├── .gitignore ├── .project-root ├── README.md ├── ckpt ├── AAV │ ├── mutations_0 │ │ └── percentile_0.0_1.0 │ │ │ ├── cnn_oracle.ckpt │ │ │ └── config.yaml │ ├── mutations_6 │ │ └── percentile_0.2_0.4 │ │ │ ├── tik-gamma-1_smoothed │ │ │ └── ham1_n-250K │ │ │ │ ├── config.yaml │ │ │ │ └── predictor.ckpt │ │ │ └── unsmoothed │ │ │ └── predictor │ │ │ ├── config.yaml │ │ │ └── predictor.ckpt │ └── mutations_7 │ │ └── percentile_0.0_0.3 │ │ ├── tik-gamma-1_smoothed │ │ └── ham1_n-250K │ │ │ ├── config.yaml │ │ │ └── predictor.ckpt │ │ └── unsmoothed │ │ └── predictor │ │ ├── config.yaml │ │ └── predictor.ckpt └── GFP │ ├── mutations_0 │ └── percentile_0.0_1.0 │ │ ├── cnn_oracle.ckpt │ │ └── config.yaml │ ├── mutations_6 │ └── percentile_0.2_0.4 │ │ ├── tik-gamma-1_smoothed │ │ └── ham1_n-250K │ │ │ ├── config.yaml │ │ │ └── predictor.ckpt │ │ └── unsmoothed │ │ └── predictor │ │ ├── config.yaml │ │ └── predictor.ckpt │ └── mutations_7 │ └── percentile_0.0_0.3 │ ├── tik-gamma-1_smoothed │ └── ham1_n-250K │ │ ├── config.yaml │ │ └── predictor.ckpt │ └── unsmoothed │ └── predictor │ ├── config.yaml │ └── predictor.ckpt ├── configs ├── GS.yaml ├── GWG.yaml ├── __init__.py ├── evaluate.yaml ├── experiment │ ├── evaluate │ │ ├── AAV-hard-smoothed.yaml │ │ ├── AAV-hard-unsmoothed.yaml │ │ ├── AAV-medium-smoothed.yaml │ │ ├── AAV-medium-unsmoothed.yaml │ │ ├── GFP-hard-smoothed.yaml │ │ ├── GFP-hard-unsmoothed.yaml │ │ ├── GFP-medium-smoothed.yaml │ │ └── GFP-medium-unsmoothed.yaml │ ├── generate │ │ ├── AAV-hard-smoothed.yaml │ │ ├── AAV-hard-unsmoothed.yaml │ │ ├── AAV-medium-smoothed.yaml │ │ ├── AAV-medium-unsmoothed.yaml │ │ ├── GFP-hard-smoothed.yaml │ │ ├── GFP-hard-unsmoothed.yaml │ │ ├── GFP-medium-smoothed.yaml │ │ └── GFP-medium-unsmoothed.yaml │ ├── smooth │ │ ├── AAV-hard.yaml │ │ ├── AAV-medium.yaml │ │ ├── GFP-hard.yaml │ │ └── GFP-medium.yaml │ └── train │ │ ├── AAV-hard-smoothed.yaml │ │ ├── AAV-hard-unsmoothed.yaml │ │ ├── AAV-medium-smoothed.yaml │ │ ├── AAV-medium-unsmoothed.yaml │ │ ├── AAV-oracle.yaml │ │ ├── GFP-hard-smoothed.yaml │ │ ├── GFP-hard-unsmoothed.yaml │ │ ├── GFP-medium-smoothed.yaml │ │ ├── GFP-medium-unsmoothed.yaml │ │ └── GFP-oracle.yaml ├── extras │ ├── default.yaml │ └── hydra │ │ └── default.yaml ├── paths │ └── default.yaml └── train_predictor.yaml ├── data ├── AAV │ └── ground_truth.csv └── GFP │ └── ground_truth.csv ├── environment.yaml ├── ggs ├── GS.py ├── GWG.py ├── __init__.py ├── data │ ├── __init__.py │ ├── data_module.py │ ├── predictor_data_module.py │ ├── sequence_dataset.py │ └── utils │ │ ├── __init__.py │ │ └── tokenize.py ├── evaluate.py ├── models │ ├── GWG_module.py │ ├── __init__.py │ ├── predictor_module.py │ └── predictors.py ├── train_predictor.py └── utils │ ├── __init__.py │ ├── instantiators.py │ ├── logging_utils.py │ ├── pylogger.py │ ├── rich_utils.py │ └── utils.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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