_VISIBLE_DEVICES=3 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size 4B \ - --data_dir /root/MOE_DNA/ICLR/data/microbes_cds_filtered.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/cai \ - --max_prompt_bp 2100 \ - --max_output_bp 2100 \ - --temperature $temp \ - --min_length 600 \ - --max_length 1000 \ - --presence_penalty $presence_penalty \ - --frequency_penalty $frequency_penalty \ - --repetition_penalty $repetition_penalty \ - - done - done - done -done - - - - -export prompt=500 -CUDA_VISIBLE_DEVICES=0 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size 4B \ - --data_dir /root/data/cami2/marine_plant_30_known.tsv \ - --output_dir /root/MOE_DNA/ICLR/generated/known/$prompt/ \ - --max_prompt_bp $prompt \ - --max_output_bp -1 \ - --temperature 1.0 \ - --min_length 2000 \ - --max_length 2000 \ - --presence_penalty 0.5 \ - --frequency_penalty 0.5 \ - --repetition_penalty 1.0 - - -export prompt=2000 -CUDA_VISIBLE_DEVICES=3 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size 4B \ - --data_dir /root/MOE_DNA/ICLR/data/coding_non_coding.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/coding_non_coding \ - --max_prompt_bp $prompt \ - --max_output_bp -1 \ - --temperature 1.0 \ - --min_length 600 \ - --max_length 1000 \ - --presence_penalty 0.5 \ - --frequency_penalty 0.5 \ - --repetition_penalty 1.0 - - -export prompt=2000 -for model_size in 500M 100M -do - CUDA_VISIBLE_DEVICES=3 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size ${model_size} \ - --data_dir /root/data/cami2/marine_plant_20_unknown.tsv \ - --output_dir /root/MOE_DNA/ICLR/generated/unknown/${prompt}_${model_size}/ \ - --max_prompt_bp $prompt \ - --max_output_bp 2000 \ - --temperature 1.0 \ - --min_length 600 \ - --max_length 1000 \ - --presence_penalty 0.5 \ - --frequency_penalty 0.5 \ - --repetition_penalty 1.0 -done - - -export temp=1 -CUDA_VISIBLE_DEVICES=3 python run_evo.py \ - --temperature $temp \ - --data_dir /root/MOE_DNA/ICLR/data/microbes_cds_filtered.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/cai \ - --start_idx 0 \ - --end_idx 233 - - -export temp=1 -CUDA_VISIBLE_DEVICES=4 python run_evo.py \ - --temperature $temp \ - --data_dir /root/MOE_DNA/ICLR/data/microbes_cds_filtered.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/cai \ - --start_idx 233 \ - --end_idx 466 - - - -export temp=1 -CUDA_VISIBLE_DEVICES=5 python run_evo.py \ - --temperature $temp \ - --data_dir /root/MOE_DNA/ICLR/data/microbes_cds_filtered.csv \ - --output_dir /root/MOE_DNA/ICLR/generated/cai \ - --start_idx 466 \ - --end_idx 700 - - -export temp=1 -CUDA_VISIBLE_DEVICES=3 python run_evo.py \ - --temperature $temp \ - --data_dir /root/data/cami2/marine_plant_30_known.tsv \ - --output_dir /root/MOE_DNA/ICLR/generated/known \ - --start_idx 0 \ - --end_idx 1500 - - -export temp=1 -CUDA_VISIBLE_DEVICES=4 python run_evo.py \ - --temperature $temp \ - --data_dir /root/data/cami2/marine_plant_30_known.tsv \ - --output_dir /root/MOE_DNA/ICLR/generated/known \ - --start_idx 1500 \ - --end_idx 3000 - - -export prompt=1000 -export model_size=4B -CUDA_VISIBLE_DEVICES=2 python generate_go.py \ - --num_generation_from_each_prompt 1 \ - --model_size ${model_size} \ - --data_dir /root/data/cami2/marine_plant_30_known.tsv \ - --output_dir /root/MOE_DNA/ICLR/generated/known/${prompt}_${model_size}/ \ - --max_prompt_bp $prompt \ - --max_output_bp 2048 \ - --temperature 1.0 \ - --min_length 600 \ - --max_length 600 \ - --presence_penalty 0.5 \ - --frequency_penalty 0.5 \ - --repetition_penalty 1.0 - - - - - -python display_distribution.py \ - -i ./CODE_NON_CODE/orf_stick/ \ - -o ./CODE_NON_CODE/orf_stick_pdf_new/ \ - -f best_orf_length \ - -s '[["ground truth", [1, 501]], ["genlsm", [501, 1001]], ["we", [1001, 1501]], ["evo", [1501, 2001]]]' - - diff --git a/dnabert/delete.py b/dnabert/delete.py deleted file mode 100644 index f0b89324..00000000 --- a/dnabert/delete.py +++ /dev/null @@ -1,19 +0,0 @@ -import os -import shutil - -def delete_checkpoint_folders(directory): - if not os.path.exists(directory): - print(f"目录 {directory} 不存在！") - return - - for item in os.listdir(directory): - item_path = os.path.join(directory, item) - if os.path.isdir(item_path) and item.startswith("checkpoint"): - print(f"正在删除: {item_path}") - shutil.rmtree(item_path) - - print("删除完成！") - -if __name__ == "__main__": - target_directory = "/projects/p32013/DNABERT-meta/dnabert/output_pipe" - delete_checkpoint_folders(target_directory) diff --git a/dnabert/pipeline.sh b/dnabert/pipeline.sh deleted file mode 100644 index c033edc2..00000000 --- a/dnabert/pipeline.sh +++ /dev/null @@ -1,82 +0,0 @@ -export WANDB_DISABLED=true - -export DATA_CACHE_DIR=".hf_data" -export MODEL_CACHE_DIR=".hf_cache" - -cd /projects/p32013/DNABERT-meta/dnabert - -tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4" "reconstructed" "covid") - -for task in "${tasks[@]}"; do - python train.py \ - --model_name_or_path "zhihan1996/DNABERT-2-117M" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/${task}" \ - --kmer -1 \ - --run_name "dnabert_${task}" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 200 \ - --output_dir "output_pipe/${task}/origin" \ - --save_total_limit 1 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model True - - python train.py \ - --model_name_or_path "zhihan1996/DNABERT-2-117M" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/${task}/invert" \ - --kmer -1 \ - --run_name "dnabert_${task}" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 200 \ - --output_dir "output_pipe/${task}/invert" \ - --save_total_limit 1 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model True - - python train.py \ - --model_name_or_path "zhihan1996/DNABERT-2-117M" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/${task}/noninvert" \ - --kmer -1 \ - --run_name "dnabert_${task}" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 200 \ - --output_dir "output_pipe/${task}/noninvert" \ - --save_total_limit 1 \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model True -done diff --git a/dnabert/run.sh b/dnabert/run.sh deleted file mode 100644 index 5b48b0a6..00000000 --- a/dnabert/run.sh +++ /dev/null @@ -1,36 +0,0 @@ -export WANDB_DISABLED=true - -export DATA_CACHE_DIR=".hf_data" -export MODEL_CACHE_DIR=".hf_cache" - -module load gcc/12.3.0-gcc - -cd /projects/p32013/DNABERT-meta/dnabert - -tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") - -for task in "${tasks[@]}"; do - python train.py \ - --model_name_or_path "zhihan1996/DNABERT-2-117M" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/${task}/all" \ - --kmer -1 \ - --run_name "hyena_dna_${task}" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 200 \ - --output_dir "/scratch/hlv8980/Attack_Benchmark/models/dnabert/${task}/all" \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model False - -done diff --git a/dnabert/self.sh b/dnabert/self.sh deleted file mode 100644 index abb51cbc..00000000 --- a/dnabert/self.sh +++ /dev/null @@ -1,36 +0,0 @@ -export WANDB_DISABLED=true - -export DATA_CACHE_DIR=".hf_data" -export MODEL_CACHE_DIR=".hf_cache" - -module load gcc/12.3.0-gcc - -cd /projects/p32013/DNABERT-meta/dnabert - -tasks=("H3" "H3K14ac" "H3K36me3" "H3K4me1" "H3K4me2" "H3K4me3" "H3K79me3" "H3K9ac" "H4" "H4ac" "prom_core_all" "prom_core_notata" "prom_core_tata" "prom_300_all" "prom_300_notata" "prom_300_tata" "tf0" "tf1" "tf2" "tf3" "tf4" "0" "1" "2" "3" "4") - -for task in "${tasks[@]}"; do - python train.py \ - --model_name_or_path "zhihan1996/DNABERT-2-117M" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/${task}/all" \ - --kmer -1 \ - --run_name "hyena_dna_${task}" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 10000 \ - --output_dir "output_pipe/${task}/self" \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model False - -done diff --git a/dnabert/train.py b/dnabert/train.py deleted file mode 100644 index 1992e17a..00000000 --- a/dnabert/train.py +++ /dev/null @@ -1,342 +0,0 @@ -import os -import csv -import copy -import json -import logging -from dataclasses import dataclass, field -from typing import Optional, Dict, Sequence, Tuple, List - -import torch -import transformers -from transformers.models.bert.configuration_bert import BertConfig -import sklearn -import numpy as np -from torch.utils.data import Dataset - -from peft import ( - LoraConfig, - get_peft_model, - get_peft_model_state_dict, -) - - -@dataclass -class ModelArguments: - model_name_or_path: Optional[str] = field(default="facebook/opt-125m") - use_lora: bool = field(default=False, metadata={"help": "whether to use LoRA"}) - lora_r: int = field(default=16, metadata={"help": "hidden dimension for LoRA"}) - lora_alpha: int = field(default=32, metadata={"help": "alpha for LoRA"}) - lora_dropout: float = field(default=0.05, metadata={"help": "dropout rate for LoRA"}) - lora_target_modules: str = field(default="query,value", metadata={"help": "where to perform LoRA"}) - - -@dataclass -class DataArguments: - data_path: str = field(default=None, metadata={"help": "Path to the training data."