├── .gitignore ├── LICENSE ├── README.md ├── blat_class_A1A2_experiments.ipynb ├── distances.ipynb ├── models ├── geoml │ ├── __init__.py │ ├── curve.py │ ├── discretized_manifold.py │ ├── geodesics.py │ └── manifold.py └── vae_geometric.py ├── scripts ├── blat_class_A1A2_preprocessing.py └── needleman_wunsch.py └── tape ├── .ipynb_checkpoints └── Representation visuzalization-checkpoint.ipynb ├── LICENSE ├── MANIFEST.in ├── PF00144_full.txt ├── PF00144_full_length_sequences_labeled.fasta ├── README.md ├── Representation_visuzalization.ipynb ├── cleanup_results.sh ├── config ├── resnet_config.json ├── transformer_config.json └── transformer_tiny_config.json ├── data └── unilanguage │ └── combine_data.py ├── data_refs.bib ├── download_data.sh ├── download_data_aws.sh ├── embeddings ├── labels.npy ├── lstm_all.npy ├── lstm_beta.npy ├── resnet_all.npy ├── resnet_beta.npy ├── transformer_all.npy └── transformer_beta.npy ├── environment.yml ├── example.fasta ├── examples ├── adding_model.py └── adding_task.py ├── gridsearch_config.json ├── mypy.ini ├── requirements.txt ├── scripts ├── fix_lmdb.py ├── generate_plots.py ├── lmdb_to_fasta.py ├── tfrecord_to_json.py └── tfrecord_to_lmdb.py ├── setup.py ├── tape ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── datasets.cpython-38.pyc │ ├── errors.cpython-38.pyc │ ├── main.cpython-38.pyc │ ├── metrics.cpython-38.pyc │ ├── optimization.cpython-38.pyc │ ├── registry.cpython-38.pyc │ ├── tokenizers.cpython-38.pyc │ ├── training.cpython-38.pyc │ └── visualization.cpython-38.pyc ├── datasets.py ├── errors.py ├── main.py ├── metrics.py ├── models │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── file_utils.cpython-38.pyc │ │ ├── modeling_autoencoder.cpython-38.pyc │ │ ├── modeling_bert.cpython-38.pyc │ │ ├── modeling_bottleneck.cpython-38.pyc │ │ ├── modeling_lstm.cpython-38.pyc │ │ ├── modeling_onehot.cpython-38.pyc │ │ ├── modeling_resnet.cpython-38.pyc │ │ ├── modeling_trrosetta.cpython-38.pyc │ │ ├── modeling_unirep.cpython-38.pyc │ │ └── modeling_utils.cpython-38.pyc │ ├── file_utils.py │ ├── modeling_autoencoder.py │ ├── modeling_bert.py │ ├── modeling_bottleneck.py │ ├── modeling_lstm.py │ ├── modeling_onehot.py │ ├── modeling_resnet.py │ ├── modeling_trrosetta.py │ ├── modeling_unirep.py │ └── modeling_utils.py ├── optimization.py ├── registry.py ├── tokenizers.py ├── training.py ├── utils │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── _sampler.cpython-38.pyc │ │ ├── distributed_utils.cpython-38.pyc │ │ ├── setup_utils.cpython-38.pyc │ │ └── utils.cpython-38.pyc │ ├── _sampler.py │ ├── distributed_utils.py │ ├── setup_utils.py │ └── utils.py └── visualization.py ├── tape_proteins.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── requires.txt └── top_level.txt ├── tests ├── test_basic.py └── test_forceDownload.py └── tox.ini /.gitignore: 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