{ "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 } } }