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Fix PaccMann integration
- #447
#447
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tereshchuk1
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Fix PaccMann integration
#447
tereshchuk1
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Commits on Apr 23, 2026
Implementierung PaccMann
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Implementierung PaccMann
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Merge branch 'development' into development
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Commits on Apr 27, 2026
Pytoda hinzugefügt zu PaccMann
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Commits on Jul 3, 2026
fix: remove top-level pytoda imports, fix SMILES loading
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fix: resolve merge conflicts with upstream/development
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fix: mypy - remove None annotation for hyperparameters
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fix: mypy - initialize hyperparameters as empty dict
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Commits on Jul 16, 2026
refactor: remove dead PaccMann confidence-estimation path (forward(confidence=...), _associate_language, utils/interpret.py, vendored pytoda) and unused gene_projection/smiles_projection/alpha_proj…
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fix: make PaccMann gene_list a hyperparameter and use gene_list=None for the TOY test, so the model no longer requires the gene_list_paccmann_network_prop panel on toy data
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documentation for PaccMann model was added
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Commits on Aug 7, 2026
docs: add PaccMann to the model overview table in usage.rst
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Commits on Aug 8, 2026
feat: select the best PaccMann epoch on the early stopping set
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fix: align PaccMann SMILES handling with upstream and drop dead code
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Commits on Aug 9, 2026
feat: augment PaccMann drugs with equivalent SMILES strings
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refactor: drop historical residue from the PaccMann port
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Commits on Aug 18, 2026
refactor: rewrite PaccMann as a standalone module, fixing early stopping and dropping upstream cruft
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Merge branch 'development' into pr-388
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