├── Experiments ├── benchmark.py ├── data_prep.py ├── figures │ ├── Fig_2.pdf │ ├── Fig_3.pdf │ ├── Fig_4.pdf │ ├── Fig_5.pdf │ ├── R_scripts │ │ ├── main_figures.R │ │ ├── suppl_figures.R │ │ └── vis_utils.R │ ├── fig_1.pdf │ ├── sup_fig_1.pdf │ ├── sup_fig_2.pdf │ ├── sup_fig_3.pdf │ ├── sup_fig_4.pdf │ ├── sup_fig_5.pdf │ └── sup_fig_6.pdf ├── optimization.py ├── pretrain_lstm.py ├── train_an_included_model.py └── use_your_own_data.py ├── LICENCE ├── MoleculeACE ├── Data │ ├── __init__.py │ ├── benchmark_data │ │ ├── CHEMBL1862_Ki.csv │ │ ├── CHEMBL1871_Ki.csv │ │ ├── CHEMBL2034_Ki.csv │ │ ├── CHEMBL2047_EC50.csv │ │ ├── CHEMBL204_Ki.csv │ │ ├── CHEMBL2147_Ki.csv │ │ ├── CHEMBL214_Ki.csv │ │ ├── CHEMBL218_EC50.csv │ │ ├── CHEMBL219_Ki.csv │ │ ├── CHEMBL228_Ki.csv │ │ ├── CHEMBL231_Ki.csv │ │ ├── CHEMBL233_Ki.csv │ │ ├── CHEMBL234_Ki.csv │ │ ├── CHEMBL235_EC50.csv │ │ ├── CHEMBL236_Ki.csv │ │ ├── CHEMBL237_EC50.csv │ │ ├── CHEMBL237_Ki.csv │ │ ├── CHEMBL238_Ki.csv │ │ ├── CHEMBL239_EC50.csv │ │ ├── CHEMBL244_Ki.csv │ │ ├── CHEMBL262_Ki.csv │ │ ├── CHEMBL264_Ki.csv │ │ ├── CHEMBL2835_Ki.csv │ │ ├── CHEMBL287_Ki.csv │ │ ├── CHEMBL2971_Ki.csv │ │ ├── CHEMBL3979_EC50.csv │ │ ├── CHEMBL4005_Ki.csv │ │ ├── CHEMBL4203_Ki.csv │ │ ├── CHEMBL4616_EC50.csv │ │ ├── CHEMBL4792_Ki.csv │ │ ├── __init__.py │ │ ├── metadata │ │ │ └── datasets.csv │ │ ├── old │ │ │ ├── CHEMBL1862_Ki.csv │ │ │ ├── CHEMBL1871_Ki.csv │ │ │ ├── CHEMBL2034_Ki.csv │ │ │ ├── CHEMBL2047_EC50.csv │ │ │ ├── CHEMBL204_Ki.csv │ │ │ ├── CHEMBL2147_Ki.csv │ │ │ ├── CHEMBL214_Ki.csv │ │ │ ├── CHEMBL218_EC50.csv │ │ │ ├── CHEMBL219_Ki.csv │ │ │ ├── CHEMBL228_Ki.csv │ │ │ ├── CHEMBL231_Ki.csv │ │ │ ├── CHEMBL233_Ki.csv │ │ │ ├── CHEMBL234_Ki.csv │ │ │ ├── CHEMBL235_EC50.csv │ │ │ ├── CHEMBL236_Ki.csv │ │ │ ├── CHEMBL237_EC50.csv │ │ │ ├── CHEMBL237_Ki.csv │ │ │ ├── CHEMBL238_Ki.csv │ │ │ ├── CHEMBL239_EC50.csv │ │ │ ├── CHEMBL244_Ki.csv │ │ │ ├── CHEMBL262_Ki.csv │ │ │ ├── CHEMBL264_Ki.csv │ │ │ ├── CHEMBL2835_Ki.csv │ │ │ ├── CHEMBL287_Ki.csv │ │ │ ├── CHEMBL2971_Ki.csv │ │ │ ├── CHEMBL3979_EC50.csv │ │ │ ├── CHEMBL4005_Ki.csv │ │ │ ├── CHEMBL4203_Ki.csv │ │ │ ├── CHEMBL4616_EC50.csv │ │ │ └── CHEMBL4792_Ki.csv │ │ └── raw │ │ │ ├── CHEMBL1862_Ki.csv │ │ │ ├── CHEMBL1871_Ki.csv │ │ │ ├── CHEMBL2034_Ki.csv │ │ │ ├── CHEMBL2047_EC50.csv │ │ │ ├── CHEMBL204_Ki.csv │ │ │ ├── CHEMBL2147_Ki.csv │ │ │ ├── CHEMBL214_Ki.csv │ │ │ ├── CHEMBL218_EC50.csv │ │ │ ├── CHEMBL219_Ki.csv │ │ │ ├── CHEMBL228_Ki.csv │ │ │ ├── CHEMBL231_Ki.csv │ │ │ ├── CHEMBL233_Ki.csv │ │ │ ├── CHEMBL234_Ki.csv │ │ │ ├── CHEMBL235_EC50.csv │ │ │ ├── CHEMBL236_Ki.csv │ │ │ ├── CHEMBL237_EC50.csv │ │ │ ├── CHEMBL237_Ki.csv │ │ │ ├── CHEMBL238_Ki.csv │ │ │ ├── CHEMBL239_EC50.csv │ │ │ ├── CHEMBL244_Ki.csv │ │ │ ├── CHEMBL262_Ki.csv │ │ │ ├── CHEMBL264_Ki.csv │ │ │ ├── CHEMBL2835_Ki.csv │ │ │ ├── CHEMBL287_Ki.csv │ │ │ ├── CHEMBL2971_Ki.csv │ │ │ ├── CHEMBL3979_EC50.csv │ │ │ ├── CHEMBL4005_Ki.csv │ │ │ ├── CHEMBL4203_Ki.csv │ │ │ ├── CHEMBL4616_EC50.csv │ │ │ └── CHEMBL4792_Ki.csv │ ├── configures │ │ ├── __init__.py │ │ ├── benchmark │ │ │ ├── CHEMBL1862_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL1871_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL2034_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL2047_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL204_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL2147_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL214_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL218_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL219_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL228_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL231_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL233_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL234_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL235_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL236_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL237_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL237_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL238_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL239_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL244_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL262_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL264_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL2835_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL287_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL2971_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL3979_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL4005_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL4203_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL4616_EC50 │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ ├── CHEMBL4792_Ki │ │ │ │ ├── AFP_GRAPH.yml │ │ │ │ ├── CNN_SMILES.yml │ │ │ │ ├── GAT_GRAPH.yml │ │ │ │ ├── GBM_ECFP.yml │ │ │ │ ├── GBM_MACCS.yml │ │ │ │ ├── GBM_PHYSCHEM.yml │ │ │ │ ├── GBM_WHIM.yml │ │ │ │ ├── GCN_GRAPH.yml │ │ │ │ ├── KNN_ECFP.yml │ │ │ │ ├── KNN_MACCS.yml │ │ │ │ ├── KNN_PHYSCHEM.yml │ │ │ │ ├── KNN_WHIM.yml │ │ │ │ ├── LSTM_SMILES.yml │ │ │ │ ├── MLP_ECFP.yml │ │ │ │ ├── MPNN_GRAPH.yml │ │ │ │ ├── RF_ECFP.yml │ │ │ │ ├── RF_MACCS.yml │ │ │ │ ├── RF_PHYSCHEM.yml │ │ │ │ ├── RF_WHIM.yml │ │ │ │ ├── SVM_ECFP.yml │ │ │ │ ├── SVM_MACCS.yml │ │ │ │ ├── SVM_PHYSCHEM.yml │ │ │ │ ├── SVM_WHIM.yml │ │ │ │ ├── Transformer_TOKENS.yml │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ └── default │ │ │ ├── AFP.yml │ │ │ ├── CNN.yml │ │ │ ├── GAT.yml │ │ │ ├── GBM.yml │ │ │ ├── GCN.yml │ │ │ ├── GIN.yml │ │ │ ├── KNN.yml │ │ │ ├── LSTM.yml │ │ │ ├── MLP.yml │ │ │ ├── MPNN.yml │ │ │ ├── RF.yml │ │ │ ├── SMILES.yml │ │ │ ├── SVM.yml │ │ │ ├── TRANSFORMER.yml │ │ │ └── __init__.py │ └── results │ │ ├── MoleculeACE_results.csv │ │ └── MoleculeACE_results_old.csv ├── __init__.py ├── benchmark │ ├── __init__.py │ ├── cliffs.py │ ├── const.py │ ├── data_fetching │ │ ├── __init__.py │ │ ├── exp_property_curation.py │ │ ├── fetch_chembl.py │ │ ├── main_curator.py │ │ └── molecule_preparation.py │ ├── data_prep.py │ ├── featurization.py │ └── utils.py └── models │ ├── __init__.py │ ├── attentivefp.py │ ├── cnn.py │ ├── gat.py │ ├── gcn.py │ ├── lstm.py │ ├── ml.py │ ├── mlp.py │ ├── mpnn.py │ ├── optimize.py │ ├── transformer.py │ └── utils.py ├── README.md ├── img ├── MoleculeACE.png ├── cliff_example.png └── moleculeACE_example.png └── setup.py /Experiments/figures/Fig_2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/Experiments/figures/Fig_2.pdf -------------------------------------------------------------------------------- /Experiments/figures/Fig_3.pdf: 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/MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 278 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 277 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 2 7 | node_hidden: 128 8 | transformer_hidden: 64 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 114 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 224 4 | fc_hidden: 512 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1862_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | epochs: 306 2 | hidden: 256 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 220 3 | fc_hidden: 256 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 4 7 | n_gat_layers: 1 8 | node_hidden: 64 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 205 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 4 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 30 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 32 3 | epochs: 166 4 | fc_hidden: 512 5 | lr: 5.0e-05 6 | message_steps: 1 7 | n_fc_layers: 3 8 | node_hidden: 64 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL1871_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 81 3 | hidden_channels: 128 4 | lr: 0.0005 5 | num_layers: 1 6 | num_timesteps: 4 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 10 2 | hidden: 128 3 | kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 194 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 1 8 | node_hidden: 512 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 61 3 | fc_hidden: 128 4 | lr: 0.0005 5 | n_conv_layers: 2 6 | n_fc_layers: 3 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 41 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 291 4 | fc_hidden: 128 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 1 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2034_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 70 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 0.0005 6 | n_fc_layers: 2 7 | n_gat_layers: 2 8 | node_hidden: 512 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 144 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 2 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 191 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2047_EC50/RF_WHIM.yml: 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node_hidden: 512 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 184 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 3 7 | node_hidden: 512 8 | transformer_hidden: 64 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 56 4 | fc_hidden: 128 5 | lr: 0.0005 6 | message_steps: 4 7 | n_fc_layers: 3 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL204_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 248 3 | fc_hidden: 256 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 223 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 4 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 100 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 64 3 | epochs: 196 4 | fc_hidden: 128 5 | lr: 5.0e-05 6 | message_steps: 1 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | 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-------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2147_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 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kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 209 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 5 7 | n_gat_layers: 4 8 | node_hidden: 512 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 230 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 4 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 102 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 32 3 | epochs: 300 4 | fc_hidden: 256 5 | lr: 0.0005 6 | message_steps: 2 7 | n_fc_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | 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10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL214_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | 