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2,276 changes: 1,125 additions & 1,151 deletions
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docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb
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docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html
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docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.ipynb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "task": "building", | ||
| "data": { | ||
| "input_column": "canonical", | ||
| "response_column": "molwt_gt_330", | ||
| "training_dataset_file": "tests/data/DRD2/subset-50/train.csv", | ||
| "test_dataset_file": "tests/data/DRD2/subset-50/test.csv" | ||
| }, | ||
| "metadata": { | ||
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| "best_trial": null, | ||
| "best_value": null, | ||
| "n_trials": 15 | ||
| }, | ||
| "descriptor": | ||
| { "name": "SmilesFromFile", | ||
| "parameters": { | ||
| } | ||
| } | ||
| , | ||
| "settings": { | ||
| "mode": "classification", | ||
| "direction": "maximize" | ||
| }, | ||
| "algorithm": { | ||
| "name": "CalibratedClassifierCVWithVA", | ||
| "parameters": { | ||
| "method": "vennabers", | ||
| "n_folds": 2, | ||
| "ensemble": "True", | ||
| "estimator": { | ||
| "name": "ChemPropHyperoptClassifier", | ||
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| "epochs": 4, | ||
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| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| { | ||
| "task": "optimization", | ||
| "data": { | ||
| "input_column": "canonical", | ||
| "response_column": "molwt", | ||
| "training_dataset_file": "tests/data/DRD2/subset-50/train.csv" | ||
| }, | ||
| "descriptors": [ | ||
| { | ||
| "name": "SmilesFromFile", | ||
| "parameters": { | ||
| } | ||
| } | ||
| ], | ||
| "settings": { | ||
| "mode": "regression", | ||
| "cross_validation": 2, | ||
| "direction": "maximize", | ||
| "n_trials": 3 | ||
| }, | ||
| "algorithms": [ | ||
| { | ||
| "name": "ChemPropRegressorPretrained", | ||
| "parameters": { | ||
| "pretrained_model": "tests/data/DRD2/drd2_reg.pkl" | ||
| } | ||
| } | ||
| ] | ||
| } |
29 changes: 29 additions & 0 deletions
29
examples/optimization/ChemProp_drd2_50_retrain_cls_error.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| { | ||
| "task": "optimization", | ||
| "data": { | ||
| "input_column": "canonical", | ||
| "response_column": "molwt", | ||
| "training_dataset_file": "tests/data/DRD2/subset-50/train.csv" | ||
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| "direction": "maximize", | ||
| "n_trials": 3 | ||
| }, | ||
| "algorithms": [ | ||
| { | ||
| "name": "ChemPropRegressorPretrained", | ||
| "parameters": { | ||
| "pretrained_model": "tests/data/DRD2/drd2_cls.pkl" | ||
| } | ||
| } | ||
| ] | ||
| } |
36 changes: 36 additions & 0 deletions
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examples/optimization/ChemProp_drd2_50_retrain_missingfile.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| { | ||
| "task": "optimization", | ||
| "data": { | ||
| "input_column": "canonical", | ||
| "response_column": "molwt", | ||
| "training_dataset_file": "tests/data/DRD2/subset-50/train.csv" | ||
| }, | ||
| "descriptors": [ | ||
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| "name": "SmilesFromFile", | ||
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| "settings": { | ||
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| "random_seed": 643 | ||
| }, | ||
| "algorithms": [ | ||
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| "pretrained_model": "missing.pkl" | ||
| } | ||
| }, | ||
| { | ||
| "name": "ChemPropRegressorPretrained", | ||
| "parameters": { | ||
| "pretrained_model": "tests/data/DRD2/drd2_reg.pkl" | ||
| } | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| { | ||
| "task": "optimization", | ||
| "data": { | ||
| "input_column": "Smiles", | ||
| "response_column": "Class", | ||
| "training_dataset_file": "tests/data/peptide/toxinpred3/train.csv", | ||
| "test_dataset_file": "tests/data/peptide/toxinpred3/test.csv", | ||
| "aux_column": "Peptide", | ||
| "aux_transform": { | ||
| "name": "ZScales", | ||
| "parameters": { | ||
| } | ||
| } | ||
| }, | ||
| "descriptors": [ | ||
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| { | ||
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| { | ||
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| ] | ||
| } | ||
| } | ||
| ], | ||
| "settings": { | ||
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| }, | ||
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| }, | ||
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| } | ||
| }, | ||
| { | ||
| "name": "KNeighborsClassifier", | ||
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| "low": 1, | ||
| "high": 3 | ||
| }, | ||
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| "metric": ["minkowski", "euclidean", "manhattan"] | ||
| } | ||
| }, | ||
| { "name": "SVC", | ||
| "parameters": { | ||
| "C": { | ||
| "low": 1e-7, | ||
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| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| { | ||
| "task": "optimization", | ||
| "data": { | ||
| "input_column": "Structure", | ||
| "response_column": "Permeability", | ||
| "training_dataset_file": "train/data/peptide/permeability/train.csv" | ||
| }, | ||
| "descriptors": [ | ||
| { | ||
| "name": "ECFP", | ||
| "parameters": { | ||
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| "nBits": 2048 | ||
| } | ||
| }, | ||
| { | ||
| "name": "SmilesFromFile", | ||
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| } | ||
| } | ||
| ], | ||
| "settings": { | ||
| "mode": "regression", | ||
| "cross_validation": 5, | ||
| "shuffle": true, | ||
| "direction": "maximize", | ||
| "n_trials": 15, | ||
| "random_seed": 2, | ||
| "n_jobs": 1 | ||
| }, | ||
| "algorithms": [ | ||
| { | ||
| "name": "RandomForestRegressor", | ||
| "parameters": { | ||
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| }, | ||
| "n_estimators": { | ||
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| }, | ||
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| "auto", | ||
| "sqrt", | ||
| "log2" | ||
| ] | ||
| } | ||
| }, | ||
| { | ||
| "name": "KNeighborsRegressor", | ||
| "parameters": { | ||
| "n_neighbors": { | ||
| "low": 1, | ||
| "high": 3 | ||
| }, | ||
| "weights": ["uniform", "distance"], | ||
| "metric": ["minkowski", "euclidean", "manhattan"] | ||
| } | ||
| }, | ||
| { | ||
| "name": "SVR", | ||
| "parameters": { | ||
| "C": { | ||
| "low": 1e-7, | ||
| "high": 1e7 | ||
| }, | ||
| "gamma": { | ||
| "low": 1e-9, | ||
| "high": 1000 | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "name": "Ridge", | ||
| "parameters": { | ||
| "alpha": { | ||
| "low": 1, | ||
| "high": 2 | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "name": "Lasso", | ||
| "parameters": { | ||
| "alpha": { | ||
| "low": 1, | ||
| "high": 2 | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "name": "ChemPropHyperoptRegressor", | ||
| "parameters": { | ||
| "ensemble_size": 1, | ||
| "epochs": 4, | ||
| "num_iters": 1 | ||
| } | ||
| } | ||
| ] | ||
| } | ||
|
|
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