Datasets:
Download Data/Generation_Model/Connection/MPNN/SMALL/eval_test.json from qingxin1999/pepforge-fig-data: direct link, hf CLI and curl.
- Browser
- Download file 7.46 kB
-
https://huggingface.co/datasets/qingxin1999/pepforge-fig-data/resolve/main/Data/Generation_Model/Connection/MPNN/SMALL/eval_test.json
- Command line
-
hf download hf://datasets/qingxin1999/pepforge-fig-data/Data/Generation_Model/Connection/MPNN/SMALL/eval_test.json
-
curl -L -o eval_test.json https://huggingface.co/datasets/qingxin1999/pepforge-fig-data/resolve/main/Data/Generation_Model/Connection/MPNN/SMALL/eval_test.json
7.46 kB
| { | |
| "checkpoint": "/net/work/wangq/CycAMP/Scripts/Generation_Model/Models_ckpt/260226_connection/MPNN/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": "mpnn", | |
| "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": "2026-02-26T18:27:24.343663" | |
| }, | |
| "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": { | |
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| "loss": 0.040401963454659726, | |
| "total_edges_evaluated": 62647, | |
| "total_graphs": 38381, | |
| "missing_required_connection_rate": 0.003543419921315234, | |
| "fast_check_fail_rate": 0.0032828743388655843, | |
| "fast_check_fail_reasons": { | |
| "blocks_disconnected": 126 | |
| }, | |
| "gt_edge_count_mean": 1.500230467849735, | |
| "over_connect_rate": 0.06257202120304217, | |
| "under_connect_rate": 0.04747637704540217 | |
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| "head1_graph_gate": { | |
| "description": "Graph-level: does this molecule need special connections?", | |
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| "recall": 0.978681723899516, | |
| "f1": 0.9490445859872612, | |
| "accuracy": 0.9762382428805919, | |
| "mcc": 0.9342981604945385 | |
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| "head2_edge_exist": { | |
| "description": "Edge-level binary: does this candidate edge exist? (cascade filter)", | |
| "threshold": 0.5, | |
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| "tn": 49035, | |
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| "precision": 0.9553934105611555, | |
| "recall": 0.9755741608418466, | |
| "f1": 0.9653783301029909, | |
| "accuracy": 0.9854582023081712, | |
| "mcc": 0.956259495901017 | |
| }, | |
| "head3_edge_type": { | |
| "description": "Edge type classification: given edge exists, what type is it?", | |
| "type_given_exist": { | |
| "correct": 12701, | |
| "total": 12701, | |
| "accuracy": 1.0 | |
| }, | |
| "pred_edge_count_mean": 1.5153261120073749, | |
| "gt_edge_count_mean": 1.500230467849735, | |
| "edge_level": { | |
| "description": "Edge-level type classification (per candidate edge)", | |
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