├── .gitattributes ├── .gitignore ├── Image └── DeepHop.jpg ├── LICENSE ├── README.md ├── data ├── cond-test.txt ├── cond-train.txt ├── cond-val.txt ├── src-test.txt ├── src-train.txt ├── src-val.txt ├── tgt-test.txt ├── tgt-train.txt └── tgt-val.txt ├── deephop ├── Graph3dConv.py ├── calc_SC_RDKit.py ├── calc_scaffold_smilarity.py ├── data_loader.py ├── env.yaml ├── graph_embedding.py ├── make_pair.py ├── onmt │ ├── GAT.py │ ├── GATGATE.py │ ├── GCN.py │ ├── MPNNs │ │ ├── MPNN.py │ │ ├── MPNNv2.py │ │ ├── MPNNv3.py │ │ ├── MessageFunction.py │ │ ├── UpdateFunction.py │ │ └── nnet.py │ ├── MYGCN.py │ ├── __init__.py │ ├── decoders │ │ ├── __init__.py │ │ ├── cnn_decoder.py │ │ ├── decoder.py │ │ ├── ensemble.py │ │ └── transformer.py │ ├── encoders │ │ ├── __init__.py │ │ ├── audio_encoder.py │ │ ├── cnn_encoder.py │ │ ├── encoder.py │ │ ├── image_encoder.py │ │ ├── mean_encoder.py │ │ ├── rnn_encoder.py │ │ └── transformer.py │ ├── inputters │ │ ├── __init__.py │ │ ├── audio_dataset.py │ │ ├── dataset_base.py │ │ ├── image_dataset.py │ │ ├── inputter.py │ │ └── text_dataset.py │ ├── model_builder.py │ ├── models │ │ ├── __init__.py │ │ ├── model.py │ │ ├── model_saver.py │ │ ├── sru.py │ │ └── stacked_rnn.py │ ├── modules │ │ ├── __init__.py │ │ ├── average_attn.py │ │ ├── conv_multi_step_attention.py │ │ ├── copy_generator.py │ │ ├── embeddings.py │ │ ├── gate.py │ │ ├── global_attention.py │ │ ├── multi_headed_attn.py │ │ ├── position_ffn.py │ │ ├── sparse_activations.py │ │ ├── sparse_losses.py │ │ ├── structured_attention.py │ │ ├── util_class.py │ │ └── weight_norm.py │ ├── myutils.py │ ├── opts.py │ ├── tests │ │ ├── output_hyp.txt │ │ ├── pull_request_chk.sh │ │ ├── rebuild_test_models.sh │ │ ├── test_attention.py │ │ ├── test_models.py │ │ ├── test_models.sh │ │ ├── test_preprocess.py │ │ └── test_simple.py │ ├── train_single.py │ ├── trainer.py │ ├── translate │ │ ├── __init__.py │ │ ├── beam.py │ │ ├── penalties.py │ │ ├── translation.py │ │ ├── translation_server.py │ │ └── translator.py │ └── utils │ │ ├── __init__.py │ │ ├── cnn_factory.py │ │ ├── distributed.py │ │ ├── logging.py │ │ ├── loss.py │ │ ├── masking.py │ │ ├── misc.py │ │ ├── optimizers.py │ │ ├── report_manager.py │ │ ├── rnn_factory.py │ │ └── statistics.py ├── preprocess.py ├── protein_emb.pkl ├── pvalue_score_predictions.py ├── replace_torchtext │ ├── batch.py │ ├── field.py │ └── iterator.py ├── split_data.py ├── train.py └── translate.py ├── known_pvalue_data ├── CHEMBL1868.csv ├── CHEMBL1906.csv ├── CHEMBL1907601.csv ├── CHEMBL1907602.csv ├── CHEMBL1974.csv ├── CHEMBL2094127.csv ├── CHEMBL2095191.csv ├── CHEMBL2111367.csv ├── CHEMBL2147.csv ├── CHEMBL2148.csv ├── CHEMBL2276.csv ├── CHEMBL2431.csv ├── CHEMBL2534.csv ├── CHEMBL258.csv ├── CHEMBL2637.csv ├── CHEMBL267.csv ├── CHEMBL2695.csv ├── CHEMBL2828.csv ├── CHEMBL2835.csv ├── CHEMBL2850.csv ├── CHEMBL299.csv ├── CHEMBL3130.csv ├── CHEMBL3145.csv ├── CHEMBL3231.csv ├── CHEMBL3234.csv ├── CHEMBL3267.csv ├── CHEMBL3529.csv ├── CHEMBL3582.csv ├── CHEMBL3650.csv ├── CHEMBL3778.csv ├── CHEMBL3788.csv ├── CHEMBL3861.csv ├── CHEMBL3905.csv ├── CHEMBL4005.csv ├── CHEMBL4203.csv ├── CHEMBL4204.csv ├── CHEMBL4247.csv ├── CHEMBL4501.csv ├── CHEMBL4523.csv ├── CHEMBL4578.csv ├── CHEMBL4722.csv ├── CHEMBL4816.csv ├── CHEMBL4898.csv ├── CHEMBL5145.csv ├── CHEMBL5407.csv └── CHEMBL5543.csv └── score ├── data_loader.py ├── env.yaml ├── evaluate.py ├── mtdnn.py ├── summary_one_task.py ├── total_mtr ├── seed0 │ ├── checkpoint │ ├── ckpt-43.data-00000-of-00002 │ ├── ckpt-43.data-00001-of-00002 │ └── ckpt-43.index ├── seed1 │ ├── checkpoint │ ├── ckpt-53.data-00000-of-00002 │ ├── ckpt-53.data-00001-of-00002 │ └── ckpt-53.index └── seed2 │ ├── checkpoint │ ├── ckpt-37.data-00000-of-00002 │ ├── ckpt-37.data-00001-of-00002 │ └── ckpt-37.index ├── train.py └── util.py /.gitattributes: -------------------------------------------------------------------------------- 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