├── .github └── workflows │ ├── deploy.yaml │ └── test.yaml ├── .gitignore ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── ProtMamba_ssm ├── __init__.py ├── dataloaders.py ├── fim.py ├── modules.py ├── trainer.py └── utils.py ├── README.html ├── README.md ├── README_files └── libs │ ├── bootstrap │ ├── bootstrap-icons.css │ ├── bootstrap-icons.woff │ ├── bootstrap.min.css │ └── bootstrap.min.js │ ├── clipboard │ └── clipboard.min.js │ └── quarto-html │ ├── anchor.min.js │ ├── popper.min.js │ ├── quarto-syntax-highlighting.css │ ├── quarto.js │ ├── tippy.css │ └── tippy.umd.min.js ├── configs ├── default_config.yaml └── default_config_fim-finetuning.yaml ├── data ├── cluster_testing_set.txt ├── cluster_training_set.txt ├── example_msa.a3m ├── example_pretrained_model │ ├── config.json │ ├── optimizer.pt │ ├── pytorch_model.bin │ ├── rng_state.pth │ ├── scheduler.pt │ └── trainer_state.json └── logo.jpeg ├── requirements.txt ├── settings.ini ├── setup.py ├── tests ├── generation │ ├── figures_sampled_sequences.ipynb │ ├── sample_sequences.ipynb │ ├── score_sequences.ipynb │ └── test_model.ipynb ├── proteingym │ ├── mmseqs_search.py │ ├── nb_proteingym.ipynb │ └── proteingym.py └── utils.py └── train.py /.github/workflows/deploy.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bitbol-Lab/ProtMamba-ssm/HEAD/.github/workflows/deploy.yaml -------------------------------------------------------------------------------- /.github/workflows/test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bitbol-Lab/ProtMamba-ssm/HEAD/.github/workflows/test.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bitbol-Lab/ProtMamba-ssm/HEAD/.gitignore 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