}) - kmer: int = field(default=-1, metadata={"help": "k-mer for input sequence. -1 means not using k-mer."}) - - -@dataclass -class TrainingArguments(transformers.TrainingArguments): - cache_dir: Optional[str] = field(default=None) - run_name: str = field(default="run") - optim: str = field(default="adamw_torch") - model_max_length: int = field(default=512, metadata={"help": "Maximum sequence length."}) - gradient_accumulation_steps: int = field(default=1) - per_device_train_batch_size: int = field(default=1) - per_device_eval_batch_size: int = field(default=1) - num_train_epochs: int = field(default=1) - fp16: bool = field(default=False) - logging_steps: int = field(default=100) - save_steps: int = field(default=100) - eval_steps: int = field(default=100) - evaluation_strategy: str = field(default="steps"), - warmup_steps: int = field(default=50) - weight_decay: float = field(default=0.01) - learning_rate: float = field(default=1e-4) - save_total_limit: int = field(default=1) - load_best_model_at_end: bool = field(default=True) - output_dir: str = field(default="output") - find_unused_parameters: bool = field(default=False) - checkpointing: bool = field(default=False) - dataloader_pin_memory: bool = field(default=False) - eval_and_save_results: bool = field(default=True) - save_model: bool = field(default=False) - seed: int = field(default=42) - regression: bool = field(default=False) - - -def safe_save_model_for_hf_trainer(trainer: transformers.Trainer, output_dir: str): - """Collects the state dict and dump to disk.""" - state_dict = trainer.model.state_dict() - if trainer.args.should_save: - cpu_state_dict = {key: value.cpu() for key, value in state_dict.items()} - del state_dict - trainer._save(output_dir, state_dict=cpu_state_dict) # noqa - -def save_model(trainer: transformers.Trainer, output_dir: str): - """Save the model, optimizer state, and other information.""" - if trainer.args.should_save: - # Save the model - trainer.save_model(output_dir) - - # Save the optimizer state (if available) - if trainer.optimizer is not None: - optimizer_state_dict = trainer.optimizer.state_dict() - torch.save(optimizer_state_dict, os.path.join(output_dir, 'optimizer_state_dict.pth')) - - print(f"Model and optimizer state saved to {output_dir}") - - -""" -Get the reversed complement of the original DNA sequence. -""" -def get_alter_of_dna_sequence(sequence: str): - MAP = {"A": "T", "T": "A", "C": "G", "G": "C"} - # return "".join([MAP[c] for c in reversed(sequence)]) - return "".join([MAP[c] for c in sequence]) - -""" -Transform a dna sequence to k-mer string -""" -def generate_kmer_str(sequence: str, k: int) -> str: - """Generate k-mer string from DNA sequence.""" - return " ".join([sequence[i:i+k] for i in range(len(sequence) - k + 1)]) - - -""" -Load or generate k-mer string for each DNA sequence. The generated k-mer string will be saved to the same directory as the original data with the same name but with a suffix of "_{k}mer". -""" -def load_or_generate_kmer(data_path: str, texts: List[str], k: int) -> List[str]: - """Load or generate k-mer string for each DNA sequence.""" - kmer_path = data_path.replace(".csv", f"_{k}mer.json") - if os.path.exists(kmer_path): - logging.warning(f"Loading k-mer from {kmer_path}...") - with open(kmer_path, "r") as f: - kmer = json.load(f) - else: - logging.warning(f"Generating k-mer...") - kmer = [generate_kmer_str(text, k) for text in texts] - with open(kmer_path, "w") as f: - logging.warning(f"Saving k-mer to {kmer_path}...") - json.dump(kmer, f) - - return kmer - -class SupervisedDataset(Dataset): - """Dataset for supervised fine-tuning.""" - - def __init__(self, - data_path: str, - tokenizer: transformers.PreTrainedTokenizer, - kmer: int = -1, - regression: bool = False): - - super(SupervisedDataset, self).__init__() - - # load data from the disk - with open(data_path, "r") as f: - data = list(csv.reader(f))[1:] - if len(data[0]) == 2: - # data is in the format of [text, label] - logging.warning("Perform single sequence classification...") - texts = [d[0] for d in data] - labels = [float(d[1]) for d in data] if regression else [int(d[1]) for d in data] - elif len(data[0]) == 3: - # data is in the format of [text1, text2, label] - logging.warning("Perform sequence-pair classification...") - texts = [[d[0], d[1]] for d in data] - labels = [float(d[2]) for d in data] if regression else [int(d[2]) for d in data] - else: - raise ValueError("Data format not supported.") - - if kmer != -1: - # only write file on the first process - if torch.distributed.get_rank() not in [0, -1]: - torch.distributed.barrier() - - logging.warning(f"Using {kmer}-mer as input...") - texts = load_or_generate_kmer(data_path, texts, kmer) - - if torch.distributed.get_rank() == 0: - torch.distributed.barrier() - - output = tokenizer( - texts, - return_tensors="pt", - padding="longest", - max_length=tokenizer.model_max_length, - truncation=True, - # pad_to_multiple_of=512, - ) - - self.input_ids = torch.clip(output["input_ids"], max=4104) #if "InstaDeepAI" in tokenizer.name_or_path else output["input_ids"] - # print(torch.max(self.input_ids)) - # print(len(tokenizer)) - self.attention_mask = self.input_ids.ne(tokenizer.pad_token_id) - self.labels = labels - self.num_labels = len(set(labels)) if not regression else 1 - - def __len__(self): - return len(self.input_ids) - - def __getitem__(self, i) -> Dict[str, torch.Tensor]: - return dict(input_ids=self.input_ids[i], labels=self.labels[i]) - - -@dataclass -class DataCollatorForSupervisedDataset(object): - """Collate examples for supervised fine-tuning.""" - - def __init__(self, tokenizer: transformers.PreTrainedTokenizer, apply_attention_mask: bool = True, regression: bool = False): - self.tokenizer = tokenizer - self.apply_attention_mask = apply_attention_mask - self.regression = regression - - def __call__(self, instances: Sequence[Dict]) -> Dict[str, torch.Tensor]: - input_ids, labels = tuple([instance[key] for instance in instances] for key in ("input_ids", "labels")) - input_ids = torch.nn.utils.rnn.pad_sequence( - input_ids, batch_first=True, padding_value=self.tokenizer.pad_token_id - ) - labels = torch.Tensor(labels).long() if not self.regression else torch.Tensor(labels).float() - return dict( - input_ids=input_ids, - labels=labels, - attention_mask=input_ids.ne(self.tokenizer.pad_token_id), - ) if self.apply_attention_mask else dict(input_ids=input_ids, labels=labels) - -""" -Manually calculate the accuracy, f1, matthews_correlation, precision, recall with sklearn. -""" -def calculate_metric_with_sklearn(logits: np.ndarray, labels: np.ndarray): - if logits.ndim == 3: - # Reshape logits to 2D if needed - logits = logits.reshape(-1, logits.shape[-1]) - predictions = np.argmax(logits, axis=-1) - valid_mask = labels != -100 # Exclude padding tokens (assuming -100 is the padding token ID) - valid_predictions = predictions[valid_mask] - valid_labels = labels[valid_mask] - return { - "accuracy": sklearn.metrics.accuracy_score(valid_labels, valid_predictions), - "f1": sklearn.metrics.f1_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - "matthews_correlation": sklearn.metrics.matthews_corrcoef( - valid_labels, valid_predictions - ), - "precision": sklearn.metrics.precision_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - "recall": sklearn.metrics.recall_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - } - - -""" -Compute metrics used for huggingface trainer. -""" -def compute_metrics_classification(eval_pred): - logits, labels = eval_pred - if isinstance(logits, tuple): # Unpack logits if it's a tuple - logits = logits[0] - return calculate_metric_with_sklearn(logits, labels) - -def compute_metrics_regression(eval_pred): - logits, labels = eval_pred - if isinstance(logits, tuple): # Unpack logits if it's a tuple - logits = logits[0] - return { - "mse": sklearn.metrics.mean_squared_error(labels, logits), - "mae": sklearn.metrics.mean_absolute_error(labels, logits), - } - - -def train(): - parser = transformers.HfArgumentParser((ModelArguments, DataArguments, TrainingArguments)) - model_args, data_args, training_args = parser.parse_args_into_dataclasses() - - # load tokenizer - tokenizer = transformers.AutoTokenizer.from_pretrained( - model_args.model_name_or_path, - cache_dir=training_args.cache_dir, - model_max_length=training_args.model_max_length, - padding_side="right", - use_fast=True, - trust_remote_code=True, - ) - - if "InstaDeepAI" in model_args.model_name_or_path: - tokenizer.eos_token = tokenizer.pad_token - - # define datasets and data collator - train_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "train.