| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/MPNN/MEDIUM/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": "mpnn", |
| "d_model": 512, |
| "hidden": 1024, |
| "num_layers": 4, |
| "num_edge_types": 10, |
| "dropout": 0.25, |
| "max_nodes": 256 |
| }, |
| "evaluation": { |
| "device": "cuda", |
| "batch_size": 256, |
| "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": "2026-02-26T19:59:47.342516" |
| }, |
| "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": 0.05696277729753433, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.003647638154295094, |
| "fast_check_fail_rate": 0.003439201688335374, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 132 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.054044710762848586, |
| "under_connect_rate": 0.048743950218944454 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8504, |
| "fp": 821, |
| "fn": 174, |
| "tn": 28882, |
| "precision": 0.9119571045576408, |
| "recall": 0.9799492970730583, |
| "f1": 0.9447314336499473, |
| "accuracy": 0.9740757145462599, |
| "mcc": 0.9288498849968012 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12680, |
| "fp": 501, |
| "fn": 339, |
| "tn": 49127, |
| "total": 62647, |
| "precision": 0.9619907442530916, |
| "recall": 0.9739611337276288, |
| "f1": 0.96793893129771, |
| "accuracy": 0.9865915367056682, |
| "mcc": 0.9594918638564396 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12680, |
| "total": 12680, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5051855266190366, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8159, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1190, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1082, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1304, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 3, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 12, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 911 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9865779927448609, |
| "recall": 0.9911321671525753, |
| "f1": 0.9888498363834687, |
| "support": 8232, |
| "tp": 8159, |
| "fp": 111, |
| "fn": 73 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9384858044164038, |
| "recall": 0.9770114942528736, |
| "f1": 0.9573612228479486, |
| "support": 1218, |
| "tp": 1190, |
| "fp": 78, |
| "fn": 28 |
| }, |
| { |
| "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": 0.902418682235196, |
| "recall": 0.9482909728308502, |
| "f1": 0.9247863247863248, |
| "support": 1141, |
| "tp": 1082, |
| "fp": 117, |
| "fn": 59 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.919605077574048, |
| "recall": 0.9546120058565154, |
| "f1": 0.9367816091954023, |
| "support": 1366, |
| "tp": 1304, |
| "fp": 114, |
| "fn": 62 |
| }, |
| { |
| "class_id": 6, |
| "class_name": "Trp-Cys", |
| "precision": 0.75, |
| "recall": 1.0, |
| "f1": 0.8571428571428571, |
| "support": 3, |
| "tp": 3, |
| "fp": 1, |
| "fn": 0 |
| }, |
| { |
| "class_id": 7, |
| "class_name": "Lanthionin", |
| "precision": 0.8571428571428571, |
| "recall": 0.7058823529411765, |
| "f1": 0.7741935483870968, |
| "support": 17, |
| "tp": 12, |
| "fp": 2, |
| "fn": 5 |
| }, |
| { |
| "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": 0.922998986828774, |
| "recall": 0.8905180840664711, |
| "f1": 0.9064676616915422, |
| "support": 1023, |
| "tp": 911, |
| "fp": 76, |
| "fn": 112 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8984800344481165, |
| "recall": 0.9408274530111626, |
| "f1": 0.9161480482075804, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9619907442530916, |
| "recall": 0.9739611337276288, |
| "f1": 0.96793893129771, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 140, |
| "fast_check_fail": 132, |
| "ok": 8406 |
| } |
| } |
| } |
