| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/MPNN/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": "mpnn", |
| "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": "2026-02-26T18:50:51.726299" |
| }, |
| "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": 0.12958097883766048, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.004403220343399078, |
| "fast_check_fail_rate": 0.003699747270785024, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 142 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.049896289467619266, |
| "under_connect_rate": 0.05266190366443881 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8521, |
| "fp": 874, |
| "fn": 157, |
| "tn": 28829, |
| "precision": 0.9069717935071847, |
| "recall": 0.9819082737958055, |
| "f1": 0.9429535771592984, |
| "accuracy": 0.9731377504494412, |
| "mcc": 0.9266697104242205 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12649, |
| "fp": 409, |
| "fn": 370, |
| "tn": 49219, |
| "total": 62647, |
| "precision": 0.9686782049318425, |
| "recall": 0.9715799984637837, |
| "f1": 0.9701269317789624, |
| "accuracy": 0.9875652465401376, |
| "mcc": 0.9622771931086612 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12649, |
| "total": 12649, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.496197280479373, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8157, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1180, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1078, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1313, |
| 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, |
| 886 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9863361547762999, |
| "recall": 0.9908892128279884, |
| "f1": 0.9886074415222399, |
| "support": 8232, |
| "tp": 8157, |
| "fp": 113, |
| "fn": 75 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9546925566343042, |
| "recall": 0.9688013136288999, |
| "f1": 0.9616951915240425, |
| "support": 1218, |
| "tp": 1180, |
| "fp": 56, |
| "fn": 38 |
| }, |
| { |
| "class_id": 3, |
| "class_name": "Sulfanilamide", |
| "precision": 1.0, |
| "recall": 1.0, |
| "f1": 1.0, |
| "support": 9, |
| "tp": 9, |
| "fp": 0, |
| "fn": 0 |
| }, |
| { |
| "class_id": 4, |
| "class_name": "Disulfide", |
| "precision": 0.9120135363790186, |
| "recall": 0.9447852760736196, |
| "f1": 0.9281102023245802, |
| "support": 1141, |
| "tp": 1078, |
| "fp": 104, |
| "fn": 63 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9351851851851852, |
| "recall": 0.9612005856515373, |
| "f1": 0.948014440433213, |
| "support": 1366, |
| "tp": 1313, |
| "fp": 91, |
| "fn": 53 |
| }, |
| { |
| "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": 0.8666666666666667, |
| "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": 0.9557713052858684, |
| "recall": 0.8660801564027371, |
| "f1": 0.9087179487179488, |
| "support": 1023, |
| "tp": 886, |
| "fp": 41, |
| "fn": 137 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.9188618126686947, |
| "recall": 0.9440513807708582, |
| "f1": 0.9285743371162037, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9686782049318425, |
| "recall": 0.9715799984637837, |
| "f1": 0.9701269317789624, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 169, |
| "fast_check_fail": 142, |
| "ok": 8367 |
| } |
| } |
| } |