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - val_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "dev.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - test_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "test.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - apply_attention_mask = ("hyena" not in model_args.model_name_or_path) and ("caduceus" not in model_args.model_name_or_path) - data_collator = DataCollatorForSupervisedDataset(tokenizer=tokenizer, apply_attention_mask=apply_attention_mask, regression=training_args.regression) - - - # load model - config = BertConfig.from_pretrained(model_args.model_name_or_path, num_labels=train_dataset.num_labels, trust_remote_code=True) - model = transformers.AutoModelForSequenceClassification.from_pretrained( - model_args.model_name_or_path, - config=config, - cache_dir=training_args.cache_dir, - trust_remote_code=True, - ) - - # configure LoRA - if model_args.use_lora: - lora_config = LoraConfig( - r=model_args.lora_r, - lora_alpha=model_args.lora_alpha, - target_modules=list(model_args.lora_target_modules.split(",")), - lora_dropout=model_args.lora_dropout, - bias="none", - task_type="SEQ_CLS", - inference_mode=False, - ) - model = get_peft_model(model, lora_config) - model.print_trainable_parameters() - - # define trainer - trainer = transformers.Trainer( - model=model, - tokenizer=tokenizer, - args=training_args, - compute_metrics=compute_metrics_regression if training_args.regression else compute_metrics_classification, - train_dataset=train_dataset, - eval_dataset=val_dataset, - data_collator=data_collator - ) - trainer.train() - - if training_args.save_model: - trainer.save_state() - # safe_save_model_for_hf_trainer(trainer=trainer, output_dir=training_args.output_dir) - save_model(trainer=trainer, output_dir=training_args.output_dir) - - # get the evaluation results from trainer - if training_args.eval_and_save_results: - results_path = os.path.join(training_args.output_dir, "results", str(training_args.seed)) - results = trainer.evaluate(eval_dataset=test_dataset) - print(results) - os.makedirs(results_path, exist_ok=True) - with open(os.path.join(results_path, "eval_results.json"), "w") as f: - json.dump(results, f) - - - - -if __name__ == "__main__": - train() diff --git a/fimba-attack/.hf_cache/.locks/models--zhihan1996--DNABERT-2-117M/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec.lock b/fimba-attack/.hf_cache/.locks/models--zhihan1996--DNABERT-2-117M/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec.lock deleted file mode 100644 index e69de29b..00000000 diff --git a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/blobs/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec b/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/blobs/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec deleted file mode 100644 index b27bed3d..00000000 --- a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/blobs/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2022 MosaicML Examples authors -# SPDX-License-Identifier: Apache-2.0 - -from transformers.configuration_utils import PretrainedConfig - - -class BertConfig(PretrainedConfig): - - def __init__( - self, - alibi_starting_size: int = 512, - attention_probs_dropout_prob: float = 0.0, - **kwargs, - ): - """Configuration class for MosaicBert. - - Args: - alibi_starting_size (int): Use `alibi_starting_size` to determine how large of an alibi tensor to - create when initializing the model. You should be able to ignore this parameter in most cases. - Defaults to 512. - attention_probs_dropout_prob (float): By default, turn off attention dropout in Mosaic BERT - (otherwise, Flash Attention will be off by default). Defaults to 0.0. - """ - super().__init__( - attention_probs_dropout_prob=attention_probs_dropout_prob, **kwargs) - self.alibi_starting_size = alibi_starting_size diff --git a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/refs/main b/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/refs/main deleted file mode 100644 index e48ab4d5..00000000 --- a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/refs/main +++ /dev/null @@ -1 +0,0 @@ -d064dece8a8b41d9fb8729fbe3435278786931f1 \ No newline at end of file diff --git a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/snapshots/d064dece8a8b41d9fb8729fbe3435278786931f1/configuration_bert.py b/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/snapshots/d064dece8a8b41d9fb8729fbe3435278786931f1/configuration_bert.py deleted file mode 120000 index 3f4b0ff7..00000000 --- a/fimba-attack/.hf_cache/models--zhihan1996--DNABERT-2-117M/snapshots/d064dece8a8b41d9fb8729fbe3435278786931f1/configuration_bert.py +++ /dev/null @@ -1 +0,0 @@ -../../blobs/b27bed3d8ae09cd13fe64f8805bc2aef24e1ffec \ No newline at end of file diff --git a/fimba-attack/run.sh b/fimba-attack/run.sh index c9b21aef..5f890a56 100644 --- a/fimba-attack/run.sh +++ b/fimba-attack/run.sh @@ -9,8 +9,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 \ --max_seq_length 128 --batch_size 1 \ --dataset_name $task --model_type ${model} \ @@ -18,12 +18,12 @@ do --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 64 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done @@ -40,8 +40,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 \ --max_seq_length 128 --batch_size 1 \ --dataset_name $task --model_type ${model} \ @@ -49,12 +49,12 @@ do --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 64 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done @@ -71,8 +71,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 \ --max_seq_length 128 --batch_size 1 \ --dataset_name $task --model_type ${model} \ @@ -80,12 +80,12 @@ do --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 64 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/fimba-attack/run_dnabert.sh b/fimba-attack/run_dnabert.sh index c1514295..e47c375f 100644 --- a/fimba-attack/run_dnabert.sh +++ b/fimba-attack/run_dnabert.sh @@ -9,8 +9,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" # python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - # --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - # --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + # --data_dir GUE/${task}/fimba \ + # --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ # --task_name $task --num_label 2 \ # --max_seq_length 128 --batch_size 1 \ # --dataset_name $task --model_type ${model} \ @@ -18,12 +18,12 @@ do # --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 32 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/fimba-attack/run_hyena.sh b/fimba-attack/run_hyena.sh index abbb65c3..72de2910 100644 --- a/fimba-attack/run_hyena.sh +++ b/fimba-attack/run_hyena.sh @@ -9,8 +9,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 \ --max_seq_length 128 --batch_size 1 \ --dataset_name $task --model_type ${model} \ @@ -18,12 +18,12 @@ do --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 64 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/fimba-attack/run_nt1.sh b/fimba-attack/run_nt1.sh index aee26d15..43653259 100644 --- a/fimba-attack/run_nt1.sh +++ b/fimba-attack/run_nt1.sh @@ -10,8 +10,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" # python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - # --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - # --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + # --data_dir GUE/${task}/fimba \ + # --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ # --task_name $task --num_label 2 \ # --max_seq_length 128 --batch_size 1 \ # --dataset_name $task --model_type ${model} \ @@ -19,12 +19,12 @@ do # --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 8 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/fimba-attack/run_nt2.sh b/fimba-attack/run_nt2.sh index 3a5f3d4c..728004ab 100644 --- a/fimba-attack/run_nt2.sh +++ b/fimba-attack/run_nt2.sh @@ -9,8 +9,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" # python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - # --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - # --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + # --data_dir GUE/${task}/fimba \ + # --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ # --task_name $task --num_label 2 \ # --max_seq_length 128 --batch_size 1 \ # --dataset_name $task --model_type ${model} \ @@ -18,12 +18,12 @@ do # --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 32 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/fimba-attack/run_og.sh b/fimba-attack/run_og.sh index 9f9b88e9..6b2f1ec3 100644 --- a/fimba-attack/run_og.sh +++ b/fimba-attack/run_og.sh @@ -9,8 +9,8 @@ for task in "${tasks[@]}" do echo "Running task: $task" # python "${SCRIPT_DIR}/shap_dl_analysis2.py" \ - # --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - # --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + # --data_dir GUE/${task}/fimba \ + # --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ # --task_name $task --num_label 2 \ # --max_seq_length 128 --batch_size 1 \ # --dataset_name $task --model_type ${model} \ @@ -18,12 +18,12 @@ do # --shap_output_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" python "${SCRIPT_DIR}/runatk_standalone.py" \ - --data_dir /projects/p32013/DNABERT-meta/GUE/${task}/fimba \ - --model_name_or_path /scratch/hlv8980/Attack_Benchmark/models/${model}/${task}/origin \ + --data_dir GUE/${task}/fimba \ + --model_name_or_path /scratch/anonymous/Attack_Benchmark/models/${model}/${task}/origin \ --task_name $task --num_label 2 --max_seq_length 128 \ --shap_file "${SCRIPT_DIR}/shap_dicts/shap_${model}_fimba_$task.pkl" \ --increase_fn --batch_size 32 --model_type ${model} \ - --output_dir /projects/p32013/DNABERT-meta/fimba-attack/results/${model} \ + --output_dir fimba-attack/results/${model} \ --overwrite_cache --overwrite_output_dir done diff --git a/metadata/PGD_origin.py b/metadata/PGD_origin.py index 627d34a3..21eeee99 100644 --- a/metadata/PGD_origin.py +++ b/metadata/PGD_origin.py @@ -5,8 +5,8 @@ import shutil # 源文件和目标文件路径 -src_path = '/projects/p32013/DNABERT-meta/metadata/BERTAttack/og.json' -dst_path = '/projects/p32013/DNABERT-meta/metadata/FREELB/og-PGD.json' +src_path = 'metadata/BERTAttack/og.json' +dst_path = 'metadata/FREELB/og-PGD.json' # 先备份目标文件 shutil.copyfile(dst_path, dst_path + '.bak') diff --git a/metadata/avg_query.py b/metadata/avg_query.py index 77ee2f1c..39d44de3 100644 --- a/metadata/avg_query.py +++ b/metadata/avg_query.py @@ -30,8 +30,8 @@ def compute_average_query(json_path): def main(): # 根据实际情况修改这两行路径 - results_dir = '/projects/p32013/DNABERT-meta/BERT-Attack/results/hyena' - meta_file = '/projects/p32013/DNABERT-meta/metadata/BERTAttack/hyena.json' + results_dir = 'BERT-Attack/results/hyena' + meta_file = 'metadata/BERTAttack/hyena.json' if not os.path.isdir(results_dir): print(f'ERROR: 目录不存在 {results_dir}', file=sys.stderr) diff --git a/metadata/avg_query_defense.py b/metadata/avg_query_defense.py index f70319af..dc67bb0d 100644 --- a/metadata/avg_query_defense.py +++ b/metadata/avg_query_defense.py @@ -30,8 +30,8 @@ def compute_average_query(json_path): def main(): # 请根据实际情况修改这两行路径 - results_dir = '/projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena' - meta_file = '/projects/p32013/DNABERT-meta/metadata/FREELB/hyena-BERTAttack.json' + results_dir = 'BERT-Attack/results/freelb/hyena' + meta_file = 'metadata/FREELB/hyena-BERTAttack.json' if not os.path.isdir(results_dir): print(f'ERROR: 目录不存在 {results_dir}', file=sys.stderr) diff --git a/metadata/change_value.py b/metadata/change_value.py index a5dc430b..383d67e0 100644 --- a/metadata/change_value.py +++ b/metadata/change_value.py @@ -30,7 +30,7 @@ def update_file(path): print(f'已更新：{os.path.basename(path)}') def main(): - folder = "/projects/p32013/DNABERT-meta/metadata/AT" + folder = "metadata/AT" for name in os.listdir(folder): if name.lower().endswith('.json'): update_file(os.path.join(folder, name)) diff --git a/metadata/generate.py b/metadata/generate.py index b4382a12..28856e29 100644 --- a/metadata/generate.py +++ b/metadata/generate.py @@ -31,8 +31,8 @@ def normalize(name): return re.sub(r"[_\-]", "", name).lower() def main(): - base_dir = "/projects/p32013/DNABERT-meta/TextFooler/output/FreeLB/og" - json_file = "/projects/p32013/DNABERT-meta/metadata/FREELB/og-TextFooler.json" + base_dir = "TextFooler/output/FreeLB/og" + json_file = "metadata/FREELB/og-TextFooler.json" if not os.path.isdir(base_dir): print(f"ERROR: 找不到目录 {base_dir}", file=sys.stderr) diff --git a/metadata/generate1.py b/metadata/generate1.py index 3f73d213..9cec5b1b 100644 --- a/metadata/generate1.py +++ b/metadata/generate1.py @@ -21,8 +21,8 @@ def normalize(name): return re.sub(r"[_\-]", "", name).lower() def main(): - results_dir = "/projects/p32013/DNABERT-meta/PGD/results/FreeLB/dnabert" - json_file = "/projects/p32013/DNABERT-meta/metadata/FREELB/DNABERT2-PGD.json" + results_dir = "PGD/results/FreeLB/dnabert" + json_file = "metadata/FREELB/DNABERT2-PGD.json" # 1) 收集所有 final accuracy parsed = {} diff --git a/metadata/generate2.py b/metadata/generate2.py index 673a6919..94968f00 100644 --- a/metadata/generate2.py +++ b/metadata/generate2.py @@ -99,5 +99,5 @@ def update_orign_acc_from_baseline(json_file: str, baseline_str: str): tf4 0.485172 """ -json_path = "/projects/p32013/DNABERT-meta/metadata/PGD/og.json" +json_path = "metadata/PGD/og.json" update_orign_acc_from_baseline(json_path, baseline_data) diff --git a/metadata/generate3.py b/metadata/generate3.py index e94772e2..954aeae8 100644 --- a/metadata/generate3.py +++ b/metadata/generate3.py @@ -23,8 +23,8 @@ def parse_all_results(path: str): return m1["accuracy"], m2["accuracy"] def main(): - results_dir = "/projects/p32013/DNABERT-meta/fimba-attack/results/og" - meta_json = "/projects/p32013/DNABERT-meta/metadata/FIMBA/og.json" + results_dir = "fimba-attack/results/og" + meta_json = "metadata/FIMBA/og.json" # 1) 收集所有子文件夹的指标 parsed = {} diff --git a/metadata/generate_bertattack.py b/metadata/generate_bertattack.py index b254855a..42f1cb1e 100644 --- a/metadata/generate_bertattack.py +++ b/metadata/generate_bertattack.py @@ -72,6 +72,6 @@ def update_bertattack_from_csv(json_path: str, csv_path: str): print(f"✔ 已写入 {json_path}") # 调用示例 -json_file = "/projects/p32013/DNABERT-meta/metadata/FREELB/hyena-BERTAttack.json" -csv_file = "/projects/p32013/DNABERT-meta/BERT-Attack/results/freelb/hyena/attack_results.csv" +json_file = "metadata/FREELB/hyena-BERTAttack.json" +csv_file = "BERT-Attack/results/freelb/hyena/attack_results.csv" update_bertattack_from_csv(json_file, csv_file) diff --git a/metadata/rename.py b/metadata/rename.py index f7a62fb7..9ba8cf3e 100644 --- a/metadata/rename.py +++ b/metadata/rename.py @@ -28,7 +28,7 @@ def update_json_file(path): print(f"Updated {os.path.basename(path)}") def main(): - folder = "/projects/p32013/DNABERT-meta/metadata/AT" + folder = "metadata/AT" for filename in os.listdir(folder): if filename.lower().endswith(".json"): fullpath = os.path.join(folder, filename) diff --git a/run.py b/run.py index bbd012b7..8f8395c6 100644 --- a/run.py +++ b/run.py @@ -3,10 +3,10 @@ # You need to initialize GenoArmory with a model and tokenizer. # For visualization, you don't need a real model/tokenizer, so you can use None if the method doesn't use them. gen = GenoArmory(model=None, tokenizer=None) -params_file = '/projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json' +params_file = 'scripts/PGD/pgd_dnabert.json' # gen.visualization( -# folder_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test', -# output_pdf_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test' +# folder_path='BERT-Attack/results/meta/test', +# output_pdf_path='BERT-Attack/results/meta/test' # ) @@ -21,6 +21,6 @@ gen.attack( attack_method='pgd', - model_path='magicslabnu/GERM', + model_path='anonymous_model', **kwargs ) \ No newline at end of file diff --git a/run.sh b/run.sh index a9942f2b..dc739616 100644 --- a/run.sh +++ b/run.sh @@ -1,21 +1,19 @@ -cd /projects/p32013/DNABERT-meta - ## Visualization -# python GenoArmory.py --model_path magicslabnu/GERM visualize --folder_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test --save_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test/frequency.pdf +# python GenoArmory.py --model_path anonymous_model visualize --folder_path BERT-Attack/results/meta/test --save_path BERT-Attack/results/meta/test/frequency.pdf ## Attack -# python GenoArmory.py --model_path magicslabnu/GERM attack --method pgd --params_file /projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json -# python GenoArmory.py --model_path magicslabnu/GERM attack --method fimba --params_file /projects/p32013/DNABERT-meta/scripts/FIMBA/fimba_dnabert.json -# python GenoArmory.py --model_path magicslabnu/GERM attack --method textfooler --params_file /projects/p32013/DNABERT-meta/scripts/TextFooler/textfooler_dnabert.json -# python GenoArmory.py --model_path magicslabnu/GERM attack --method bertattack --params_file /projects/p32013/DNABERT-meta/scripts/BertAttack/bertattack_dnabert.json +# python GenoArmory.py --model_path anonymous_model attack --method pgd --params_file scripts/PGD/pgd_dnabert.json +# python GenoArmory.py --model_path anonymous_model attack --method fimba --params_file scripts/FIMBA/fimba_dnabert.json +# python GenoArmory.py --model_path anonymous_model attack --method textfooler --params_file scripts/TextFooler/textfooler_dnabert.json +# python GenoArmory.py --model_path anonymous_model attack --method bertattack --params_file scripts/BertAttack/bertattack_dnabert.json ## Defense -python GenoArmory.py --model_path magicslabnu/GERM defense --method freelb --params_file /projects/p32013/DNABERT-meta/scripts/FreeLB/freelb_pgd_dnabert.json -# python GenoArmory.py --model_path magicslabnu/GERM defense --method adfar --params_file /projects/p32013/DNABERT-meta/scripts/ADFAR/adfar_pgd_dnabert.json -# python GenoArmory.py --model_path magicslabnu/GERM defense --method at --params_file /projects/p32013/DNABERT-meta/scripts/AT/at_pgd_dnabert.json +python GenoArmory.py --model_path anonymous_model defense --method freelb --params_file scripts/FreeLB/freelb_pgd_dnabert.json +# python GenoArmory.py --model_path anonymous_model defense --method adfar --params_file scripts/ADFAR/adfar_pgd_dnabert.json +# python GenoArmory.py --model_path anonymous_model defense --method at --params_file scripts/AT/at_pgd_dnabert.json ## Read Metadata -# python GenoArmory.py --model_path magicslabnu/GERM read --type attack --method TextFooler --model_name dnabert -# python GenoArmory.py --model_path magicslabnu/GERM read --type defense --method ADFAR --model_name dnabert --attack_method textfooler +# python GenoArmory.py --model_path anonymous_model read --type attack --method TextFooler --model_name dnabert +# python GenoArmory.py --model_path anonymous_model read --type defense --method ADFAR --model_name dnabert --attack_method textfooler diff --git a/scripts/ADFAR/adfar_pgd_dnabert.json b/scripts/ADFAR/adfar_pgd_dnabert.json index 6240e2aa..83004fe3 100644 --- a/scripts/ADFAR/adfar_pgd_dnabert.json +++ b/scripts/ADFAR/adfar_pgd_dnabert.json @@ -18,7 +18,7 @@ "num_train_epochs": 5, "learning_rate": 3e-5, "attack_methods": "pgd", - "target_model_path": "magicslabnu/DNABERT-2-finetuned-H3", + "target_model_path": "anonymous/DNABERT-2-finetuned-H3", "tokenizer_path": "zhihan1996/DNABERT-2-117M", "output_base_dir": "test/PGD", "task_name": "0", diff --git a/scripts/BertAttack/bertattack_dnabert.json b/scripts/BertAttack/bertattack_dnabert.json index f29bfb7e..a9067bd4 100644 --- a/scripts/BertAttack/bertattack_dnabert.json +++ b/scripts/BertAttack/bertattack_dnabert.json @@ -1,7 +1,7 @@ { "model": "dnabert", "data_path": "GUE/H3/cat.csv", - "tgt_path": "magicslabnu/DNABERT-2-finetuned-H3", + "tgt_path": "anonymous/DNABERT-2-finetuned-H3", "mlm_path": "zhihan1996/DNABERT-2-117M", "output_dir": "test/BertAttack/H3", "num_label": 2, diff --git a/scripts/FIMBA/fimba_dnabert.json b/scripts/FIMBA/fimba_dnabert.json index 77463cc0..a5df34ab 100644 --- a/scripts/FIMBA/fimba_dnabert.json +++ b/scripts/FIMBA/fimba_dnabert.json @@ -3,7 +3,7 @@ "H3" ], "model": "dnabert", - "target_model_path": "magicslabnu/DNABERT-2-finetuned-H3", + "target_model_path": "anonymous/DNABERT-2-finetuned-H3", "tokenizer_path": "zhihan1996/DNABERT-2-117M", "output_dir_base": "test/FIMBA", "targert_model": "bert", diff --git a/scripts/FreeLB/freelb_pgd_dnabert.json b/scripts/FreeLB/freelb_pgd_dnabert.json index 34d7a911..2e94eb8b 100644 --- a/scripts/FreeLB/freelb_pgd_dnabert.json +++ b/scripts/FreeLB/freelb_pgd_dnabert.json @@ -6,7 +6,7 @@ "attack_methods": "pgd", "attack_model_type": "dnabert", "base_dir": "GUE", - "target_model_path": "magicslabnu/DNABERT-2-finetuned-H3", + "target_model_path": "anonymous/DNABERT-2-finetuned-H3", "tokenizer_path": "zhihan1996/DNABERT-2-117M", "output_dir_base": "test/FreeLB", "attack_script_path": "PGD/pgd.py", diff --git a/scripts/PGD/pgd_dnabert.json b/scripts/PGD/pgd_dnabert.json index 613c6854..68ab8504 100644 --- a/scripts/PGD/pgd_dnabert.json +++ b/scripts/PGD/pgd_dnabert.json @@ -4,7 +4,7 @@ ], "model": "dnabert", "data_base_dir": "GUE", - "model_base_dir": "magicslabnu/DNABERT-2-finetuned-H3", + "model_base_dir": "anonymous/DNABERT-2-finetuned-H3", "output_base_dir": "test/PGD", "tokenizer_base_dir": "zhihan1996/DNABERT-2-117M", "model_type": "bert", diff --git a/scripts/PGD/pgd_genomeocean.json b/scripts/PGD/pgd_genomeocean.json index f9657a10..ec45f8b6 100644 --- a/scripts/PGD/pgd_genomeocean.json +++ b/scripts/PGD/pgd_genomeocean.json @@ -4,7 +4,7 @@ ], "model": "GenomeOcean", "data_base_dir": "GUE", - "model_base_dir": "magicslabnu/GenomeOcean-100M-finetuned-H3", + "model_base_dir": "anonymous/GenomeOcean-100M-finetuned-H3", "output_base_dir": "test/PGD", "tokenizer_base_dir": "pGenomeOcean/GenomeOcean-100M", "model_type": "og", diff --git a/scripts/PGD/pgd_hyena.json b/scripts/PGD/pgd_hyena.json index 984053ce..f14d5c93 100644 --- a/scripts/PGD/pgd_hyena.json +++ b/scripts/PGD/pgd_hyena.json @@ -4,7 +4,7 @@ ], "model": "HyenaDNA", "data_base_dir": "GUE", - "model_base_dir": "magicslabnu/Hyena-small-32k_seqlen-finetuned-H3", + "model_base_dir": "anonymous/Hyena-small-32k_seqlen-finetuned-H3", "output_base_dir": "test/PGD", "tokenizer_base_dir": "LongSafari/hyenadna-small-32k-seqlen-hf", "model_type": "hyena", diff --git a/scripts/PGD/pgd_nt1.json b/scripts/PGD/pgd_nt1.json index 8134fe7b..8df38819 100644 --- a/scripts/PGD/pgd_nt1.json +++ b/scripts/PGD/pgd_nt1.json @@ -4,7 +4,7 @@ ], "model": "NT1", "data_base_dir": "GUE", - "model_base_dir": "magicslabnu/NT1-500M-human_ref-finetuned-H3", + "model_base_dir": "anonymous/NT1-500M-human_ref-finetuned-H3", "output_base_dir": "test/PGD", "tokenizer_base_dir": "InstaDeepAI/nucleotide-transformer-500m-human-ref", "model_type": "nt1", diff --git a/scripts/PGD/pgd_nt2.json b/scripts/PGD/pgd_nt2.json index fc62747c..beaf059c 100644 --- a/scripts/PGD/pgd_nt2.json +++ b/scripts/PGD/pgd_nt2.json @@ -4,7 +4,7 @@ ], "model": "NT2", "data_base_dir": "GUE", - "model_base_dir": "magicslabnu/NT2-500M-multi_species-finetuned-H3", + "model_base_dir": "anonymous/NT2-500M-multi_species-finetuned-H3", "output_base_dir": "test/PGD", "tokenizer_base_dir": "InstaDeepAI/nucleotide-transformer-v2-500m-multi-species", "model_type": "nt2", diff --git a/scripts/TextFooler/textfooler_dnabert.json b/scripts/TextFooler/textfooler_dnabert.json index b006b2f2..8f0121c0 100644 --- a/scripts/TextFooler/textfooler_dnabert.json +++ b/scripts/TextFooler/textfooler_dnabert.json @@ -4,7 +4,7 @@ ], "model": "bert", "base_dir": "GUE", - "target_model_path": "magicslabnu/DNABERT-2-finetuned-H3", + "target_model_path": "anonymous/DNABERT-2-finetuned-H3", "tokenizer_path": "zhihan1996/DNABERT-2-117M", "output_dir_base": "test/TextFooler", "targert_model": "bert", diff --git a/setup.py b/setup.py index 37b2f1c0..36dd8a27 100644 --- a/setup.py +++ b/setup.py @@ -6,12 +6,9 @@ setup( name="genoarmory", version="0.1.0", - author="Robin Luo & Jerry Qiu", - author_email="robinluo2027@u.northwestern.edu", description="A DNA sequence Adversial attack and defense benchmark", long_description=long_description, long_description_content_type="text/markdown", - url="https://github.com/MAGICS-LAB/DNAAttack", packages=find_packages(), classifiers=[ "Development Status :: 3 - Alpha", diff --git a/test/AT/H3/checkpoint-752/config.json b/test/AT/H3/checkpoint-752/config.json deleted file mode 100644 index fbb193fd..00000000 --- a/test/AT/H3/checkpoint-752/config.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "alibi_starting_size": 512, - "architectures": [ - "BertForSequenceClassification" - ], - "attention_probs_dropout_prob": 0.0, - "auto_map": { - "AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig", - "AutoModel": "zhihan1996/DNABERT-2-117M--bert_layers.BertModel", - "AutoModelForMaskedLM": "zhihan1996/DNABERT-2-117M--bert_layers.BertForMaskedLM", - "AutoModelForSequenceClassification": "zhihan1996/DNABERT-2-117M--bert_layers.BertForSequenceClassification" - }, - "classifier_dropout": null, - "gradient_checkpointing": false, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 512, - "model_type": "bert", - "num_attention_heads": 12, - "num_hidden_layers": 12, - "pad_token_id": 0, - "position_embedding_type": "absolute", - "problem_type": "single_label_classification", - "torch_dtype": "float32", - "transformers_version": "4.51.3", - "type_vocab_size": 2, - "use_cache": true, - "vocab_size": 4096 -} diff --git a/test/AT/H3/checkpoint-752/special_tokens_map.json b/test/AT/H3/checkpoint-752/special_tokens_map.json deleted file mode 100644 index 9bbecc17..00000000 --- a/test/AT/H3/checkpoint-752/special_tokens_map.