{ "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GAT/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": "gat", "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": "2026-02-26T17:24:34.864721" }, "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": 0.0371660907295146, "total_edges_evaluated": 62647, "total_graphs": 38381, "missing_required_connection_rate": 0.004064511086214534, "fast_check_fail_rate": 0.0033349834553555143, "fast_check_fail_reasons": { "blocks_disconnected": 128 }, "gt_edge_count_mean": 1.500230467849735, "over_connect_rate": 0.05957593915648767, "under_connect_rate": 0.049550587693016825 }, "head1_graph_gate": { "description": "Graph-level: does this molecule need special connections?", "threshold": 0.5, "tp": 8474, "fp": 578, "fn": 204, "tn": 29125, "precision": 0.9361467079098542, "recall": 0.9764922793270339, "f1": 0.9558939650310209, "accuracy": 0.9796253354524374, "mcc": 0.9430093039478985 }, "head2_edge_exist": { "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", "threshold": 0.5, "tp": 12679, "fp": 501, "fn": 340, "tn": 49127, "total": 62647, "precision": 0.9619878603945372, "recall": 0.9738843229126661, "f1": 0.967899538150311, "accuracy": 0.9865755742493655, "mcc": 0.9594420996219537 }, "head3_edge_type": { "description": "Edge type classification: given edge exists, what type is it?", "type_given_exist": { "correct": 12679, "total": 12679, "accuracy": 1.0 }, "pred_edge_count_mean": 1.5106015210878083, "gt_edge_count_mean": 1.500230467849735, "edge_level": { "description": "Edge-level type classification (per candidate edge)", "confusion_matrix": [ [ 8152, 0, 0, 0, 0, 0, 0, 0, 0 ], [ 0, 1188, 0, 0, 0, 0, 0, 0, 0 ], [ 0, 0, 9, 0, 0, 0, 0, 0, 0 ], [ 0, 0, 0, 1099, 0, 0, 0, 0, 0 ], [ 0, 0, 0, 0, 1303, 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": 0.9882409989089587, "recall": 0.9902818270165209, "f1": 0.9892603604150234, "support": 8232, "tp": 8152, "fp": 97, "fn": 80 }, { "class_id": 2, "class_name": "PG_Amide", "precision": 0.945859872611465, "recall": 0.9753694581280788, "f1": 0.9603880355699272, "support": 1218, "tp": 1188, "fp": 68, "fn": 30 }, { "class_id": 3, "class_name": "Sulfanilamide", "precision": 0.75, "recall": 1.0, "f1": 0.8571428571428571, "support": 9, "tp": 9, "fp": 3, "fn": 0 }, { "class_id": 4, "class_name": "Disulfide", "precision": 0.8978758169934641, "recall": 0.9631901840490797, "f1": 0.9293868921775897, "support": 1141, "tp": 1099, "fp": 125, "fn": 42 }, { "class_id": 5, "class_name": "Ester", "precision": 0.9169598874032372, "recall": 0.9538799414348462, "f1": 0.9350556153570148, "support": 1366, "tp": 1303, "fp": 118, "fn": 63 }, { "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": 0.6875, "recall": 0.6470588235294118, "f1": 0.6666666666666667, "support": 17, "tp": 11, "fp": 5, "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": 0.917766497461929, "recall": 0.8836754643206256, "f1": 0.900398406374502, "support": 1023, "tp": 904, "fp": 81, "fn": 119 } ], "macro_avg": { "precision": 0.8348104424966626, "recall": 0.9348284109420626, "f1": 0.8730384947501334, "support": 62647 }, "micro_avg": { "precision": 0.9619878603945372, "recall": 0.9738843229126661, "f1": 0.967899538150311, "support": 62647 } } }, "stage_breakdown": { "missing_required": 156, "fast_check_fail": 128, "ok": 8394 } } }