| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GCN/SMALL/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": "gcn", |
| "d_model": 384, |
| "hidden": 768, |
| "num_layers": 3, |
| "num_edge_types": 10, |
| "dropout": 0.2, |
| "max_nodes": 256 |
| }, |
| "evaluation": { |
| "device": "cuda", |
| "batch_size": 512, |
| "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": "2026-02-26T17:22:23.611900" |
| }, |
| "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": 0.03621956246740826, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.003699747270785024, |
| "fast_check_fail_rate": 0.0031004924311508297, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 119 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.06614427287393408, |
| "under_connect_rate": 0.04805254666973957 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8438, |
| "fp": 635, |
| "fn": 240, |
| "tn": 29068, |
| "precision": 0.9300121238840516, |
| "recall": 0.9723438580318046, |
| "f1": 0.9507070024223988, |
| "accuracy": 0.9772022615356557, |
| "mcc": 0.9362810126299366 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12701, |
| "fp": 731, |
| "fn": 318, |
| "tn": 48897, |
| "total": 62647, |
| "precision": 0.945577724836212, |
| "recall": 0.9755741608418466, |
| "f1": 0.9603417640164833, |
| "accuracy": 0.9832553833383881, |
| "mcc": 0.9499183022379412 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12701, |
| "total": 12701, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5198202350772068, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8154, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1191, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1109, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1310, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 3, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 11, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 904 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.981699975921021, |
| "recall": 0.9905247813411079, |
| "f1": 0.9860926351433065, |
| "support": 8232, |
| "tp": 8154, |
| "fp": 152, |
| "fn": 78 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9189814814814815, |
| "recall": 0.9778325123152709, |
| "f1": 0.9474940334128878, |
| "support": 1218, |
| "tp": 1191, |
| "fp": 105, |
| "fn": 27 |
| }, |
| { |
| "class_id": 3, |
| "class_name": "Sulfanilamide", |
| "precision": 0.8181818181818182, |
| "recall": 1.0, |
| "f1": 0.9, |
| "support": 9, |
| "tp": 9, |
| "fp": 2, |
| "fn": 0 |
| }, |
| { |
| "class_id": 4, |
| "class_name": "Disulfide", |
| "precision": 0.8472116119174943, |
| "recall": 0.971954425942156, |
| "f1": 0.9053061224489796, |
| "support": 1141, |
| "tp": 1109, |
| "fp": 200, |
| "fn": 32 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.8991077556623198, |
| "recall": 0.95900439238653, |
| "f1": 0.9280906836698548, |
| "support": 1366, |
| "tp": 1310, |
| "fp": 147, |
| "fn": 56 |
| }, |
| { |
| "class_id": 6, |
| "class_name": "Trp-Cys", |
| "precision": 0.5, |
| "recall": 1.0, |
| "f1": 0.6666666666666666, |
| "support": 3, |
| "tp": 3, |
| "fp": 3, |
| "fn": 0 |
| }, |
| { |
| "class_id": 7, |
| "class_name": "Lanthionin", |
| "precision": 0.9166666666666666, |
| "recall": 0.6470588235294118, |
| "f1": 0.7586206896551724, |
| "support": 17, |
| "tp": 11, |
| "fp": 1, |
| "fn": 6 |
| }, |
| { |
| "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": 0.8828125, |
| "recall": 0.8836754643206256, |
| "f1": 0.8832437713727406, |
| "support": 1023, |
| "tp": 904, |
| "fp": 120, |
| "fn": 119 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8526391909913013, |
| "recall": 0.9366722666483446, |
| "f1": 0.8808772838611735, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.945577724836212, |
| "recall": 0.9755741608418466, |
| "f1": 0.9603417640164833, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 142, |
| "fast_check_fail": 119, |
| "ok": 8417 |
| } |
| } |
| } |