├── .gitignore ├── LICENSE ├── README.md ├── config └── config.yml ├── example_notebook.ipynb ├── main.py ├── results ├── KaplanMeier_TCGA-BRCA.png ├── shap_CNV_Basal.png ├── shap_CNV_Her2.png ├── shap_CNV_LumA.png ├── shap_CNV_LumB.png ├── shap_methyl_Basal.png ├── shap_methyl_Her2.png ├── shap_methyl_LumA.png └── shap_methyl_LumB.png ├── splits ├── PANCAN │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── TCGA-BLCA │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── TCGA-BRCA │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── TCGA-GBM │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── TCGA-LUAD │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── TCGA-OV │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt └── TCGA-UCEC │ ├── split_test_1.txt │ ├── split_test_2.txt │ ├── split_test_3.txt │ ├── split_test_4.txt │ ├── split_test_5.txt │ ├── split_train_1.txt │ ├── split_train_2.txt │ ├── split_train_3.txt │ ├── split_train_4.txt │ ├── split_train_5.txt │ ├── split_val_1.txt │ ├── split_val_2.txt │ ├── split_val_3.txt │ ├── split_val_4.txt │ └── split_val_5.txt ├── src ├── config │ └── samples.txt ├── datasets │ └── multi_omics_dataset.py ├── debug │ └── print_layer.py ├── decoders │ ├── decoder.py │ └── probabilistic_decoder.py ├── encoders │ ├── encoder.py │ └── probabilistic_encoder.py ├── ex_vae │ └── shap_vae.py ├── loss │ ├── classification_loss.py │ ├── consensus_loss.py │ ├── mmd_loss.py │ └── survival_loss.py ├── metrics │ ├── classification.py │ └── survival.py ├── models │ ├── autoencoder.py │ └── vae.py ├── network │ └── customics.py ├── tasks │ ├── classification.py │ └── survival.py └── tools │ ├── core_utils.py │ ├── net_utils.py │ ├── prepare_dataset.py │ └── utils.py └── toy_data ├── gene_exp.txt ├── labels.txt ├── methyl.txt └── protein.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HakimBenkirane/CustOmics/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HakimBenkirane/CustOmics/HEAD/LICENSE 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