| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GCN/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": "gcn", |
| "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": "2026-02-26T17:35:14.790422" |
| }, |
| "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": 0.03858662127733342, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.003230765222375655, |
| "fast_check_fail_rate": 0.003439201688335374, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 132 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.05980640700622263, |
| "under_connect_rate": 0.04713067527079973 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8459, |
| "fp": 677, |
| "fn": 219, |
| "tn": 29026, |
| "precision": 0.9258975481611208, |
| "recall": 0.9747637704540216, |
| "f1": 0.9497024811945661, |
| "accuracy": 0.9766551158125114, |
| "mcc": 0.9350397001558348 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12704, |
| "fp": 588, |
| "fn": 315, |
| "tn": 49040, |
| "total": 62647, |
| "precision": 0.9557628648811315, |
| "recall": 0.9758045932867347, |
| "f1": 0.9656797537151762, |
| "accuracy": 0.9855859019585934, |
| "mcc": 0.9566407274913443 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12704, |
| "total": 12704, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5134823692094952, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8168, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1172, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1098, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1309, |
| 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, |
| 923 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9842149656585131, |
| "recall": 0.9922254616132167, |
| "f1": 0.9882039804004598, |
| "support": 8232, |
| "tp": 8168, |
| "fp": 131, |
| "fn": 64 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9338645418326693, |
| "recall": 0.9622331691297209, |
| "f1": 0.947836635665184, |
| "support": 1218, |
| "tp": 1172, |
| "fp": 83, |
| "fn": 46 |
| }, |
| { |
| "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": 0.8805132317562149, |
| "recall": 0.9623137598597721, |
| "f1": 0.9195979899497486, |
| "support": 1141, |
| "tp": 1098, |
| "fp": 149, |
| "fn": 43 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9173090399439383, |
| "recall": 0.958272327964861, |
| "f1": 0.9373433583959899, |
| "support": 1366, |
| "tp": 1309, |
| "fp": 118, |
| "fn": 57 |
| }, |
| { |
| "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": 0.8, |
| "recall": 0.7058823529411765, |
| "f1": 0.7500000000000001, |
| "support": 17, |
| "tp": 12, |
| "fp": 3, |
| "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": 0.9031311154598826, |
| "recall": 0.9022482893450635, |
| "f1": 0.9026894865525672, |
| "support": 1023, |
| "tp": 923, |
| "fp": 99, |
| "fn": 100 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8607006246582162, |
| "recall": 0.9425750400948678, |
| "f1": 0.8942280448161001, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9557628648811315, |
| "recall": 0.9758045932867347, |
| "f1": 0.9656797537151762, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 124, |
| "fast_check_fail": 132, |
| "ok": 8422 |
| } |
| } |
| } |