├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── data ├── AbrahamAcree2014_Octsol_partialSmiles.csv ├── BradleyDoublePlusGoodMeltingPointDataset.csv ├── Delaney2004.txt ├── nr-ahr-eval.smiles ├── nr-ahr-test.smiles ├── nr-ahr-traintest.smiles ├── nr-ahr.smiles ├── nr-ar-eval.smiles ├── nr-ar-lbd-eval.smiles ├── nr-ar-lbd-test.smiles ├── nr-ar-lbd-traintest.smiles ├── nr-ar-lbd.smiles ├── nr-ar-test.smiles ├── nr-ar-traintest.smiles ├── nr-ar.smiles ├── nr-aromatase-eval.smiles ├── nr-aromatase-test.smiles ├── nr-aromatase-traintest.smiles ├── nr-aromatase.smiles ├── nr-er-eval.smiles ├── nr-er-lbd-eval.smiles ├── nr-er-lbd-test.smiles ├── nr-er-lbd-traintest.smiles ├── nr-er-lbd.smiles ├── nr-er-test.smiles ├── nr-er-traintest.smiles ├── nr-er.smiles ├── nr-ppar-gamma-eval.smiles ├── nr-ppar-gamma-test.smiles ├── nr-ppar-gamma-traintest.smiles ├── nr-ppar-gamma.smiles ├── sr-are-eval.smiles ├── sr-are-test.smiles ├── sr-are-traintest.smiles ├── sr-are.smiles ├── sr-atad5-eval.smiles ├── sr-atad5-test.smiles ├── sr-atad5-traintest.smiles ├── sr-atad5.smiles ├── sr-hse-eval.smiles ├── sr-hse-test.smiles ├── sr-hse-traintest.smiles ├── sr-hse.smiles ├── sr-mmp-eval.smiles ├── sr-mmp-test.smiles ├── sr-mmp-traintest.smiles ├── sr-mmp.smiles ├── sr-p53-eval.smiles ├── sr-p53-test.smiles ├── sr-p53-traintest.smiles ├── sr-p53.smiles ├── tox21-eval.smiles ├── tox21-test.smiles ├── tox21-traintest.smiles └── tox21.smiles ├── inputs ├── Ab-oct.cfg ├── Br-tm.cfg ├── De-aq.cfg ├── SVM_baselines │ ├── Ab-oct-SVM-linear-2a.cfg │ ├── Ab-oct-SVM-linear-2b.cfg │ ├── Ab-oct-SVM-linear-2c.cfg │ ├── Ab-oct-SVM-linear-a.cfg │ ├── Ab-oct-SVM-linear-b.cfg │ ├── Ab-oct-SVM-linear-c.cfg │ ├── Ab-oct-SVM-rbf-2a.cfg │ ├── Ab-oct-SVM-rbf-2b.cfg │ ├── Ab-oct-SVM-rbf-2c.cfg │ ├── Ab-oct-SVM-rbf-a.cfg │ ├── Ab-oct-SVM-rbf-b.cfg │ ├── Ab-oct-SVM-rbf-c.cfg │ ├── Ab-oct-SVM-tanimoto-2a.cfg │ ├── Ab-oct-SVM-tanimoto-2b.cfg │ ├── Ab-oct-SVM-tanimoto-2c.cfg │ ├── Ab-oct-SVM-tanimoto-a.cfg │ ├── Ab-oct-SVM-tanimoto-b.cfg │ ├── Ab-oct-SVM-tanimoto-c.cfg │ ├── Br-tm-SVM-linear-2a.cfg │ ├── Br-tm-SVM-linear-2b.cfg │ ├── Br-tm-SVM-linear-2c.cfg │ ├── Br-tm-SVM-linear-a.cfg │ ├── Br-tm-SVM-linear-b.cfg │ ├── Br-tm-SVM-linear-c.cfg │ ├── Br-tm-SVM-rbf-2a.cfg │ ├── Br-tm-SVM-rbf-2b.cfg │ ├── Br-tm-SVM-rbf-2c.cfg │ ├── Br-tm-SVM-rbf-a.cfg │ ├── Br-tm-SVM-rbf-b.cfg │ ├── Br-tm-SVM-rbf-c.cfg │ ├── Br-tm-SVM-tanimoto-2a.cfg │ ├── Br-tm-SVM-tanimoto-2b.cfg │ ├── Br-tm-SVM-tanimoto-2c.cfg │ ├── Br-tm-SVM-tanimoto-a.cfg │ ├── Br-tm-SVM-tanimoto-b.cfg │ ├── Br-tm-SVM-tanimoto-c.cfg │ ├── De-aq-SVM-linear-2a.cfg │ ├── De-aq-SVM-linear-2b.cfg │ ├── De-aq-SVM-linear-2c.cfg │ ├── De-aq-SVM-linear-a.cfg │ ├── De-aq-SVM-linear-b.cfg │ ├── De-aq-SVM-linear-c.cfg │ ├── De-aq-SVM-rbf-2a.cfg │ ├── De-aq-SVM-rbf-2b.cfg │ ├── De-aq-SVM-rbf-2c.cfg │ ├── De-aq-SVM-rbf-a.cfg │ ├── De-aq-SVM-rbf-b.cfg │ ├── De-aq-SVM-rbf-c.cfg │ ├── De-aq-SVM-tanimoto-2a.cfg │ ├── De-aq-SVM-tanimoto-2b.cfg │ ├── De-aq-SVM-tanimoto-2c.cfg │ ├── De-aq-SVM-tanimoto-a.cfg │ ├── De-aq-SVM-tanimoto-b.cfg │ ├── De-aq-SVM-tanimoto-c.cfg │ └── SVM.sh ├── run_tox.sh ├── tox21 │ ├── tox21_ahr.cfg │ ├── tox21_ar-lbd.cfg │ ├── tox21_ar.cfg │ ├── tox21_are.cfg │ ├── tox21_aromatase.cfg │ ├── tox21_atad5.cfg │ ├── tox21_er-lbd.cfg │ ├── tox21_er.cfg │ ├── tox21_hse.cfg │ ├── tox21_mmp.cfg │ ├── tox21_p53.cfg │ └── tox21_ppar-gamma.cfg ├── tox21_Morgan │ ├── tox21_ahr.cfg │ ├── tox21_ar-lbd.cfg │ ├── tox21_ar.cfg │ ├── tox21_are.cfg │ ├── tox21_aromatase.cfg │ ├── tox21_atad5.cfg │ ├── tox21_er-lbd.cfg │ ├── tox21_er.cfg │ ├── tox21_hse.cfg │ ├── tox21_mmp.cfg │ ├── tox21_p53.cfg │ └── tox21_ppar-gamma.cfg ├── tox21_Morgan2 │ ├── tox21_ahr.cfg │ ├── tox21_ar-lbd.cfg │ ├── tox21_ar.cfg │ ├── tox21_are.cfg │ ├── tox21_aromatase.cfg │ ├── tox21_atad5.cfg │ ├── tox21_er-lbd.cfg │ ├── tox21_er.cfg │ ├── tox21_hse.cfg │ ├── tox21_mmp.cfg │ ├── tox21_p53.cfg │ └── tox21_ppar-gamma.cfg └── tox21_all_traintest_MSE_fullsize.cfg ├── main ├── __init__.py ├── core.py ├── data.py ├── main_cv.py ├── main_nested_cv.py ├── similar_residuals.py ├── svm_cv.py ├── test.py └── test_index_removal.py ├── models └── __init__.py ├── scripts ├── coley_abraham.tdf ├── coley_bradley.tdf ├── coley_delaney.tdf ├── coley_tox21-eval.tdf ├── coley_tox21-test.tdf ├── coley_tox21-traintest.tdf ├── coley_tox21.tdf ├── consensus_test_from_CV.py ├── preprocess_tox21.py ├── preprocess_tox21_test.py └── save_data.py └── utils ├── GraphEmbedding.py ├── GraphEmbedding_sumAfter.py ├── __init__.py ├── neural_fp.py ├── parse_cfg.py ├── parsing.py ├── reset_layers.py ├── saving.py └── stats.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/connorcoley/conv_qsar_fast/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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