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-------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 237 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 223 3 | fc_hidden: 256 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 3 7 | n_gat_layers: 1 8 | node_hidden: 512 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 104 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 3 7 | node_hidden: 512 8 | transformer_hidden: 512 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 35 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 4 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 80 4 | fc_hidden: 256 5 | lr: 5.0e-05 6 | message_steps: 2 7 | n_fc_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | 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1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL218_EC50/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 200 3 | hidden_channels: 256 4 | lr: 5.0e-05 5 | num_layers: 2 6 | num_timesteps: 4 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 388 2 | hidden: 256 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 184 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 300 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 1 7 | node_hidden: 128 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 152 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 290 4 | fc_hidden: 256 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL219_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 193 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 1 8 | node_hidden: 512 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 95 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 1 7 | node_hidden: 512 8 | transformer_hidden: 512 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 147 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 32 3 | epochs: 255 4 | fc_hidden: 128 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL228_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 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kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 196 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 2 8 | node_hidden: 512 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 132 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 2 7 | node_hidden: 512 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 27 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 98 4 | fc_hidden: 512 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 3 8 | node_hidden: 64 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | 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10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL231_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | 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-------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 22 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 149 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 1 8 | node_hidden: 256 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 117 3 | fc_hidden: 512 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 4 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 157 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 254 4 | fc_hidden: 256 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 1 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL233_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 200 3 | hidden_channels: 256 4 | lr: 5.0e-05 5 | num_layers: 2 6 | num_timesteps: 4 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 35 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 159 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 66 3 | fc_hidden: 128 4 | lr: 0.0005 5 | n_conv_layers: 2 6 | n_fc_layers: 5 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 180 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 32 3 | epochs: 300 4 | fc_hidden: 128 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 64 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | 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-------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL234_Ki/__init__.py: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 296 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 2 8 | node_hidden: 512 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 102 3 | fc_hidden: 128 4 | lr: 0.0005 5 | n_conv_layers: 3 6 | n_fc_layers: 4 7 | node_hidden: 128 8 | transformer_hidden: 64 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 218 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 32 3 | epochs: 65 4 | fc_hidden: 128 5 | lr: 0.0005 6 | message_steps: 2 7 | n_fc_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | 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-------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL235_EC50/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 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kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 164 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 3 7 | n_gat_layers: 2 8 | node_hidden: 512 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 228 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 3 7 | node_hidden: 512 8 | transformer_hidden: 64 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 