Add checkpoints: ProtSolM/**

ProtSolM/ankh-large/lr5e-4_bt12k_ga8.json

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+{"hidden_size": 1536, "num_attention_head": 8, "attention_probs_dropout": 0.1, "plm_model": "ElnaggarLab/ankh-large", "pooling_method": "mean", "pooling_dropout": 0.1, "dataset": "tyang816/ProtSolM", "dataset_config": "data/ProtSolM/ProtSolM_HF.json", "normalize": null, "num_labels": 2, "problem_type": "single_label_classification", "pdb_type": null, "train_file": null, "valid_file": null, "test_file": null, "metrics": ["accuracy", "mcc", "f1", "precision", "recall", "auroc"], "seed": 3407, "learning_rate": 0.0005, "scheduler": null, "warmup_steps": 0, "num_workers": 4, "batch_size": null, "batch_token": 12000, "num_epochs": 100, "max_seq_len": -1, "gradient_accumulation_steps": 8, "max_grad_norm": -1, "patience": 10, "monitor": "accuracy", "monitor_strategy": "max", "training_method": "freeze", "structure_seq": [], "output_model_name": "lr5e-4_bt12k_ga8.pt", "output_root": "ckpt", "output_dir": "ckpt/ProtSolM/ankh-large", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

ProtSolM/ankh-large/lr5e-4_bt12k_ga8.pt

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ProtSolM/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.json

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+{"hidden_size": 1280, "num_attention_head": 8, "attention_probs_dropout": 0.1, "plm_model": "facebook/esm2_t33_650M_UR50D", "pooling_method": "mean", "pooling_dropout": 0.1, "dataset": "tyang816/ProtSolM", "dataset_config": "data/ProtSolM/ProtSolM_HF.json", "normalize": null, "num_labels": 2, "problem_type": "single_label_classification", "pdb_type": null, "train_file": null, "valid_file": null, "test_file": null, "metrics": ["accuracy", "mcc", "f1", "precision", "recall", "auroc"], "seed": 3407, "learning_rate": 0.0005, "scheduler": null, "warmup_steps": 0, "num_workers": 4, "batch_size": null, "batch_token": 12000, "num_epochs": 100, "max_seq_len": -1, "gradient_accumulation_steps": 8, "max_grad_norm": -1, "patience": 10, "monitor": "accuracy", "monitor_strategy": "max", "training_method": "freeze", "structure_seq": [], "output_model_name": "lr5e-4_bt12k_ga8.pt", "output_root": "ckpt", "output_dir": "ckpt/ProtSolM/esm2_t33_650M_UR50D", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

ProtSolM/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.pt

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ProtSolM/prot_bert/lr5e-4_bt12k_ga8.json

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+{"hidden_size": 1024, "num_attention_head": 8, "attention_probs_dropout": 0.1, "plm_model": "RostLab/prot_bert", "pooling_method": "mean", "pooling_dropout": 0.1, "dataset": "tyang816/ProtSolM", "dataset_config": "data/ProtSolM/ProtSolM_HF.json", "normalize": null, "num_labels": 2, "problem_type": "single_label_classification", "pdb_type": null, "train_file": null, "valid_file": null, "test_file": null, "metrics": ["accuracy", "mcc", "f1", "precision", "recall", "auroc"], "seed": 3407, "learning_rate": 0.0005, "scheduler": null, "warmup_steps": 0, "num_workers": 4, "batch_size": null, "batch_token": 12000, "num_epochs": 100, "max_seq_len": -1, "gradient_accumulation_steps": 8, "max_grad_norm": -1, "patience": 10, "monitor": "accuracy", "monitor_strategy": "max", "training_method": "freeze", "structure_seq": [], "output_model_name": "lr5e-4_bt12k_ga8.pt", "output_root": "ckpt", "output_dir": "ckpt/ProtSolM/prot_bert", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

ProtSolM/prot_bert/lr5e-4_bt12k_ga8.pt

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ProtSolM/prot_t5_xl_uniref50/lr5e-4_bt12k_ga8.json

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+{"hidden_size": 1024, "num_attention_head": 8, "attention_probs_dropout": 0.1, "plm_model": "RostLab/prot_t5_xl_uniref50", "pooling_method": "mean", "pooling_dropout": 0.1, "dataset": "tyang816/ProtSolM", "dataset_config": "data/ProtSolM/ProtSolM_HF.json", "normalize": null, "num_labels": 2, "problem_type": "single_label_classification", "pdb_type": null, "train_file": null, "valid_file": null, "test_file": null, "metrics": ["accuracy", "mcc", "f1", "precision", "recall", "auroc"], "seed": 3407, "learning_rate": 0.0005, "scheduler": null, "warmup_steps": 0, "num_workers": 4, "batch_size": null, "batch_token": 12000, "num_epochs": 100, "max_seq_len": -1, "gradient_accumulation_steps": 8, "max_grad_norm": -1, "patience": 10, "monitor": "accuracy", "monitor_strategy": "max", "training_method": "freeze", "structure_seq": [], "output_model_name": "lr5e-4_bt12k_ga8.pt", "output_root": "ckpt", "output_dir": "ckpt/ProtSolM/prot_t5_xl_uniref50", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

ProtSolM/prot_t5_xl_uniref50/lr5e-4_bt12k_ga8.pt

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