qingxin1999's picture
Restructure: all figure data under Data/ prefix
b5f096e verified
Raw
History Blame Contribute Delete
7.44 kB
{
"checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/GAT/SMALL/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": 384,
"hidden": 768,
"num_layers": 3,
"num_edge_types": 10,
"dropout": 0.2,
"max_nodes": 256
},
"evaluation": {
"device": "cuda",
"batch_size": 512,
"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": "2026-02-26T17:24:34.864721"
},
"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": 0.0371660907295146,
"total_edges_evaluated": 62647,
"total_graphs": 38381,
"missing_required_connection_rate": 0.004064511086214534,
"fast_check_fail_rate": 0.0033349834553555143,
"fast_check_fail_reasons": {
"blocks_disconnected": 128
},
"gt_edge_count_mean": 1.500230467849735,
"over_connect_rate": 0.05957593915648767,
"under_connect_rate": 0.049550587693016825
},
"head1_graph_gate": {
"description": "Graph-level: does this molecule need special connections?",
"threshold": 0.5,
"tp": 8474,
"fp": 578,
"fn": 204,
"tn": 29125,
"precision": 0.9361467079098542,
"recall": 0.9764922793270339,
"f1": 0.9558939650310209,
"accuracy": 0.9796253354524374,
"mcc": 0.9430093039478985
},
"head2_edge_exist": {
"description": "Edge-level binary: does this candidate edge exist? (cascade filter)",
"threshold": 0.5,
"tp": 12679,
"fp": 501,
"fn": 340,
"tn": 49127,
"total": 62647,
"precision": 0.9619878603945372,
"recall": 0.9738843229126661,
"f1": 0.967899538150311,
"accuracy": 0.9865755742493655,
"mcc": 0.9594420996219537
},
"head3_edge_type": {
"description": "Edge type classification: given edge exists, what type is it?",
"type_given_exist": {
"correct": 12679,
"total": 12679,
"accuracy": 1.0
},
"pred_edge_count_mean": 1.5106015210878083,
"gt_edge_count_mean": 1.500230467849735,
"edge_level": {
"description": "Edge-level type classification (per candidate edge)",
"confusion_matrix": [
[
8152,
0,
0,
0,
0,
0,
0,
0,
0
],
[
0,
1188,
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,
1303,
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,
904
]
],
"per_class": [
{
"class_id": 1,
"class_name": "Amide",
"precision": 0.9882409989089587,
"recall": 0.9902818270165209,
"f1": 0.9892603604150234,
"support": 8232,
"tp": 8152,
"fp": 97,
"fn": 80
},
{
"class_id": 2,
"class_name": "PG_Amide",
"precision": 0.945859872611465,
"recall": 0.9753694581280788,
"f1": 0.9603880355699272,
"support": 1218,
"tp": 1188,
"fp": 68,
"fn": 30
},
{
"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": 0.8978758169934641,
"recall": 0.9631901840490797,
"f1": 0.9293868921775897,
"support": 1141,
"tp": 1099,
"fp": 125,
"fn": 42
},
{
"class_id": 5,
"class_name": "Ester",
"precision": 0.9169598874032372,
"recall": 0.9538799414348462,
"f1": 0.9350556153570148,
"support": 1366,
"tp": 1303,
"fp": 118,
"fn": 63
},
{
"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": 0.6875,
"recall": 0.6470588235294118,
"f1": 0.6666666666666667,
"support": 17,
"tp": 11,
"fp": 5,
"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": 0.917766497461929,
"recall": 0.8836754643206256,
"f1": 0.900398406374502,
"support": 1023,
"tp": 904,
"fp": 81,
"fn": 119
}
],
"macro_avg": {
"precision": 0.8348104424966626,
"recall": 0.9348284109420626,
"f1": 0.8730384947501334,
"support": 62647
},
"micro_avg": {
"precision": 0.9619878603945372,
"recall": 0.9738843229126661,
"f1": 0.967899538150311,
"support": 62647
}
}
},
"stage_breakdown": {
"missing_required": 156,
"fast_check_fail": 128,
"ok": 8394
}
}
}