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/MPNN/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": "mpnn",
"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": "2026-02-26T18:50:51.726299"
},
"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": 0.12958097883766048,
"total_edges_evaluated": 62647,
"total_graphs": 38381,
"missing_required_connection_rate": 0.004403220343399078,
"fast_check_fail_rate": 0.003699747270785024,
"fast_check_fail_reasons": {
"blocks_disconnected": 142
},
"gt_edge_count_mean": 1.500230467849735,
"over_connect_rate": 0.049896289467619266,
"under_connect_rate": 0.05266190366443881
},
"head1_graph_gate": {
"description": "Graph-level: does this molecule need special connections?",
"threshold": 0.5,
"tp": 8521,
"fp": 874,
"fn": 157,
"tn": 28829,
"precision": 0.9069717935071847,
"recall": 0.9819082737958055,
"f1": 0.9429535771592984,
"accuracy": 0.9731377504494412,
"mcc": 0.9266697104242205
},
"head2_edge_exist": {
"description": "Edge-level binary: does this candidate edge exist? (cascade filter)",
"threshold": 0.5,
"tp": 12649,
"fp": 409,
"fn": 370,
"tn": 49219,
"total": 62647,
"precision": 0.9686782049318425,
"recall": 0.9715799984637837,
"f1": 0.9701269317789624,
"accuracy": 0.9875652465401376,
"mcc": 0.9622771931086612
},
"head3_edge_type": {
"description": "Edge type classification: given edge exists, what type is it?",
"type_given_exist": {
"correct": 12649,
"total": 12649,
"accuracy": 1.0
},
"pred_edge_count_mean": 1.496197280479373,
"gt_edge_count_mean": 1.500230467849735,
"edge_level": {
"description": "Edge-level type classification (per candidate edge)",
"confusion_matrix": [
[
8157,
0,
0,
0,
0,
0,
0,
0,
0
],
[
0,
1180,
0,
0,
0,
0,
0,
0,
0
],
[
0,
0,
9,
0,
0,
0,
0,
0,
0
],
[
0,
0,
0,
1078,
0,
0,
0,
0,
0
],
[
0,
0,
0,
0,
1313,
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,
886
]
],
"per_class": [
{
"class_id": 1,
"class_name": "Amide",
"precision": 0.9863361547762999,
"recall": 0.9908892128279884,
"f1": 0.9886074415222399,
"support": 8232,
"tp": 8157,
"fp": 113,
"fn": 75
},
{
"class_id": 2,
"class_name": "PG_Amide",
"precision": 0.9546925566343042,
"recall": 0.9688013136288999,
"f1": 0.9616951915240425,
"support": 1218,
"tp": 1180,
"fp": 56,
"fn": 38
},
{
"class_id": 3,
"class_name": "Sulfanilamide",
"precision": 1.0,
"recall": 1.0,
"f1": 1.0,
"support": 9,
"tp": 9,
"fp": 0,
"fn": 0
},
{
"class_id": 4,
"class_name": "Disulfide",
"precision": 0.9120135363790186,
"recall": 0.9447852760736196,
"f1": 0.9281102023245802,
"support": 1141,
"tp": 1078,
"fp": 104,
"fn": 63
},
{
"class_id": 5,
"class_name": "Ester",
"precision": 0.9351851851851852,
"recall": 0.9612005856515373,
"f1": 0.948014440433213,
"support": 1366,
"tp": 1313,
"fp": 91,
"fn": 53
},
{
"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": 0.8666666666666667,
"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": 0.9557713052858684,
"recall": 0.8660801564027371,
"f1": 0.9087179487179488,
"support": 1023,
"tp": 886,
"fp": 41,
"fn": 137
}
],
"macro_avg": {
"precision": 0.9188618126686947,
"recall": 0.9440513807708582,
"f1": 0.9285743371162037,
"support": 62647
},
"micro_avg": {
"precision": 0.9686782049318425,
"recall": 0.9715799984637837,
"f1": 0.9701269317789624,
"support": 62647
}
}
},
"stage_breakdown": {
"missing_required": 169,
"fast_check_fail": 142,
"ok": 8367
}
}
}