├── LICENSE ├── README.md ├── data ├── LINCS2020 │ ├── data_example │ │ ├── ECFP4_emb2048.pickle │ │ ├── KPGT_emb2304.pickle │ │ ├── processed_data.h5 │ │ └── processed_data_id.h5 │ ├── geneinfo_processed.csv │ ├── idx2smi.pickle │ ├── landmark_geneinfo.csv │ ├── modz_x1.pickle │ ├── processed_data_id.h5 │ ├── same_random_split │ │ ├── test.h5 │ │ ├── train.h5 │ │ └── valid.h5 │ ├── same_smiles_split │ │ ├── test.h5 │ │ ├── test_external.h5 │ │ ├── train.h5 │ │ └── valid.h5 │ └── test.h5 ├── PRISM │ ├── KPGT_emb2304.pickle │ ├── screening_compound.csv │ └── smi2idx.pickle └── TranSiGen.jpg ├── requirements.txt ├── results ├── 5.Drug_response_prediction │ ├── data.csv │ └── grid_search_param.csv ├── 6.Phenotype_based_drug_repurposing │ ├── DEGs_approved_drugs.csv │ ├── DEGs_disease.csv │ └── approved_drugs.csv ├── trained_model_shRNA_vae_x1 │ └── best_model.pt ├── trained_model_shRNA_vae_x2 │ └── best_model.pt └── trained_models_164_cell_smiles_split │ └── 364039 │ └── 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