├── .DS_Store ├── .gitignore ├── GNN ├── .DS_Store ├── MyNets │ ├── .DS_Store │ ├── MyNet_Classification.py │ ├── MyNet_Regression.py │ ├── order_cls.sh │ ├── order_cls_kinase.sh │ └── order_rgs.sh ├── MyNets_Scaffold │ ├── .DS_Store │ ├── MyNet_Classification.py │ ├── checkpoints │ │ └── .DS_Store │ ├── order_cls.sh │ ├── order_cls_kinase.sh │ └── order_rgs.sh ├── Nets │ ├── .DS_Store │ ├── AttentiveFP.py │ ├── NN.py │ ├── ReduceGNN.py │ └── ReduceGNN_explain.py ├── Utils │ ├── .DS_Store │ ├── EdgeHandle.py │ ├── log2csv_cls.py │ ├── log2csv_rgs.py │ ├── logging.py │ ├── metrics.py │ └── sort_tid.py ├── configs │ └── configs.py └── logs │ └── .DS_Store ├── LICENSE ├── README.md ├── SOM ├── .DS_Store ├── AURKA_analysis.ipynb ├── AURKA_som_train.ipynb ├── fingerprints │ ├── AFP_test.csv │ ├── AFP_train.csv │ ├── AFP_val.csv │ ├── ECFP_MLP_test.csv │ ├── ECFP_MLP_train.csv │ ├── ECFP_MLP_valid.csv │ ├── ECFP_test.csv │ ├── ECFP_train.csv │ ├── ECFP_valid.csv │ ├── GNN_test.csv │ ├── GNN_train.csv │ ├── GNN_val.csv │ ├── NN_test.csv │ ├── NN_train.csv │ ├── NN_val.csv │ ├── RGNN_test.csv │ ├── RGNN_train.csv │ ├── RGNN_val.csv │ ├── ReduceAFP_test.csv │ ├── ReduceAFP_train.csv │ ├── ReduceAFP_val.csv │ ├── ReduceNN_test.csv │ ├── ReduceNN_train.csv │ └── ReduceNN_val.csv ├── maps │ ├── .DS_Store │ ├── AFP_pie.png │ ├── AFP_scatter.png │ ├── ECFP_pie.png │ ├── ECFP_scatter.png │ ├── GNN_pie.png │ ├── GNN_scatter.png │ ├── NN_pie.png │ ├── NN_scatter.png │ ├── RGNN_pie.png │ ├── RGNN_scatter.png │ ├── ReduceAFP_pie.png │ ├── ReduceAFP_scatter.png │ ├── ReduceNN_pie.png │ └── ReduceNN_scatter.png ├── models │ ├── .DS_Store │ ├── AFP_som.p │ ├── ECFP_som.p │ ├── GNN_som.p │ ├── NN_som.p │ ├── RGNN_som.p │ ├── ReduceAFP_som.p │ └── ReduceNN_som.p └── similarity │ ├── .DS_Store │ ├── AFP_ECFP_mol_sim.png │ ├── AFP_ECFP_rg_sim.png │ ├── AFP_mol_sim.png │ ├── AFP_rg_sim.png │ ├── ECFP_mol_sim.png │ ├── ECFP_rg_sim.png │ ├── GNN_ECFP_mol_sim.png │ ├── GNN_ECFP_rg_sim.png │ ├── GNN_mol_sim.png │ ├── GNN_rg_sim.png │ ├── NN_ECFP_mol_sim.png │ ├── NN_ECFP_rg_sim.png │ ├── NN_mol_sim.png │ ├── NN_rg_sim.png │ ├── RGNN_ECFP_mol_sim.png │ ├── RGNN_ECFP_rg_sim.png │ ├── RGNN_mol_sim.png │ ├── RGNN_rg_sim.png │ ├── ReduceAFP_ECFP_mol_sim.png │ ├── ReduceAFP_ECFP_rg_sim.png │ ├── ReduceAFP_mol_sim.png │ ├── ReduceAFP_rg_sim.png │ ├── ReduceNN_ECFP_mol_sim.png │ ├── ReduceNN_ECFP_rg_sim.png │ ├── ReduceNN_mol_sim.png │ └── ReduceNN_rg_sim.png ├── data ├── .DS_Store ├── benchmark │ ├── .DS_Store │ ├── BBBP │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── BBBP.csv │ │ │ ├── BBBP_ScafflodSplit_test.csv │ │ │ ├── BBBP_ScafflodSplit_train.csv │ │ │ └── BBBP_ScafflodSplit_valid.csv │ ├── ClinTox │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── clintox.csv │ │ │ ├── clintox_ScafflodSplit_test.csv │ │ │ ├── clintox_ScafflodSplit_train.csv │ │ │ └── clintox_ScafflodSplit_valid.csv │ ├── ESOL │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── ESOL.csv │ │ │ ├── ESOL_ScafflodSplit_test.csv │ │ │ ├── ESOL_ScafflodSplit_train.csv │ │ │ └── ESOL_ScafflodSplit_valid.csv │ ├── FreeSolv │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── FreeSolv.csv │ │ │ ├── FreeSolv_ScafflodSplit_test.csv │ │ │ ├── FreeSolv_ScafflodSplit_train.csv │ │ │ └── FreeSolv_ScafflodSplit_valid.csv │ ├── HIV │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── HIV.csv │ │ │ ├── HIV_ScafflodSplit_test.csv │ │ │ ├── HIV_ScafflodSplit_train.csv │ │ │ └── HIV_ScafflodSplit_valid.csv │ ├── Lipo │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── Lipophilicity.csv │ │ │ ├── Lipophilicity_ScafflodSplit_test.csv │ │ │ ├── Lipophilicity_ScafflodSplit_train.csv │ │ │ └── Lipophilicity_ScafflodSplit_valid.csv │ ├── MUV │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── muv.csv │ │ │ ├── muv_ScafflodSplit_test.csv │ │ │ ├── muv_ScafflodSplit_train.csv │ │ │ └── muv_ScafflodSplit_valid.csv │ ├── SIDER │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── sider.csv │ │ │ ├── sider_ScafflodSplit_test.csv │ │ │ ├── sider_ScafflodSplit_train.csv │ │ │ └── sider_ScafflodSplit_valid.csv │ ├── Tox21 │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── tox21.csv │ │ │ ├── tox21_ScafflodSplit_test.csv │ │ │ ├── tox21_ScafflodSplit_train.csv │ │ │ └── tox21_ScafflodSplit_valid.csv │ ├── ToxCast │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── toxcast.csv │ │ │ ├── toxcast_ScafflodSplit_test.csv │ │ │ ├── toxcast_ScafflodSplit_train.csv │ │ │ └── toxcast_ScafflodSplit_valid.csv │ └── bace │ │ ├── .DS_Store │ │ └── raw │ │ ├── bace.csv │ │ ├── bace_ScafflodSplit_test.csv │ │ ├── bace_ScafflodSplit_train.csv │ │ └── bace_ScafflodSplit_valid.csv ├── kinase │ ├── .DS_Store │ ├── AKT1 │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── AKT1.csv │ │ │ ├── AKT1_ScafflodSplit_test.csv │ │ │ ├── AKT1_ScafflodSplit_train.csv │ │ │ └── AKT1_ScafflodSplit_valid.csv │ ├── AURKA │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── AURKA.csv │ │ │ ├── AURKA_ScafflodSplit_test.csv │ │ │ ├── AURKA_ScafflodSplit_train.csv │ │ │ └── AURKA_ScafflodSplit_valid.csv │ ├── BRAF │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── BRAF.csv │ │ │ ├── BRAF_ScafflodSplit_test.csv │ │ │ ├── BRAF_ScafflodSplit_train.csv │ │ │ └── BRAF_ScafflodSplit_valid.csv │ ├── BTK │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── BTK.csv │ │ │ ├── BTK_ScafflodSplit_test.csv │ │ │ ├── BTK_ScafflodSplit_train.csv │ │ │ └── BTK_ScafflodSplit_valid.csv │ ├── CDK2 │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── CDK2.csv │ │ │ ├── CDK2_ScafflodSplit_test.csv │ │ │ ├── CDK2_ScafflodSplit_train.csv │ │ │ └── CDK2_ScafflodSplit_valid.csv │ ├── CK1 │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── CK1.csv │ │ │ ├── CK1_ScafflodSplit_test.csv │ │ │ ├── CK1_ScafflodSplit_train.csv │ │ │ └── CK1_ScafflodSplit_valid.csv │ ├── EGFR │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── EGFR.csv │ │ │ ├── EGFR_ScafflodSplit_test.csv │ │ │ ├── EGFR_ScafflodSplit_train.csv │ │ │ └── EGFR_ScafflodSplit_valid.csv │ ├── MAP4K2 │ │ ├── .DS_Store │ │ └── raw │ │ │ ├── MAP4K2.csv │ │ │ ├── MAP4K2_ScafflodSplit_test.csv │ │ │ ├── MAP4K2_ScafflodSplit_train.csv │ │ │ └── MAP4K2_ScafflodSplit_valid.csv │ ├── PIM1 │ │ 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