| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GIN/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": "gin", |
| "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": "2026-02-26T17:55:05.646178" |
| }, |
| "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": 0.04656120167052183, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.0037258018290299887, |
| "fast_check_fail_rate": 0.0033349834553555143, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 128 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.05899976953215026, |
| "under_connect_rate": 0.04885918414381194 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8497, |
| "fp": 802, |
| "fn": 181, |
| "tn": 28901, |
| "precision": 0.9137541671147436, |
| "recall": 0.9791426595989859, |
| "f1": 0.9453190187461757, |
| "accuracy": 0.9743883692451994, |
| "mcc": 0.9295686176686825 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12696, |
| "fp": 592, |
| "fn": 323, |
| "tn": 49036, |
| "total": 62647, |
| "precision": 0.9554485249849488, |
| "recall": 0.9751901067670328, |
| "f1": 0.9652183829399019, |
| "accuracy": 0.98539435248296, |
| "mcc": 0.9560560462800373 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12696, |
| "total": 12696, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5102558193132058, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8161, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1174, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1104, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 1322, |
| 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, |
| 902 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9843203473646123, |
| "recall": 0.9913751214771623, |
| "f1": 0.9878351388972947, |
| "support": 8232, |
| "tp": 8161, |
| "fp": 130, |
| "fn": 71 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9347133757961783, |
| "recall": 0.9638752052545156, |
| "f1": 0.9490703314470492, |
| "support": 1218, |
| "tp": 1174, |
| "fp": 82, |
| "fn": 44 |
| }, |
| { |
| "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": 0.8846153846153846, |
| "recall": 0.9675723049956179, |
| "f1": 0.9242360820426957, |
| "support": 1141, |
| "tp": 1104, |
| "fp": 144, |
| "fn": 37 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9136143745680718, |
| "recall": 0.9677891654465594, |
| "f1": 0.9399217916814788, |
| "support": 1366, |
| "tp": 1322, |
| "fp": 125, |
| "fn": 44 |
| }, |
| { |
| "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": 0.9166666666666666, |
| "recall": 0.6470588235294118, |
| "f1": 0.7586206896551724, |
| "support": 17, |
| "tp": 11, |
| "fp": 1, |
| "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": 0.8957298907646475, |
| "recall": 0.8817204301075269, |
| "f1": 0.8886699507389163, |
| "support": 1023, |
| "tp": 902, |
| "fp": 105, |
| "fn": 121 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8820834387629412, |
| "recall": 0.9354878945345327, |
| "f1": 0.901668961236586, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9554485249849488, |
| "recall": 0.9751901067670328, |
| "f1": 0.9652183829399019, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 143, |
| "fast_check_fail": 128, |
| "ok": 8407 |
| } |
| } |
| } |