├── .gitignore ├── EVE ├── VAE_decoder.py ├── VAE_encoder.py ├── VAE_model.py └── default_model_params.json ├── LICENSE ├── README.md ├── compute_evol_indices.py ├── data ├── MSA │ ├── P53_HUMAN_b0.1.a2m │ ├── PTEN_HUMAN_b1.0.a2m │ ├── RASH_HUMAN_b03.a2m │ └── SCN5A_HUMAN_b1.0.a2m ├── labels │ ├── ClinVar_labels_P53_PTEN_RASH_SCN5A.csv │ └── PTEN_ClinVar_labels.csv ├── mappings │ └── example_mapping.csv ├── mutations │ └── .gitkeep └── weights │ └── .gitkeep ├── examples ├── Step1_train_VAE.sh ├── Step2_compute_evol_indices_all_singles.sh └── Step3_train_GMM_and_compute_EVE_scores_all_singles.sh ├── logs └── .gitkeep ├── protein_env.yml ├── results ├── EVE_scores │ └── .gitkeep ├── GMM_parameters │ └── Default_GMM_parameters │ │ ├── GMM_model_dictionary_default │ │ └── GMM_pathogenic_cluster_index_dictionary_default ├── VAE_parameters │ └── .gitkeep ├── evol_indices │ └── .gitkeep ├── plots_histograms │ └── .gitkeep └── plots_scores_vs_labels │ └── .gitkeep ├── train_GMM_and_compute_EVE_scores.py ├── train_VAE.py └── utils ├── data_utils.py ├── default_uncertainty_threshold.json ├── performance_helpers.py └── plot_helpers.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OATML-Markslab/EVE/HEAD/.gitignore -------------------------------------------------------------------------------- /EVE/VAE_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OATML-Markslab/EVE/HEAD/EVE/VAE_decoder.py -------------------------------------------------------------------------------- /EVE/VAE_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OATML-Markslab/EVE/HEAD/EVE/VAE_encoder.py -------------------------------------------------------------------------------- /EVE/VAE_model.py: 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