130 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 64 3 | epochs: 58 4 | fc_hidden: 128 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 64 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | 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10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL236_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | 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-------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 3 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 75 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 0.0005 6 | n_fc_layers: 4 7 | n_gat_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 69 3 | fc_hidden: 128 4 | lr: 0.0005 5 | n_conv_layers: 5 6 | n_fc_layers: 3 7 | node_hidden: 128 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 31 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 64 4 | fc_hidden: 256 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 64 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_EC50/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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/MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/AFP_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 64 3 | hidden_channels: 256 4 | lr: 0.0005 5 | num_layers: 4 6 | num_timesteps: 2 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 19 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 223 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 3 7 | n_gat_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 64 10 | 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-------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 300 3 | fc_hidden: 256 4 | lr: 5.0e-06 5 | n_conv_layers: 5 6 | n_fc_layers: 3 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 191 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 271 4 | fc_hidden: 512 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 2 8 | node_hidden: 64 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL237_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 138 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 5 7 | n_gat_layers: 1 8 | node_hidden: 512 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 210 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 2 6 | n_fc_layers: 2 7 | node_hidden: 128 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 30 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 66 4 | fc_hidden: 512 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | 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-------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL238_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 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kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 201 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 3 7 | n_gat_layers: 4 8 | node_hidden: 512 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 142 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 4 7 | node_hidden: 256 8 | transformer_hidden: 512 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 113 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 115 4 | fc_hidden: 128 5 | lr: 5.0e-05 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL239_EC50/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.001 4 | kernel: rbf 5 | 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-------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 482 2 | hidden: 512 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 238 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 5 7 | n_gat_layers: 4 8 | node_hidden: 512 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 244 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 5 7 | node_hidden: 256 8 | transformer_hidden: 64 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 204 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 188 4 | fc_hidden: 512 5 | lr: 5.0e-06 6 | message_steps: 5 7 | n_fc_layers: 2 8 | node_hidden: 128 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 100 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL244_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 81 3 | hidden_channels: 256 4 | lr: 0.0005 5 | num_layers: 4 6 | num_timesteps: 2 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 446 2 | hidden: 512 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 174 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 3 7 | n_gat_layers: 5 8 | node_hidden: 256 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 156 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 5 7 | node_hidden: 512 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 169 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 128 3 | epochs: 250 4 | fc_hidden: 256 5 | lr: 5.0e-06 6 | message_steps: 3 7 | n_fc_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | 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-------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL262_Ki/__init__.py: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 250 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 2 8 | node_hidden: 256 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 133 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 3 7 | node_hidden: 256 8 | transformer_hidden: 512 