| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GAT/LARGE/best.pt", |
| "tokenizer_path": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Tokenizer/content_vocab.json", |
| "test_data_path": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Data/processed/test.jsonl", |
| "config": { |
| "arch": "gat", |
| "d_model": 768, |
| "hidden": 1536, |
| "num_layers": 6, |
| "num_edge_types": 10, |
| "dropout": 0.3, |
| "max_nodes": 256 |
| }, |
| "evaluation": { |
| "device": "cuda", |
| "batch_size": 128, |
| "seed": 42, |
| "num_samples": 38381, |
| "num_records": 38381, |
| "positive_records": 8678, |
| "negative_records": 29703, |
| "default_threshold": 0.5, |
| "type_method": "argmax", |
| "use_full_candidates": true, |
| "timestamp": "2026-02-26T19:43:53.960913" |
| }, |
| "edge_type_names": { |
| "1": "Amide", |
| "2": "PG_Amide", |
| "3": "Sulfanilamide", |
| "4": "Disulfide", |
| "5": "Ester", |
| "6": "Trp-Cys", |
| "7": "Lanthionin", |
| "8": "Bz_Stapled", |
| "9": "head2tail ring" |
| }, |
| "results": { |
| "overall": { |
| "loss": 0.05476830073700056, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.0037258018290299887, |
| "fast_check_fail_rate": 0.0038821291784997785, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 149 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.053007605439041254, |
| "under_connect_rate": 0.05001152339248675 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8526, |
| "fp": 788, |
| "fn": 152, |
| "tn": 28915, |
| "precision": 0.9153961777968649, |
| "recall": 0.9824844434201429, |
| "f1": 0.9477545575811471, |
| "accuracy": 0.9755087152497329, |
| "mcc": 0.9327800941717175 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12681, |
| "fp": 410, |
| "fn": 338, |
| "tn": 49218, |
| "total": 62647, |
| "precision": 0.9686807730501872, |
| "recall": 0.9740379445425916, |
| "f1": 0.9713519724243586, |
| "accuracy": 0.9880600826855237, |
| "mcc": 0.9638163537088555 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12681, |
| "total": 12681, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5027656141968195, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8163, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1183, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1087, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1301, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 3, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 13, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 912 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9878978579208519, |
| "recall": 0.9916180758017493, |
| "f1": 0.989754471051834, |
| "support": 8232, |
| "tp": 8163, |
| "fp": 100, |
| "fn": 69 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9540322580645161, |
| "recall": 0.9712643678160919, |
| "f1": 0.9625711960943856, |
| "support": 1218, |
| "tp": 1183, |
| "fp": 57, |
| "fn": 35 |
| }, |
| { |
| "class_id": 3, |
| "class_name": "Sulfanilamide", |
| "precision": 0.9, |
| "recall": 1.0, |
| "f1": 0.9473684210526316, |
| "support": 9, |
| "tp": 9, |
| "fp": 1, |
| "fn": 0 |
| }, |
| { |
| "class_id": 4, |
| "class_name": "Disulfide", |
| "precision": 0.9211864406779661, |
| "recall": 0.9526730937773883, |
| "f1": 0.9366652305040931, |
| "support": 1141, |
| "tp": 1087, |
| "fp": 93, |
| "fn": 54 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9299499642601858, |
| "recall": 0.9524158125915081, |
| "f1": 0.9410488245931283, |
| "support": 1366, |
| "tp": 1301, |
| "fp": 98, |
| "fn": 65 |
| }, |
| { |
| "class_id": 6, |
| "class_name": "Trp-Cys", |
| "precision": 0.6, |
| "recall": 1.0, |
| "f1": 0.7499999999999999, |
| "support": 3, |
| "tp": 3, |
| "fp": 2, |
| "fn": 0 |
| }, |
| { |
| "class_id": 7, |
| "class_name": "Lanthionin", |
| "precision": 0.8666666666666667, |
| "recall": 0.7647058823529411, |
| "f1": 0.8125, |
| "support": 17, |
| "tp": 13, |
| "fp": 2, |
| "fn": 4 |
| }, |
| { |
| "class_id": 8, |
| "class_name": "Bz_Stapled", |
| "precision": 0.9090909090909091, |
| "recall": 1.0, |
| "f1": 0.9523809523809523, |
| "support": 10, |
| "tp": 10, |
| "fp": 1, |
| "fn": 0 |
| }, |
| { |
| "class_id": 9, |
| "class_name": "head2tail ring", |
| "precision": 0.9421487603305785, |
| "recall": 0.8914956011730205, |
| "f1": 0.9161225514816673, |
| "support": 1023, |
| "tp": 912, |
| "fp": 56, |
| "fn": 111 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8901080952235192, |
| "recall": 0.9471303148347443, |
| "f1": 0.912045738573188, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9686807730501872, |
| "recall": 0.9740379445425916, |
| "f1": 0.9713519724243586, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 143, |
| "fast_check_fail": 149, |
| "ok": 8386 |
| } |
| } |
| } |