| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GIN/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": "gin", |
| "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": "2026-02-26T20:24:30.175302" |
| }, |
| "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": 0.05200071142998695, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.004455329459889008, |
| "fast_check_fail_rate": 0.0034131471300904094, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 131 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.057040792809403086, |
| "under_connect_rate": 0.05369900898824614 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8496, |
| "fp": 873, |
| "fn": 182, |
| "tn": 28830, |
| "precision": 0.9068203650336215, |
| "recall": 0.9790274256741185, |
| "f1": 0.9415415304482739, |
| "accuracy": 0.972512441051562, |
| "mcc": 0.9247661080092603 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12631, |
| "fp": 584, |
| "fn": 388, |
| "tn": 49044, |
| "total": 62647, |
| "precision": 0.955807794173288, |
| "recall": 0.9701974037944543, |
| "f1": 0.9629488450102921, |
| "accuracy": 0.9844844924737018, |
| "mcc": 0.9531798614885465 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12631, |
| "total": 12631, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5036874855957594, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8147, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1163, |
| 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, |
| 1301, |
| 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, |
| 889 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.9852460998911597, |
| "recall": 0.9896744412050534, |
| "f1": 0.9874553057390462, |
| "support": 8232, |
| "tp": 8147, |
| "fp": 122, |
| "fn": 85 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.934136546184739, |
| "recall": 0.9548440065681445, |
| "f1": 0.9443767762890783, |
| "support": 1218, |
| "tp": 1163, |
| "fp": 82, |
| "fn": 55 |
| }, |
| { |
| "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": 0.8552529182879377, |
| "recall": 0.9631901840490797, |
| "f1": 0.9060181368507831, |
| "support": 1141, |
| "tp": 1099, |
| "fp": 186, |
| "fn": 42 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9220411055988661, |
| "recall": 0.9524158125915081, |
| "f1": 0.9369823550594166, |
| "support": 1366, |
| "tp": 1301, |
| "fp": 110, |
| "fn": 65 |
| }, |
| { |
| "class_id": 6, |
| "class_name": "Trp-Cys", |
| "precision": 1.0, |
| "recall": 1.0, |
| "f1": 1.0, |
| "support": 3, |
| "tp": 3, |
| "fp": 0, |
| "fn": 0 |
| }, |
| { |
| "class_id": 7, |
| "class_name": "Lanthionin", |
| "precision": 0.7142857142857143, |
| "recall": 0.5882352941176471, |
| "f1": 0.6451612903225806, |
| "support": 17, |
| "tp": 10, |
| "fp": 4, |
| "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": 0.9212435233160622, |
| "recall": 0.8690127077223851, |
| "f1": 0.8943661971830986, |
| "support": 1023, |
| "tp": 889, |
| "fp": 76, |
| "fn": 134 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8879218685172653, |
| "recall": 0.9241524940282019, |
| "f1": 0.9026537634408681, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.955807794173288, |
| "recall": 0.9701974037944543, |
| "f1": 0.9629488450102921, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 171, |
| "fast_check_fail": 131, |
| "ok": 8376 |
| } |
| } |
| } |