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Add silu support, fix neural_nets typo #90

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5d3386c
add silu support, fix neural_nets typo
dilpath Jul 22, 2026
70551c6
review: swish
dilpath Jul 23, 2026
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2 changes: 1 addition & 1 deletion doc/examples/getting_started/problem.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ extensions:
- "net1_ps.hdf5"
hybridization_files:
- "hybridization.tsv"
neural_nets:
neural_networks:
net1:
location: "net1.yaml"
static: false
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2 changes: 1 addition & 1 deletion doc/examples/how_to_dmms/problem.yaml
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Expand Up @@ -19,7 +19,7 @@ extensions:
- "net3_input2.hdf5"
hybridization_files:
- "hybridization.tsv"
neural_nets:
neural_networks:
net3:
location: "net3.yaml"
static: true
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2 changes: 1 addition & 1 deletion doc/examples/how_to_neural_ode/problem.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ extensions:
- net1_ps.hdf5
hybridization_files:
- hybridization.tsv
neural_nets:
neural_networks:
net1:
location: net1.yaml
static: false
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2 changes: 1 addition & 1 deletion doc/examples/how_to_observable/problem.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ extensions:
- "net1_ps.hdf5"
hybridization_files:
- "hybridization.tsv"
neural_nets:
neural_networks:
net1:
location: "net1.yaml"
static: false
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3 changes: 3 additions & 0 deletions doc/layers.rst
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Expand Up @@ -176,6 +176,9 @@ Additionally, the table indicates which tools support each layer.
| moid <https://pytorch.org/docs/stable/generated/torch.nn.fun | | |
| ctional.hardsigmoid.html#torch.nn.functional.hardsigmoid>`__ | | |
+--------------------------------------------------------------+----+---+
| `silu <https://pytorch.org/docs/stable/generated/torch.nn | ✔️ | |

@sebapersson sebapersson Jul 23, 2026

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Could you here highlight this activation function is also called swish, e.g., silu (swish), as it is called swish in Lux.jl?

| .functional.silu.html#torch.nn.functional.silu>`__ | | |
+--------------------------------------------------------------+----+---+
| `mish <https://pytorch.org/docs/stable/generate | ✔️ | |
| d/torch.nn.functional.mish.html#torch.nn.functional.mish>`__ | | |
+--------------------------------------------------------------+----+---+
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2 changes: 1 addition & 1 deletion petab_sciml/problem_utils/neural_ode.py
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Expand Up @@ -208,7 +208,7 @@ def create_neural_ode_problem(
"sciml": {
"version": "0.1.0",
"required": True,
"neural_nets": {
"neural_networks": {
network_name: {
"location": network_filename,
"pre_initialization": False,
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6 changes: 4 additions & 2 deletions tests/problem_utils/test_neural_ode.py
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Expand Up @@ -152,9 +152,11 @@ def test_create_neural_ode_problem(dir_tmp):
assert problem["model_files"]["model"]["location"] == "model.xml"
assert problem["measurement_files"][0] == "measurements.tsv"

assert "net1" in problem["extensions"]["sciml"]["neural_nets"]
assert "net1" in problem["extensions"]["sciml"]["neural_networks"]
assert (
problem["extensions"]["sciml"]["neural_nets"]["net1"]["location"]
problem["extensions"]["sciml"]["neural_networks"]["net1"][
"location"
]
== "net1.yaml"
)
assert "array_files" in problem["extensions"]["sciml"]
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