├── .gitignore ├── README.md ├── configs ├── sample_eval_config.yaml └── sample_train_config.yaml ├── data ├── cleaned_openfold_training.txt └── treebase_datasets_1533.txt ├── img └── 16S_sequences.png ├── phyla ├── __init__.py ├── data │ ├── 40seqs.fasta │ └── treebase_datasets_1533.txt ├── dataset │ └── data.py ├── dataset_info │ ├── openfold_eval_large.txt │ ├── openfold_eval_medium.txt │ ├── openfold_eval_small.txt │ ├── openfold_training.txt │ └── proteingym_eval.txt ├── env │ └── enviornment.yaml ├── eval │ ├── TreeCluster.py │ ├── evo_reasoning_eval.py │ └── proteingym_summary.csv ├── model │ ├── __init__.py │ └── model.py ├── run.sh ├── run │ ├── TrainingModule.py │ └── run.py └── utils │ ├── __init__.py │ ├── eval_configs.py │ └── utils.py ├── run_phyla_test.py ├── setup.py └── tb_analysis └── chunking.py /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__/ 2 | *.pyc 3 | 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