Add checkpoints: MetalIonBinding/**

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

@@ -0,0 +1 @@
+{"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/MetalIonBinding_ESMFold", "dataset_config": "data/MetalIonBinding/MetalIonBinding_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/MetalIonBinding/ankh-large", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

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

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4349f47222e269430d197abbf6c1414b344bee2081f1a11838a3919b8691bdc9
+size 9471074

MetalIonBinding/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.json

@@ -0,0 +1 @@
+{"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/MetalIonBinding_ESMFold", "dataset_config": "data/MetalIonBinding/MetalIonBinding_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/MetalIonBinding/esm2_t33_650M_UR50D", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

MetalIonBinding/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:856b484f678802e4dab97e5081e0aafac02831e92e5cb0358917b9461849b291
+size 6582370

MetalIonBinding/prot_bert/lr5e-4_bt12k_ga8.json

@@ -0,0 +1 @@
+{"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/MetalIonBinding_ESMFold", "dataset_config": "data/MetalIonBinding/MetalIonBinding_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/MetalIonBinding/prot_bert", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

MetalIonBinding/prot_bert/lr5e-4_bt12k_ga8.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d63b9502b995876188718be578c4a5f8b41a5fd5ee912df86797765ef8e7ab9a
+size 4217954

MetalIonBinding/prot_t5_xl_uniref50/lr5e-4_bt12k_ga8.json

@@ -0,0 +1 @@
+{"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/MetalIonBinding_ESMFold", "dataset_config": "data/MetalIonBinding/MetalIonBinding_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/MetalIonBinding/prot_t5_xl_uniref50", "wandb": false, "wandb_entity": null, "wandb_project": "VenusFactory2", "wandb_run_name": null}

MetalIonBinding/prot_t5_xl_uniref50/lr5e-4_bt12k_ga8.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a88b05a44be2d7620650131949fb3311be04d6d7335e9b8792ee5d00c083c631
+size 4217954