├── .amltignore ├── .github └── workflows │ └── codeql.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── amlt_config.yml ├── amlt_config_ablations.yml ├── bin ├── calculate_supervised_metrics.py ├── create_test_sets.py ├── download_EC_annotations.py ├── download_GO_annotations.py ├── download_and_test_multiple_proteinfer_seeds.sh ├── download_and_test_proteinfer_seeds.py ├── download_swissprot.py ├── export_proteinfer.py ├── generate_label_embeddings.py ├── main.py ├── make_dataset_from_swissprot.py ├── make_proteinfer_dataset.py ├── make_zero_shot_datasets_from_proteinfer.py ├── run_baseline.py ├── run_blast.py ├── test_ablation.sh ├── test_models.py ├── test_proteinfer.py ├── umap_plots.py ├── update_go_annotations.py └── upload_to_zenodo.py ├── configs └── base_config.yaml ├── docs └── .gitkeep ├── environment.yml ├── hyperdrive_seed_replicates.yml ├── img ├── main_fig.jpg └── main_fig.pdf ├── model_card.md ├── notebooks ├── GOAnnotationsPerYear.ipynb ├── Gene Ontology Data Archive.html └── Results.ipynb ├── proteinfer_conda_requirements.yml ├── protnote ├── .gitkeep ├── __init__.py ├── data │ ├── __init__.py │ ├── collators.py │ ├── datasets.py │ └── samplers.py ├── models │ ├── ProtNote.py │ ├── ProtNoteTrainer.py │ ├── __init__.py │ ├── blast.py │ └── protein_encoders.py └── utils │ ├── __init__.py │ ├── configs.py │ ├── data.py │ ├── evaluation.py │ ├── losses.py │ ├── main_utils.py │ ├── models.py │ ├── notebooks.py │ └── proteinfer.py ├── pyproject.toml ├── setup.py └── singularity_image ├── Dockerfile └── build_image.sh /.amltignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/protnote/HEAD/.amltignore -------------------------------------------------------------------------------- /.github/workflows/codeql.yml: -------------------------------------------------------------------------------- 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