├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── chemprop_benchmarks │ ├── README.md │ ├── evaluate_predictions.ipynb │ ├── filtering_invalid_smiles.ipynb │ └── scripts │ │ ├── hiv_script.sh │ │ ├── pcba_random_nan.sh │ │ ├── pcba_random_script.sh │ │ ├── pcba_scaffold_script.sh │ │ ├── pcqm4mv4_script.sh │ │ ├── qm9_gap_script.sh │ │ ├── qm9_multitask_script.sh │ │ ├── qm9_u0_script.sh │ │ ├── sampl_script.sh │ │ └── uv_vis_script.sh ├── cliffs.ipynb ├── cliffs │ ├── 1862_Ki_hsd.eps │ ├── 1871_Ki_hsd.eps │ ├── 2034_Ki_hsd.eps │ ├── 2047_EC50_hsd.eps │ ├── 204_Ki_hsd.eps │ ├── 2147_Ki_hsd.eps │ ├── 214_Ki_hsd.eps │ ├── 218_EC50_hsd.eps │ ├── 219_Ki_hsd.eps │ ├── 228_Ki_hsd.eps │ ├── 231_Ki_hsd.eps │ ├── 233_Ki_hsd.eps │ ├── 234_Ki_hsd.eps │ ├── 235_EC50_hsd.eps │ ├── 236_Ki_hsd.eps │ ├── 237_EC50_hsd.eps │ ├── 237_Ki_hsd.eps │ ├── 238_Ki_hsd.eps │ ├── 239_EC50_hsd.eps │ ├── 244_Ki_hsd.eps │ ├── 262_Ki_hsd.eps │ ├── 264_Ki_hsd.eps │ ├── 2835_Ki_hsd.eps │ ├── 287_Ki_hsd.eps │ ├── 2971_Ki_hsd.eps │ ├── 3979_EC50_hsd.eps │ ├── 4005_Ki_hsd.eps │ ├── 4203_Ki_hsd.eps │ ├── 4616_EC50_hsd.eps │ ├── 4792_Ki_hsd.eps │ ├── combined.eps │ ├── mace_all.eps │ ├── mace_subset.eps │ └── source_data.csv ├── hsd.ipynb ├── hsd │ ├── combined.eps │ ├── combined_selected.eps │ ├── polaris-adme-fang-hclint-1_hsd.eps │ ├── polaris-adme-fang-hppb-1_hsd.eps │ ├── polaris-adme-fang-perm-1_hsd.eps │ ├── polaris-adme-fang-rclint-1_hsd.eps │ ├── polaris-adme-fang-rppb-1_hsd.eps │ ├── polaris-adme-fang-solu-1_hsd.eps │ ├── polaris-pkis2-egfr-wt-reg-v2_hsd.eps │ ├── polaris-pkis2-kit-wt-cls-v2_hsd.eps │ ├── polaris-pkis2-kit-wt-reg-v2_hsd.eps │ ├── polaris-pkis2-ret-wt-cls-v2_hsd.eps │ ├── polaris-pkis2-ret-wt-reg-v2_hsd.eps │ ├── source_data.csv │ ├── tdcommons-ames_hsd.eps │ ├── tdcommons-bbb-martins_hsd.eps │ ├── tdcommons-bioavailability-ma_hsd.eps │ ├── tdcommons-caco2-wang_hsd.eps │ ├── tdcommons-clearance-hepatocyte-az_hsd.eps │ ├── tdcommons-clearance-microsome-az_hsd.eps │ ├── tdcommons-cyp2c9-substrate-carbonmangels_hsd.eps │ ├── tdcommons-cyp2d6-substrate-carbonmangels_hsd.eps │ ├── tdcommons-cyp3a4-substrate-carbonmangels_hsd.eps │ ├── tdcommons-dili_hsd.eps │ ├── tdcommons-half-life-obach_hsd.eps │ ├── tdcommons-herg_hsd.eps │ ├── tdcommons-ld50-zhu_hsd.eps │ ├── tdcommons-lipophilicity-astrazeneca_hsd.eps │ ├── tdcommons-pgp-broccatelli_hsd.eps │ ├── tdcommons-ppbr-az_hsd.eps │ └── tdcommons-vdss-lombardo_hsd.eps ├── moleculeace_results │ ├── CheMeleon.md │ ├── ChemProp.md │ ├── ChemProp_Mordred.md │ ├── MLP_PLR_Pretrained.md │ ├── MoLFormer.md │ ├── MolCLR.md │ ├── PCA_MLP.md │ ├── PCA_MLP_Prefitted.md │ ├── RF_Mordred.md │ ├── RF_Morgan.md │ ├── fastprop.md │ └── minimol.md ├── polaris_results │ ├── CheMeleon.md │ ├── ChemProp.md │ ├── ChemProp_Mordred.md │ ├── MLP_PLR_Pretrained.md │ ├── MoLFormer.md │ ├── MolCLR.md │ ├── PCA_MLP.md │ ├── PCA_MLP_Prefitted.md │ ├── RF_Mordred.md │ ├── RF_Morgan.md │ ├── fastprop.md │ └── minimol.md ├── pretraining_size.ipynb └── pretraining_size │ ├── 10MM_mace.md │ ├── 10MM_polaris.md │ ├── 1MM_mace.md │ └── 1MM_polaris.md ├── chemeleon.svg ├── chemeleon_fingerprint.py ├── chemeleon_logo_with_background.png ├── finetuning_demo.ipynb ├── models ├── chemprop_mordred │ └── evaluate.py ├── chemprop_mpnn │ ├── evaluate.py │ └── pretrain.py ├── descriptor_mlp │ ├── evaluate.py │ ├── hopt.py │ ├── models.py │ ├── pretrain.py │ └── torchford.py ├── features.py ├── minimol │ ├── evaluate.py │ └── features.py ├── molclr │ ├── create_benchmark_csv.py │ ├── evaluate_moleculeace.py │ ├── evaluate_polaris.py │ └── train_models_polaris.py ├── molformer_transformer │ └── evaluate.py ├── pca_mlp │ ├── evaluate.py │ └── fit_pca.py ├── rf_fingerprint │ └── evaluate.py └── rf_mordred │ └── evaluate.py └── scripts ├── get_pubchem.sh ├── gpus.sh ├── run_experiments.sh └── start_screen.sh /.gitignore: -------------------------------------------------------------------------------- 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