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "cls_token": { - "content": "[CLS]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "[PAD]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "[SEP]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "[UNK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false - } -} diff --git a/test/AT/H3/checkpoint-752/tokenizer.json b/test/AT/H3/checkpoint-752/tokenizer.json deleted file mode 100644 index 24a1fa3f..00000000 --- a/test/AT/H3/checkpoint-752/tokenizer.json +++ /dev/null @@ -1,20602 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 256, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": "BatchLongest", - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "[PAD]" - }, - "added_tokens": [ - { - "id": 0, - "content": "[UNK]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 1, - "content": "[CLS]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 2, - "content": "[SEP]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 3, - "content": "[PAD]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - }, - { - "id": 4, - "content": "[MASK]", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": false, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "Whitespace" - }, - "post_processor": { - "type": "TemplateProcessing", - "single": [ - { - "SpecialToken": { - "id": "[CLS]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "A", - "type_id": 0 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 0 - } - } - ], - "pair": [ - { - "SpecialToken": { - "id": "[CLS]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "A", - "type_id": 0 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 0 - } - }, - { - "Sequence": { - "id": "B", - "type_id": 1 - } - }, - { - "SpecialToken": { - "id": "[SEP]", - "type_id": 1 - } - } - ], - "special_tokens": { - "[CLS]": { - "id": "[CLS]", - "ids": [ - 1 - ], - "tokens": [ - "[CLS]" - ] - }, - "[SEP]": { - "id": "[SEP]", - "ids": [ - 2 - ], - "tokens": [ - "[SEP]" - ] - } - } - }, - "decoder": null, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": "[UNK]", - "continuing_subword_prefix": null, - "end_of_word_suffix": null, - "fuse_unk": false, - "byte_fallback": false, - "ignore_merges": false, - "vocab": { - 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"GCTG", - "CTA" - ], - [ - "TTA", - "GTAA" - ], - [ - "TAAA", - "CATG" - ], - [ - "GTCA", - "CCA" - ], - [ - "CA", - "TCTTTT" - ], - [ - "CATA", - "TAA" - ], - [ - "TCTC", - "TCTA" - ], - [ - "TTTTA", - "TTAA" - ], - [ - "TATT", - "CTAA" - ], - [ - "GAAA", - "TTTA" - ], - [ - "CTT", - "CCCTG" - ], - [ - "TAAA", - "GATG" - ], - [ - "TA", - "CGTA" - ], - [ - "GTT", - "TATTA" - ], - [ - "GAAAA", - "GAA" - ], - [ - "CCCA", - "CCCA" - ], - [ - "CAATT", - "AAAA" - ], - [ - "CC", - "GACA" - ], - [ - "CAAA", - "GTGA" - ], - [ - "CAAA", - "CAAAA" - ], - [ - "GCAA", - "TTTT" - ], - [ - "CGATT", - "AA" - ], - [ - "TTA", - "GAGA" - ], - [ - "CTGA", - "TGA" - ], - [ - "GGA", - "GGAGG" - ], - [ - "GTCC", - "TGGG" - ], - [ - "TCA", - "TGAAA" - ], - [ - "GCAA", - "CCA" - ], - [ - "GTT", - "GGCA" - ], - [ - "GCGG", - "CGG" - ], - [ - "GTCC", - "CCA" - ], - [ - "GTA", - "GGGG" - ], - [ - "GCCA", - "TGTT" - ], - [ - "GTT", - "CGAGA" - ], - [ - "GCC", - "TATA" - ], - [ - "TAAA", - "TTCA" - ], - [ - "GG", - "CCATT" - ], - [ - "GAAAA", - "CAA" - ], - [ - "TGTG", - "TATG" - ], - [ - "GTA", - "CTC" - ], - [ - "TAGG", - "GAA" - ], - [ - "CCTT", - "GAA" - ], - [ - "TC", - "TATTTG" - ], - [ - "GAGG", - "GCA" - ], - [ - "GAAA", - "CTGA" - ], - [ - "TA", - "CGC" - ], - [ - "TA", - "CAAAAA" - ], - [ - "TCA", - "TTATT" - ], - [ - "GGAAAA", - "TT" - ], - [ - "TCAA", - "TATT" - ], - [ - "CC", - "CGTA" - ], - [ - "GGA", - "GAGAA" - ], - [ - "TTA", - "GTTA" - ], - [ - "CTCA", - "GAGA" - ], - [ - "TC", - "GAGC" - ], - [ - "CTA", - "GTCA" - ], - [ - "GATG", - "GCA" - ], - [ - "TGAA", - "CATT" - ], - [ - "CTA", - "TGGG" - ], - [ - "CACA", - "CCA" - ], - [ - "TCAA", - "TTAA" - ], - [ - "GGAA", - "CTG" - ], - [ - "TTA", - "CATG" - ], - [ - "CTT", - "TCATT" - ], - [ - "CAGC", - "TCTG" - ], - [ - "TCTTTT", - "TTTT" - ], - [ - "TAAA", - "TCTT" - ], - [ - "TGA", - "TCTA" - ], - [ - "CATA", - "CAA" - ], - [ - "GC", - "TCAAAA" - ], - [ - "GC", - "TGTGTG" - ], - [ - "TCAA", - "TCA" - ], - [ - "GATT", - "TGAA" - ], - [ - "CCAA", - "GGA" - ], - [ - "GTCC", - "TCA" - ], - [ - "GTG", - "CTCC" - ], - [ - "AAAA", - "TAA" - ], - [ - "GTGA", - "CAA" - ], - [ - "GCTCA", - "CGCCTG" - ], - [ - "CGA", - "CGG" - ], - [ - "TA", - "TCCAA" - ], - [ - "CACA", - "CATG" - ], - [ - "TCTC", - "TCTCC" - ], - [ - "TGTG", - "GTT" - ], - [ - "CTT", - "GGTA" - ], - [ - "TCTG", - "GTT" - ], - [ - "TTTA", - "TAA" - ], - [ - "CTG", - "CTTTT" - ], - [ - "TGTG", - "TCA" - ], - [ - "CACA", - "TCA" - ], - [ - "CC", - "TAATG" - ], - [ - "C", - "GTTTTTT" - ], - [ - "GCTG", - "GCA" - ], - [ - "GA", - "CGTC" - ], - [ - "TATAA", - "TTA" - ], - [ - "TACA", - "GTAA" - ], - [ - "GAAA", - "GTAA" - ], - [ - "GTC", - "TGAAA" - ], - [ - "CCCA", - "TTTT" - ], - [ - "TATA", - "TGA" - ], - [ - "CTT", - "GATA" - ], - [ - "CTT", - "TATTTT" - ], - [ - "CTT", - "TATTA" - ], - [ - "GG", - "CGAA" - ], - [ - "CCA", - "TGCC" - ], - [ - "CCTG", - "CCTT" - ], - [ - "GAAGAA", - "GAAGAA" - ], - [ - "CTGA", - "CTGA" - ], - [ - "GCC", - "CTTA" - ], - [ - "TA", - "TCTAA" - ], - [ - "GTG", - "TTTTA" - ], - [ - "TGTG", - "GCA" - ], - [ - "TATT", - "GTAA" - ], - [ - "GCCA", - "GAAA" - ], - [ - "CCCTG", - "TCTC" - ], - [ - "CACA", - "GGAA" - ], - [ - "AAAA", - "CAA" - ], - [ - "AAAAAAAA", - "AAAAAAA" - ], - [ - "TAA", - "CTCC" - ], - [ - "GCC", - "TAAA" - ], - [ - "CGA", - "GTA" - ], - [ - "TA", - "GTATT" - ], - [ - "GTATTTT", - "TAGTAGAGA" - ], - [ - "GCTG", - "CAGG" - ], - [ - "TATT", - "GAAA" - ], - [ - "CCAGCC", - "TGGG" - ], - [ - "GCTCC", - "AAA" - ], - [ - "TA", - "CGAA" - ], - [ - "GGCC", - "TCC" - ], - [ - "TATA", - "CAAA" - ], - [ - "CATG", - "GCA" - ], - [ - "CATG", - "CAA" - ], - [ - "TACA", - "CCA" - ], - [ - "CTT", - "TACCA" - ], - [ - "TACA", - "GAGA" - ], - [ - "TATT", - "CTTA" - ], - [ - "TATG", - "TCA" - ], - [ - "TCAA", - "GCA" - ], - [ - "TCAA", - "TGA" - ], - [ - "GG", - "CTCTT" - ], - [ - "GGAA", - "GTT" - ], - [ - "TCCA", - "TGTT" - ], - [ - "GCTT", - "TCC" - ], - [ - "TATG", - "TGA" - ], - [ - "GTG", - "TAGA" - ], - [ - "TTTT", - "TAAAA" - ], - [ - "GCTG", - "GAGA" - ], - [ - "GTGA", - "GAGA" - ], - [ - "CCTA", - "GAA" - ], - [ - "CCTCC", - "AAA" - ], - [ - "CCAA", - "TGA" - ], - [ - "CAGG", - "GCA" - ], - [ - "CTA", - "TGCA" - ], - [ - "CTT", - "CACC" - ], - [ - "CTA", - "CAAAA" - ], - [ - "CTCA", - "CC" - ], - [ - "GAGTA", - "TG" - ], - [ - "TA", - "GAAAAA" - ], - [ - "CTTTT", - "GAA" - ], - [ - "TAAA", - "GAGA" - ], - [ - "CATG", - "TCA" - ], - [ - "TCTTTT", - "AAA" - ], - [ - "CACA", - "GTGA" - ], - [ - "GA", - "TCTAA" - ], - [ - "TAA", - "GGTA" - ], - [ - "CATA", - "GAA" - ], - [ - "CGC", - "GCC" - ], - [ - "CAGC", - "TTA" - ], - [ - "TATA", - "GTT" - ], - [ - "CGG", - "GCC" - ], - [ - "TATC", - "CATT" - ], - [ - "TGTTTG", - "TTTT" - ], - [ - "GCTG", - "GCTG" - ], - [ - "TACA", - "GGA" - ], - [ - "CTCC", - "TTTG" - ], - [ - "CAA", - "TCTA" - ], - [ - "CCCC", - "CTG" - ], - [ - "TATA", - "CTG" - ], - [ - "CTGA", - "GCC" - ], - [ - "CGG", - "TTA" - ], - [ - "TGAA", - "GTG" - ], - [ - "GCTT", - "CCTT" - ], - [ - "TTTTA", - "TTTG" - ], - [ - "TA", - "GTGAA" - ], - [ - "CTGA", - "GGTG" - ], - [ - "TCTT", - "CTC" - ], - [ - "GACA", - "GAAA" - ], - [ - "CTGAA", - "CTGAA" - ], - [ - "CCTG", - "GGAA" - ], - [ - "TCC", - "CCAAA" - ], - [ - "TATG", - "TATT" - ], - [ - "GATT", - "TCTG" - ], - [ - "CATT", - "CAAA" - ], - [ - "CACA", - "GTT" - ], - [ - "GCTT", - "GAA" - ], - [ - "GTG", - "GATCA" - ], - [ - "CTGA", - "GTGA" - ], - [ - "TGAA", - "TTTA" - ], - [ - "TCAA", - "CAAA" - ], - [ - "GG", - "TCATT" - ], - [ - "GTAA", - "TTTA" - ], - [ - "GC", - "GACTT" - ], - [ - "CTGA", - "GAGA" - ], - [ - "GTG", - "CCCA" - ], - [ - "CTA", - "GGTT" - ], - [ - "TCC", - "TGAAA" - ], - [ - "GTC", - "CACC" - ], - [ - "TCA", - "CAGAA" - ], - [ - "GC", - "GAAAA" - ], - [ - "GTA", - "TGGG" - ], - [ - "TGAA", - "CAAA" - ], - [ - "TAAA", - "CAAAA" - ], - [ - "CC", - "GTTTT" - ], - [ - "TC", - "TCAATT" - ], - [ - "TCCA", - "GAAA" - ], - [ - "GTAA", - "CAA" - ], - [ - "GCA", - "TTTTA" - ], - [ - "TCTC", - "CATG" - ], - [ - "TTA", - "TAAAA" - ], - [ - "CAGG", - "CAA" - ], - [ - "CTAAAA", - "AAA" - ], - [ - "GTT", - "GGGA" - ], - [ - "TAAA", - "GATT" - ], - [ - "TGAA", - "GAGA" - ], - [ - "CCCC", - "TCA" - ], - [ - "TGTT", - "TATG" - ], - [ - "TCTA", - "CTG" - ], - [ - "CCAA", - "TTTT" - ], - [ - "GGTG", - "GTG" - ], - [ - "GGAA", - "CAA" - ], - [ - "TGTG", - "GGA" - ], - [ - "TCTG", - "CTA" - ], - [ - "GAA", - "CGA" - ], - [ - "GTAA", - "GTA" - ], - [ - "GTT", - "GCCA" - ], - [ - "AAAA", - "TTTT" - ], - [ - "GC", - "GCGA" - ], - [ - "GAAA", - "GATG" - ], - [ - "GTC", - "TCTCA" - ], - [ - "TCCA", - "TCAA" - ], - [ - "GCA", - "GCTA" - ], - [ - "CACA", - "TTTG" - ], - [ - "CTGA", - "CAA" - ], - [ - "TCCA", - "CC" - ], - [ - "GC", - "T" - ], - [ - "CCCA", - "CTT" - ], - [ - "GCA", - "GGTA" - ], - [ - "GAGG", - "CCA" - ], - [ - "TAAA", - "GTCA" - ], - [ - "CTG", - "GATA" - ], - [ - "CGG", - "CAA" - ] - ] - } -} \ No newline at end of file diff --git a/test/AT/H3/tokenizer_config.json b/test/AT/H3/tokenizer_config.json deleted file mode 100644 index 048e8f4c..00000000 --- a/test/AT/H3/tokenizer_config.