qingxin1999's picture
Restructure: all figure data under Data/ prefix
b5f096e verified
Raw
History Blame Contribute Delete
7.45 kB
{
"checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GAT/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": "gat",
"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": "2026-02-26T19:43:53.960913"
},
"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": 0.05476830073700056,
"total_edges_evaluated": 62647,
"total_graphs": 38381,
"missing_required_connection_rate": 0.0037258018290299887,
"fast_check_fail_rate": 0.0038821291784997785,
"fast_check_fail_reasons": {
"blocks_disconnected": 149
},
"gt_edge_count_mean": 1.500230467849735,
"over_connect_rate": 0.053007605439041254,
"under_connect_rate": 0.05001152339248675
},
"head1_graph_gate": {
"description": "Graph-level: does this molecule need special connections?",
"threshold": 0.5,
"tp": 8526,
"fp": 788,
"fn": 152,
"tn": 28915,
"precision": 0.9153961777968649,
"recall": 0.9824844434201429,
"f1": 0.9477545575811471,
"accuracy": 0.9755087152497329,
"mcc": 0.9327800941717175
},
"head2_edge_exist": {
"description": "Edge-level binary: does this candidate edge exist? (cascade filter)",
"threshold": 0.5,
"tp": 12681,
"fp": 410,
"fn": 338,
"tn": 49218,
"total": 62647,
"precision": 0.9686807730501872,
"recall": 0.9740379445425916,
"f1": 0.9713519724243586,
"accuracy": 0.9880600826855237,
"mcc": 0.9638163537088555
},
"head3_edge_type": {
"description": "Edge type classification: given edge exists, what type is it?",
"type_given_exist": {
"correct": 12681,
"total": 12681,
"accuracy": 1.0
},
"pred_edge_count_mean": 1.5027656141968195,
"gt_edge_count_mean": 1.500230467849735,
"edge_level": {
"description": "Edge-level type classification (per candidate edge)",
"confusion_matrix": [
[
8163,
0,
0,
0,
0,
0,
0,
0,
0
],
[
0,
1183,
0,
0,
0,
0,
0,
0,
0
],
[
0,
0,
9,
0,
0,
0,
0,
0,
0
],
[
0,
0,
0,
1087,
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,
13,
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": 0.9878978579208519,
"recall": 0.9916180758017493,
"f1": 0.989754471051834,
"support": 8232,
"tp": 8163,
"fp": 100,
"fn": 69
},
{
"class_id": 2,
"class_name": "PG_Amide",
"precision": 0.9540322580645161,
"recall": 0.9712643678160919,
"f1": 0.9625711960943856,
"support": 1218,
"tp": 1183,
"fp": 57,
"fn": 35
},
{
"class_id": 3,
"class_name": "Sulfanilamide",
"precision": 0.9,
"recall": 1.0,
"f1": 0.9473684210526316,
"support": 9,
"tp": 9,
"fp": 1,
"fn": 0
},
{
"class_id": 4,
"class_name": "Disulfide",
"precision": 0.9211864406779661,
"recall": 0.9526730937773883,
"f1": 0.9366652305040931,
"support": 1141,
"tp": 1087,
"fp": 93,
"fn": 54
},
{
"class_id": 5,
"class_name": "Ester",
"precision": 0.9299499642601858,
"recall": 0.9524158125915081,
"f1": 0.9410488245931283,
"support": 1366,
"tp": 1301,
"fp": 98,
"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": 0.8666666666666667,
"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": 0.9421487603305785,
"recall": 0.8914956011730205,
"f1": 0.9161225514816673,
"support": 1023,
"tp": 912,
"fp": 56,
"fn": 111
}
],
"macro_avg": {
"precision": 0.8901080952235192,
"recall": 0.9471303148347443,
"f1": 0.912045738573188,
"support": 62647
},
"micro_avg": {
"precision": 0.9686807730501872,
"recall": 0.9740379445425916,
"f1": 0.9713519724243586,
"support": 62647
}
}
},
"stage_breakdown": {
"missing_required": 143,
"fast_check_fail": 149,
"ok": 8386
}
}
}