{ "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 } } }