├── LICENSE ├── README.md ├── deepspeed.py ├── dp_config.json ├── gen_onto_protein_data.py ├── requirements.txt ├── resources ├── .DS_Store └── img │ ├── .DS_Store │ ├── main.jpg │ ├── model.png │ └── times.png ├── run_downstream.py ├── run_main.sh ├── run_pretrain.py ├── script ├── run_contact.sh ├── run_fluorescence.sh ├── run_pretrain.sh ├── run_remote_homology.sh ├── run_ss3.sh ├── run_ss8.sh └── run_stability.sh └── src ├── __pycache__ ├── dataloader.cpython-37.pyc ├── dataloader.cpython-38.pyc ├── dataset.cpython-37.pyc ├── dataset.cpython-38.pyc ├── model_configuration.cpython-37.pyc ├── models.cpython-37.pyc ├── models.cpython-38.pyc ├── op_deepspeed.cpython-37.pyc ├── op_deepspeed.cpython-38.pyc ├── optimization.cpython-37.pyc ├── optimization.cpython-38.pyc ├── sampling.cpython-37.pyc ├── sampling.cpython-38.pyc ├── trainer.cpython-37.pyc ├── trainer.cpython-38.pyc ├── training_args.cpython-37.pyc └── training_args.cpython-38.pyc ├── benchmark ├── GNN_PPI │ ├── convert.py │ 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