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 191 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 64 3 | epochs: 84 4 | fc_hidden: 128 5 | lr: 0.0005 6 | message_steps: 3 7 | n_fc_layers: 3 8 | node_hidden: 128 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | 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-------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL264_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 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kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 41 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 0.0005 6 | n_fc_layers: 3 7 | n_gat_layers: 1 8 | node_hidden: 256 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 95 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 1 7 | node_hidden: 512 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 30 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 4 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/MPNN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | edge_hidden: 256 3 | epochs: 279 4 | fc_hidden: 128 5 | lr: 5.0e-06 6 | message_steps: 4 7 | n_fc_layers: 1 8 | node_hidden: 128 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 100 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10000 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.001 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/CHEMBL2835_Ki/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/AFP_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 52 3 | hidden_channels: 256 4 | lr: 0.0005 5 | num_layers: 2 6 | num_timesteps: 5 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 43 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-05 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 84 3 | fc_hidden: 128 4 | gatv2: false 5 | lr: 0.0005 6 | n_fc_layers: 2 7 | n_gat_layers: 3 8 | node_hidden: 128 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 131 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 5 6 | n_fc_layers: 1 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 31 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL287_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | epochs: 3 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 177 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 2 8 | node_hidden: 512 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 197 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 2 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 137 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 5 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL2971_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | epochs: 481 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 161 3 | fc_hidden: 512 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 1 8 | node_hidden: 512 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 190 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 3 6 | n_fc_layers: 1 7 | node_hidden: 512 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 35 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 100 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/CHEMBL3979_EC50/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/AFP_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 94 3 | hidden_channels: 128 4 | lr: 0.0005 5 | num_layers: 3 6 | num_timesteps: 5 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 4 2 | hidden: 512 3 | kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 98 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 0.0005 6 | n_fc_layers: 2 7 | n_gat_layers: 3 8 | node_hidden: 256 9 | transformer_hidden: 64 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 108 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 1 7 | node_hidden: 512 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 195 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4005_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | epochs: 298 2 | hidden: 512 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 152 3 | fc_hidden: 128 4 | gatv2: true 5 | lr: 5.0e-05 6 | n_fc_layers: 1 7 | n_gat_layers: 3 8 | node_hidden: 512 9 | transformer_hidden: 128 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 57 3 | fc_hidden: 512 4 | lr: 0.0005 5 | n_conv_layers: 5 6 | n_fc_layers: 3 7 | node_hidden: 256 8 | transformer_hidden: 256 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 31 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 3 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1000 2 | epsilon: 0.1 3 | gamma: 1.0e-05 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/CHEMBL4203_Ki/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/AFP_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 75 3 | hidden_channels: 256 4 | lr: 0.0005 5 | num_layers: 3 6 | num_timesteps: 5 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 3 2 | hidden: 256 3 | kernel_size: 4 4 | lr: 0.0005 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 56 3 | fc_hidden: 256 4 | gatv2: true 5 | lr: 0.0005 6 | n_fc_layers: 3 7 | n_gat_layers: 4 8 | node_hidden: 256 9 | transformer_hidden: 256 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 100 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 7 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 136 3 | fc_hidden: 256 4 | lr: 5.0e-05 5 | n_conv_layers: 1 6 | n_fc_layers: 