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "added_tokens_decoder": { - "0": { - "content": "[UNK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "1": { - "content": "[CLS]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "2": { - "content": "[SEP]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "3": { - "content": "[PAD]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - }, - "4": { - "content": "[MASK]", - "lstrip": false, - "normalized": false, - "rstrip": false, - "single_word": false, - "special": true - } - }, - "clean_up_tokenization_spaces": false, - "cls_token": "[CLS]", - "extra_special_tokens": {}, - "mask_token": "[MASK]", - "model_max_length": 256, - "pad_token": "[PAD]", - "padding_side": "right", - "sep_token": "[SEP]", - "tokenizer_class": "PreTrainedTokenizer", - "unk_token": "[UNK]" -} diff --git a/test/AT/H3/trainer_state.json b/test/AT/H3/trainer_state.json deleted file mode 100644 index 3484e4b0..00000000 --- a/test/AT/H3/trainer_state.json +++ /dev/null @@ -1,64 +0,0 @@ -{ - "best_global_step": null, - "best_metric": null, - "best_model_checkpoint": null, - "epoch": 4.0, - "eval_steps": 200, - "global_step": 752, - "is_hyper_param_search": false, - "is_local_process_zero": true, - "is_world_process_zero": true, - "log_history": [ - { - "epoch": 1.0638297872340425, - "grad_norm": 4.393446922302246, - "learning_rate": 2.3717948717948718e-05, - "loss": 0.4175, - "step": 200 - }, - { - "epoch": 2.127659574468085, - "grad_norm": 3.599414348602295, - "learning_rate": 1.5170940170940172e-05, - "loss": 0.2427, - "step": 400 - }, - { - "epoch": 3.1914893617021276, - "grad_norm": 5.260833263397217, - "learning_rate": 6.623931623931625e-06, - "loss": 0.1609, - "step": 600 - }, - { - "epoch": 4.0, - "step": 752, - "total_flos": 3764005349807280.0, - "train_loss": 0.24308214289076785, - "train_runtime": 46.5411, - "train_samples_per_second": 1028.855, - "train_steps_per_second": 16.158 - } - ], - "logging_steps": 200, - "max_steps": 752, - "num_input_tokens_seen": 0, - "num_train_epochs": 4, - "save_steps": 200, - "stateful_callbacks": { - "TrainerControl": { - "args": { - "should_epoch_stop": false, - "should_evaluate": false, - "should_log": false, - "should_save": true, - "should_training_stop": true - }, - "attributes": {} - } - }, - "total_flos": 3764005349807280.0, - "train_batch_size": 64, - "trial_name": null, - "trial_params": null -} diff --git a/test/PGD/dnabert/H3/results.txt b/test/PGD/dnabert/H3/results.txt deleted file mode 100644 index a1609500..00000000 --- a/test/PGD/dnabert/H3/results.txt +++ /dev/null @@ -1,2 +0,0 @@ -Final Accuracy: 0.5264 -Average Metrics: {'accuracy': 0.527556146572104, 'f1': 0.46390537611276245, 'matthews_correlation': 0.06326471878589345, 'precision': 0.5317779442779441, 'recall': 0.527031538201751} \ No newline at end of file diff --git a/test/TextFooler/bert/H3/results_log b/test/TextFooler/bert/H3/results_log deleted file mode 100644 index e69de29b..00000000 diff --git a/test/run.sh b/test/run.sh deleted file mode 100644 index 6cc59fcb..00000000 --- a/test/run.sh +++ /dev/null @@ -1,31 +0,0 @@ -export WANDB_DISABLED=true - -export DATA_CACHE_DIR=".hf_data" -export MODEL_CACHE_DIR=".hf_cache" - -module load gcc/12.3.0-gcc - -cd /projects/p32013/DNABERT-meta/test - -python train.py \ - --model_name_or_path "magicslabnu/NT2-500M-multi_species-finetuned-tf0" \ - --data_path "/projects/p32013/DNABERT-meta/GUE/0" \ - --kmer -1 \ - --run_name "test" \ - --model_max_length 256 \ - --per_device_train_batch_size 64 \ - --per_device_eval_batch_size 64 \ - --gradient_accumulation_steps 1 \ - --learning_rate 3e-5 \ - --num_train_epochs 4 \ - --fp16 \ - --save_steps 200 \ - --output_dir "/scratch/hlv8980/Attack_Benchmark/test" \ - --evaluation_strategy steps \ - --eval_steps 200 \ - --warmup_ratio 0.05 \ - --logging_steps 100 \ - --overwrite_output_dir True \ - --log_level info \ - --find_unused_parameters False \ - --save_model False diff --git a/test/train.py b/test/train.py deleted file mode 100644 index 78fcada8..00000000 --- a/test/train.py +++ /dev/null @@ -1,343 +0,0 @@ -import os -import csv -import copy -import json -import logging -from dataclasses import dataclass, field -from typing import Optional, Dict, Sequence, Tuple, List - -import torch -import transformers -from transformers.models.bert.configuration_bert import BertConfig -import sklearn -import numpy as np -from torch.utils.data import Dataset - -from peft import ( - LoraConfig, - get_peft_model, - get_peft_model_state_dict, -) - - -@dataclass -class ModelArguments: - model_name_or_path: Optional[str] = field(default="facebook/opt-125m") - use_lora: bool = field(default=False, metadata={"help": "whether to use LoRA"}) - lora_r: int = field(default=16, metadata={"help": "hidden dimension for LoRA"}) - lora_alpha: int = field(default=32, metadata={"help": "alpha for LoRA"}) - lora_dropout: float = field(default=0.05, metadata={"help": "dropout rate for LoRA"}) - lora_target_modules: str = field(default="query,value", metadata={"help": "where to perform LoRA"}) - - -@dataclass -class DataArguments: - data_path: str = field(default=None, metadata={"help": "Path to the training data."}) - kmer: int = field(default=-1, metadata={"help": "k-mer for input sequence. -1 means not using k-mer."}) - - -@dataclass -class TrainingArguments(transformers.TrainingArguments): - cache_dir: Optional[str] = field(default=None) - run_name: str = field(default="run") - optim: str = field(default="adamw_torch") - model_max_length: int = field(default=512, metadata={"help": "Maximum sequence length."}) - gradient_accumulation_steps: int = field(default=1) - per_device_train_batch_size: int = field(default=1) - per_device_eval_batch_size: int = field(default=1) - num_train_epochs: int = field(default=1) - fp16: bool = field(default=False) - logging_steps: int = field(default=100) - save_steps: int = field(default=100) - eval_steps: int = field(default=100) - evaluation_strategy: str = field(default="steps"), - warmup_steps: int = field(default=50) - weight_decay: float = field(default=0.01) - learning_rate: float = field(default=1e-4) - save_total_limit: int = field(default=1) - load_best_model_at_end: bool = field(default=True) - output_dir: str = field(default="output") - find_unused_parameters: bool = field(default=False) - checkpointing: bool = field(default=False) - dataloader_pin_memory: bool = field(default=False) - eval_and_save_results: bool = field(default=True) - save_model: bool = field(default=False) - seed: int = field(default=42) - regression: bool = field(default=False) - - -def safe_save_model_for_hf_trainer(trainer: transformers.Trainer, output_dir: str): - """Collects the state dict and dump to disk.""" - state_dict = trainer.model.state_dict() - if trainer.args.should_save: - cpu_state_dict = {key: value.cpu() for key, value in state_dict.items()} - del state_dict - trainer._save(output_dir, state_dict=cpu_state_dict) # noqa - -def save_model(trainer: transformers.Trainer, output_dir: str): - """Save the model, optimizer state, and other information.""" - if trainer.args.should_save: - # Save the model - trainer.save_model(output_dir) - - # Save the optimizer state (if available) - if trainer.optimizer is not None: - optimizer_state_dict = trainer.optimizer.state_dict() - torch.save(optimizer_state_dict, os.path.join(output_dir, 'optimizer_state_dict.pth')) - - print(f"Model and optimizer state saved to {output_dir}") - - -""" -Get the reversed complement of the original DNA sequence. -""" -def get_alter_of_dna_sequence(sequence: str): - MAP = {"A": "T", "T": "A", "C": "G", "G": "C"} - # return "".join([MAP[c] for c in reversed(sequence)]) - return "".join([MAP[c] for c in sequence]) - -""" -Transform a dna sequence to k-mer string -""" -def generate_kmer_str(sequence: str, k: int) -> str: - """Generate k-mer string from DNA sequence.""" - return " ".join([sequence[i:i+k] for i in range(len(sequence) - k + 1)]) - - -""" -Load or generate k-mer string for each DNA sequence. The generated k-mer string will be saved to the same directory as the original data with the same name but with a suffix of "_{k}mer". -""" -def load_or_generate_kmer(data_path: str, texts: List[str], k: int) -> List[str]: - """Load or generate k-mer string for each DNA sequence.""" - kmer_path = data_path.replace(".csv", f"_{k}mer.json") - if os.path.exists(kmer_path): - logging.warning(f"Loading k-mer from {kmer_path}...") - with open(kmer_path, "r") as f: - kmer = json.load(f) - else: - logging.warning(f"Generating k-mer...") - kmer = [generate_kmer_str(text, k) for text in texts] - with open(kmer_path, "w") as f: - logging.warning(f"Saving k-mer to {kmer_path}...") - json.dump(kmer, f) - - return kmer - -class SupervisedDataset(Dataset): - """Dataset for supervised fine-tuning.""" - - def __init__(self, - data_path: str, - tokenizer: transformers.PreTrainedTokenizer, - kmer: int = -1, - regression: bool = False): - - super(SupervisedDataset, self).__init__() - - # load data from the disk - with open(data_path, "r") as f: - data = list(csv.reader(f))[1:] - if len(data[0]) == 2: - # data is in the format of [text, label] - logging.warning("Perform single sequence classification...") - texts = [d[0] for d in data] - labels = [float(d[1]) for d in data] if regression else [int(d[1]) for d in data] - elif len(data[0]) == 3: - # data is in the format of [text1, text2, label] - logging.warning("Perform sequence-pair classification...") - texts = [[d[0], d[1]] for d in data] - labels = [float(d[2]) for d in data] if regression else [int(d[2]) for d in data] - else: - raise ValueError("Data format not supported.") - - if kmer != -1: - # only write file on the first process - if torch.distributed.get_rank() not in [0, -1]: - torch.distributed.barrier() - - logging.warning(f"Using {kmer}-mer as input...") - texts = load_or_generate_kmer(data_path, texts, kmer) - - if torch.distributed.get_rank() == 0: - torch.distributed.barrier() - - output = tokenizer( - texts, - return_tensors="pt", - padding="longest", - max_length=tokenizer.model_max_length, - truncation=True, - # pad_to_multiple_of=512, - ) - - self.input_ids = torch.clip(output["input_ids"], max=4104) #if "InstaDeepAI" in tokenizer.name_or_path else output["input_ids"] - # print(torch.max(self.input_ids)) - # print(len(tokenizer)) - self.attention_mask = self.input_ids.ne(tokenizer.pad_token_id) - self.labels = labels - self.num_labels = len(set(labels)) if not regression else 1 - - def __len__(self): - return len(self.input_ids) - - def __getitem__(self, i) -> Dict[str, torch.Tensor]: - return dict(input_ids=self.input_ids[i], labels=self.labels[i]) - - -@dataclass -class DataCollatorForSupervisedDataset(object): - """Collate examples for supervised fine-tuning.""" - - def __init__(self, tokenizer: transformers.PreTrainedTokenizer, apply_attention_mask: bool = True, regression: bool = False): - self.tokenizer = tokenizer - self.apply_attention_mask = apply_attention_mask - self.regression = regression - - def __call__(self, instances: Sequence[Dict]) -> Dict[str, torch.Tensor]: - input_ids, labels = tuple([instance[key] for instance in instances] for key in ("input_ids", "labels")) - input_ids = torch.nn.utils.rnn.pad_sequence( - input_ids, batch_first=True, padding_value=self.tokenizer.pad_token_id - ) - labels = torch.Tensor(labels).long() if not self.regression else torch.Tensor(labels).float() - return dict( - input_ids=input_ids, - labels=labels, - attention_mask=input_ids.ne(self.tokenizer.pad_token_id), - ) if self.apply_attention_mask else dict(input_ids=input_ids, labels=labels) - -""" -Manually calculate the accuracy, f1, matthews_correlation, precision, recall with sklearn. -""" -def calculate_metric_with_sklearn(logits: np.ndarray, labels: np.ndarray): - if logits.ndim == 3: - # Reshape logits to 2D if needed - logits = logits.reshape(-1, logits.shape[-1]) - predictions = np.argmax(logits, axis=-1) - valid_mask = labels != -100 # Exclude padding tokens (assuming -100 is the padding token ID) - valid_predictions = predictions[valid_mask] - valid_labels = labels[valid_mask] - return { - "accuracy": sklearn.metrics.accuracy_score(valid_labels, valid_predictions), - "f1": sklearn.metrics.f1_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - "matthews_correlation": sklearn.metrics.matthews_corrcoef( - valid_labels, valid_predictions - ), - "precision": sklearn.metrics.precision_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - "recall": sklearn.metrics.recall_score( - valid_labels, valid_predictions, average="macro", zero_division=0 - ), - } - - -""" -Compute metrics used for huggingface trainer. -""" -def compute_metrics_classification(eval_pred): - logits, labels = eval_pred - if isinstance(logits, tuple): # Unpack logits if it's a tuple - logits = logits[0] - return calculate_metric_with_sklearn(logits, labels) - -def compute_metrics_regression(eval_pred): - logits, labels = eval_pred - if isinstance(logits, tuple): # Unpack logits if it's a tuple - logits = logits[0] - return { - "mse": sklearn.metrics.mean_squared_error(labels, logits), - "mae": sklearn.metrics.mean_absolute_error(labels, logits), - } - - -def train(): - parser = transformers.HfArgumentParser((ModelArguments, DataArguments, TrainingArguments)) - model_args, data_args, training_args = parser.parse_args_into_dataclasses() - - # load tokenizer - tokenizer = transformers.AutoTokenizer.from_pretrained( - model_args.model_name_or_path, - cache_dir=training_args.cache_dir, - model_max_length=training_args.model_max_length, - padding_side="right", - use_fast=True, - trust_remote_code=True, - ) - - if "InstaDeepAI" in model_args.model_name_or_path: - tokenizer.eos_token = tokenizer.pad_token - - # define datasets and data collator - train_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "train.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - val_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "dev.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - test_dataset = SupervisedDataset(tokenizer=tokenizer, - data_path=os.path.join(data_args.data_path, "test.csv"), - kmer=data_args.kmer, - regression=training_args.regression) - apply_attention_mask = ("hyena" not in model_args.model_name_or_path) and ("caduceus" not in model_args.model_name_or_path) - data_collator = DataCollatorForSupervisedDataset(tokenizer=tokenizer, apply_attention_mask=apply_attention_mask, regression=training_args.regression) - - - # load model - config = transformers.AutoConfig.from_pretrained(model_args.model_name_or_path, num_labels=train_dataset.num_labels, trust_remote_code=True) - model = transformers.AutoModelForSequenceClassification.from_pretrained( - model_args.model_name_or_path, - config=config, - cache_dir=training_args.cache_dir, - trust_remote_code=True, - ) - print(model) - - # configure LoRA - if model_args.use_lora: - lora_config = LoraConfig( - r=model_args.lora_r, - lora_alpha=model_args.lora_alpha, - target_modules=list(model_args.lora_target_modules.split(",")), - lora_dropout=model_args.lora_dropout, - bias="none", - task_type="SEQ_CLS", - inference_mode=False, - ) - model = get_peft_model(model, lora_config) - model.print_trainable_parameters() - - # define trainer - trainer = transformers.Trainer( - model=model, - tokenizer=tokenizer, - args=training_args, - compute_metrics=compute_metrics_regression if training_args.regression else compute_metrics_classification, - train_dataset=train_dataset, - eval_dataset=val_dataset, - data_collator=data_collator - ) - trainer.train() - - if training_args.save_model: - trainer.save_state() - # safe_save_model_for_hf_trainer(trainer=trainer, output_dir=training_args.output_dir) - save_model(trainer=trainer, output_dir=training_args.output_dir) - - # get the evaluation results from trainer - if training_args.eval_and_save_results: - results_path = os.path.join(training_args.output_dir, "results", str(training_args.seed)) - results = trainer.evaluate(eval_dataset=test_dataset) - print(results) - os.makedirs(results_path, exist_ok=True) - with open(os.path.join(results_path, "eval_results.json"), "w") as f: - json.dump(results, f) - - - - -if __name__ == "__main__": - train()