| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GCN/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": "gcn", |
| "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": "2026-02-26T18:01:49.898417" |
| }, |
| "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": 0.044091945643659064, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.0036736927125400587, |
| "fast_check_fail_rate": 0.0034131471300904094, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 131 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.05623415533533072, |
| "under_connect_rate": 0.04793731274487209 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8453, |
| "fp": 660, |
| "fn": 225, |
| "tn": 29043, |
| "precision": 0.9275759903434654, |
| "recall": 0.9740723669048168, |
| "f1": 0.9502557472879545, |
| "accuracy": 0.976941715953206, |
| "mcc": 0.9357339280412161 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12706, |
| "fp": 667, |
| "fn": 313, |
| "tn": 48961, |
| "total": 62647, |
| "precision": 0.9501233829357661, |
| "recall": 0.9759582149166602, |
| "f1": 0.9628675356168537, |
| "accuracy": 0.9843567928232796, |
| "mcc": 0.9530985926027946 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12706, |
| "total": 12706, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5074902051163863, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8155, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1194, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1102, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1305, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 3, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 918 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9831223628691983, |
| "recall": 0.9906462585034014, |
| "f1": 0.9868699703515459, |
| "support": 8232, |
| "tp": 8155, |
| "fp": 140, |
| "fn": 77 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9128440366972477, |
| "recall": 0.9802955665024631, |
| "f1": 0.9453681710213777, |
| "support": 1218, |
| "tp": 1194, |
| "fp": 114, |
| "fn": 24 |
| }, |
| { |
| "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": 0.8569206842923794, |
| "recall": 0.9658194566170026, |
| "f1": 0.908117016893284, |
| "support": 1141, |
| "tp": 1102, |
| "fp": 184, |
| "fn": 39 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9113128491620112, |
| "recall": 0.9553440702781845, |
| "f1": 0.9328091493924232, |
| "support": 1366, |
| "tp": 1305, |
| "fp": 127, |
| "fn": 61 |
| }, |
| { |
| "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": 0.9090909090909091, |
| "recall": 0.5882352941176471, |
| "f1": 0.7142857142857143, |
| "support": 17, |
| "tp": 10, |
| "fp": 1, |
| "fn": 7 |
| }, |
| { |
| "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": 0.9062191510365252, |
| "recall": 0.8973607038123167, |
| "f1": 0.9017681728880156, |
| "support": 1023, |
| "tp": 918, |
| "fp": 95, |
| "fn": 105 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8563091911578886, |
| "recall": 0.9308557055367793, |
| "f1": 0.8786962015422201, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9501233829357661, |
| "recall": 0.9759582149166602, |
| "f1": 0.9628675356168537, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 141, |
| "fast_check_fail": 131, |
| "ok": 8406 |
| } |
| } |
| } |