3 7 | node_hidden: 256 8 | transformer_hidden: 128 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 21 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 19 3 | hidden: 1024 4 | lr: 5.0e-05 5 | n_layers: 4 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 100 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 100 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 1000 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 1000 2 | epsilon: 0.1 3 | gamma: 0.0001 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/CHEMBL4616_EC50/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/AFP_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 76 3 | hidden_channels: 256 4 | lr: 0.0005 5 | num_layers: 3 6 | num_timesteps: 4 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/CNN_SMILES.yml: -------------------------------------------------------------------------------- 1 | epochs: 232 2 | hidden: 1024 3 | kernel_size: 4 4 | lr: 5.0e-06 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GAT_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 176 3 | fc_hidden: 256 4 | gatv2: false 5 | lr: 5.0e-05 6 | n_fc_layers: 2 7 | n_gat_layers: 3 8 | node_hidden: 128 9 | transformer_hidden: 512 10 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GBM_ECFP.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 400 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GBM_MACCS.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GBM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 5 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GBM_WHIM.yml: -------------------------------------------------------------------------------- 1 | learning_rate: 0.1 2 | max_depth: 6 3 | max_features: sqrt 4 | max_leaf_nodes: null 5 | min_samples_leaf: 1 6 | min_samples_split: 2 7 | n_estimators: 200 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/GCN_GRAPH.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 99 3 | fc_hidden: 128 4 | lr: 5.0e-05 5 | n_conv_layers: 4 6 | n_fc_layers: 3 7 | node_hidden: 256 8 | transformer_hidden: 512 9 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/KNN_ECFP.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 5 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/KNN_MACCS.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/KNN_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 3 3 | weights: uniform 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/KNN_WHIM.yml: -------------------------------------------------------------------------------- 1 | metric: euclidean 2 | n_neighbors: 11 3 | weights: distance 4 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/LSTM_SMILES.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 2 | hidden_0: 1024 3 | hidden_1: 256 4 | dropout: 0.4 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/MLP_ECFP.yml: -------------------------------------------------------------------------------- 1 | dropout: 0 2 | epochs: 263 3 | hidden: 1024 4 | lr: 5.0e-06 5 | n_layers: 2 6 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/RF_ECFP.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/RF_MACCS.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/RF_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 500 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/RF_WHIM.yml: -------------------------------------------------------------------------------- 1 | n_estimators: 250 2 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/SVM_ECFP.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/SVM_MACCS.yml: -------------------------------------------------------------------------------- 1 | C: 100 2 | epsilon: 0.1 3 | gamma: 0.01 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/SVM_PHYSCHEM.yml: -------------------------------------------------------------------------------- 1 | C: 1 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/SVM_WHIM.yml: -------------------------------------------------------------------------------- 1 | C: 10 2 | epsilon: 0.1 3 | gamma: 0.1 4 | kernel: rbf 5 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/Transformer_TOKENS.yml: -------------------------------------------------------------------------------- 1 | lr: 0.0005 -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/CHEMBL4792_Ki/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/benchmark/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/benchmark/__init__.py -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/default/RF.yml: -------------------------------------------------------------------------------- 1 | # The number of trees in the forest. 2 | n_estimators: 3 | - 100 4 | - 250 5 | - 500 6 | - 1000 7 | 8 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/default/TRANSFORMER.yml: -------------------------------------------------------------------------------- 1 | #Hyperparameters for the ChemBerta Transformer regressor 2 | 3 | # N epochs with early stopping of Transformer models 4 | epochs: 100 5 | # starting learning rate 6 | lr: 0.00005 7 | -------------------------------------------------------------------------------- /MoleculeACE/Data/configures/default/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molML/MoleculeACE/7e6de0bd2968c56589c580f2a397f01c531ede26/MoleculeACE/Data/configures/default/__init__.py 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