Datasets:
Download Data/Generation_Model/Connection/MPNN/LARGE/eval_test.json from qingxin1999/pepforge-fig-data: direct link, hf CLI and curl.
- Browser
- Download file 7.44 kB
-
https://huggingface.co/datasets/qingxin1999/pepforge-fig-data/resolve/main/Data/Generation_Model/Connection/MPNN/LARGE/eval_test.json
- Command line
-
hf download hf://datasets/qingxin1999/pepforge-fig-data/Data/Generation_Model/Connection/MPNN/LARGE/eval_test.json
-
curl -L -o eval_test.json https://huggingface.co/datasets/qingxin1999/pepforge-fig-data/resolve/main/Data/Generation_Model/Connection/MPNN/LARGE/eval_test.json
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 | |
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| "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, | |
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| "fn": 157, | |
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| "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, | |
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| "fp": 409, | |
| "fn": 370, | |
| "tn": 49219, | |
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| "precision": 0.9686782049318425, | |
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| "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)", | |
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