| { |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GAT/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": "gat", |
| "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": "2026-02-26T17:36:02.499430" |
| }, |
| "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": 0.03255900404269002, |
| "total_edges_evaluated": 62647, |
| "total_graphs": 38381, |
| "missing_required_connection_rate": 0.003569474479560199, |
| "fast_check_fail_rate": 0.0034131471300904094, |
| "fast_check_fail_reasons": { |
| "blocks_disconnected": 131 |
| }, |
| "gt_edge_count_mean": 1.500230467849735, |
| "over_connect_rate": 0.06291772297764461, |
| "under_connect_rate": 0.04770684489513713 |
| }, |
| "head1_graph_gate": { |
| "description": "Graph-level: does this molecule need special connections?", |
| "threshold": 0.5, |
| "tp": 8472, |
| "fp": 545, |
| "fn": 206, |
| "tn": 29158, |
| "precision": 0.9395586115115893, |
| "recall": 0.976261811477299, |
| "f1": 0.9575586323820289, |
| "accuracy": 0.9804330267580313, |
| "mcc": 0.9451432352169156 |
| }, |
| "head2_edge_exist": { |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", |
| "threshold": 0.5, |
| "tp": 12700, |
| "fp": 498, |
| "fn": 319, |
| "tn": 49130, |
| "total": 62647, |
| "precision": 0.9622670101530535, |
| "recall": 0.9754973500268838, |
| "f1": 0.9688370141511233, |
| "accuracy": 0.9869586732006321, |
| "mcc": 0.9606271964214377 |
| }, |
| "head3_edge_type": { |
| "description": "Edge type classification: given edge exists, what type is it?", |
| "type_given_exist": { |
| "correct": 12700, |
| "total": 12700, |
| "accuracy": 1.0 |
| }, |
| "pred_edge_count_mean": 1.5165936851809172, |
| "gt_edge_count_mean": 1.500230467849735, |
| "edge_level": { |
| "description": "Edge-level type classification (per candidate edge)", |
| "confusion_matrix": [ |
| [ |
| 8165, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 1185, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 9, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 1101, |
| 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, |
| 14, |
| 0, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 10, |
| 0 |
| ], |
| [ |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 0, |
| 912 |
| ] |
| ], |
| "per_class": [ |
| { |
| "class_id": 1, |
| "class_name": "Amide", |
| "precision": 0.986945485313671, |
| "recall": 0.9918610301263362, |
| "f1": 0.9893971523780672, |
| "support": 8232, |
| "tp": 8165, |
| "fp": 108, |
| "fn": 67 |
| }, |
| { |
| "class_id": 2, |
| "class_name": "PG_Amide", |
| "precision": 0.9510433386837881, |
| "recall": 0.9729064039408867, |
| "f1": 0.9618506493506493, |
| "support": 1218, |
| "tp": 1185, |
| "fp": 61, |
| "fn": 33 |
| }, |
| { |
| "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": 0.9017199017199017, |
| "recall": 0.964943032427695, |
| "f1": 0.9322607959356477, |
| "support": 1141, |
| "tp": 1101, |
| "fp": 120, |
| "fn": 40 |
| }, |
| { |
| "class_id": 5, |
| "class_name": "Ester", |
| "precision": 0.9213881019830028, |
| "recall": 0.9524158125915081, |
| "f1": 0.9366450683945285, |
| "support": 1366, |
| "tp": 1301, |
| "fp": 111, |
| "fn": 65 |
| }, |
| { |
| "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": 0.7368421052631579, |
| "recall": 0.8235294117647058, |
| "f1": 0.7777777777777778, |
| "support": 17, |
| "tp": 14, |
| "fp": 5, |
| "fn": 3 |
| }, |
| { |
| "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": 0.912, |
| "recall": 0.8914956011730205, |
| "f1": 0.9016312407315867, |
| "support": 1023, |
| "tp": 912, |
| "fp": 88, |
| "fn": 111 |
| } |
| ], |
| "macro_avg": { |
| "precision": 0.8596901844706942, |
| "recall": 0.955239032447128, |
| "f1": 0.9002159596610233, |
| "support": 62647 |
| }, |
| "micro_avg": { |
| "precision": 0.9622670101530535, |
| "recall": 0.9754973500268838, |
| "f1": 0.9688370141511233, |
| "support": 62647 |
| } |
| } |
| }, |
| "stage_breakdown": { |
| "missing_required": 137, |
| "fast_check_fail": 131, |
| "ok": 8410 |
| } |
| } |
| } |