Datasets:
Download inputs/mutation/protocol.json from GENTEL-Lab/AlphaEnzyme-data: direct link, hf CLI and curl.
- Browser
- Download file 15.7 kB
-
https://huggingface.co/datasets/GENTEL-Lab/AlphaEnzyme-data/resolve/main/inputs/mutation/protocol.json
- Command line
-
hf download hf://datasets/GENTEL-Lab/AlphaEnzyme-data/inputs/mutation/protocol.json
-
curl -L -o protocol.json https://huggingface.co/datasets/GENTEL-Lab/AlphaEnzyme-data/resolve/main/inputs/mutation/protocol.json
15.7 kB
| { | |
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| "OXDA_RHOTO_Vanella_2023_activity", | |
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| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
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| "AMIE_PSEAE_Wrenbeck_2017", | |
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| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
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| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
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| "RASH_HUMAN_Bandaru_2017" | |
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| "dropout": 0.2, | |
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| "batch_size": 512, | |
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| "lr": 0.0002, | |
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| "OXDA_RHOTO_Vanella_2023_activity", | |
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| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
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| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "LGK_LIPST_Klesmith_2015", | |
| "test": "HEM3_HUMAN_Loggerenberg_2023" | |
| }, | |
| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "OTC_HUMAN_Lo_2023", | |
| "test": "LGK_LIPST_Klesmith_2015" | |
| }, | |
| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
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| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "OXDA_RHOTO_Vanella_2023_activity", | |
| "test": "OTC_HUMAN_Lo_2023" | |
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| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "PTEN_HUMAN_Mighell_2018", | |
| "test": "OXDA_RHOTO_Vanella_2023_activity" | |
| }, | |
| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "Q59976_STRSQ_Romero_2015", | |
| "test": "PTEN_HUMAN_Mighell_2018" | |
| }, | |
| { | |
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| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018" | |
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| "train": [ | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015" | |
| ], | |
| "valid": "AMIE_PSEAE_Wrenbeck_2017", | |
| "test": "RASH_HUMAN_Bandaru_2017" | |
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| "neural_and_tree_configs": [ | |
| { | |
| "id": "nn_paired", | |
| "kind": "nn", | |
| "view": "paired", | |
| "normalization": "total", | |
| "target": "zscore", | |
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| "balanced": false | |
| }, | |
| { | |
| "id": "nn_paired_within", | |
| "kind": "nn", | |
| "view": "paired", | |
| "normalization": "within_protein", | |
| "target": "zscore", | |
| "rank_weight": 0.05, | |
| "balanced": false | |
| }, | |
| { | |
| "id": "nn_paired_meta", | |
| "kind": "nn", | |
| "view": "paired_meta", | |
| "normalization": "within_protein", | |
| "target": "gaussian_rank", | |
| "rank_weight": 0.2, | |
| "balanced": true | |
| }, | |
| { | |
| "id": "nn_raw", | |
| "kind": "nn", | |
| "view": "raw", | |
| "normalization": "within_protein", | |
| "target": "gaussian_rank", | |
| "rank_weight": 0.2, | |
| "balanced": true | |
| }, | |
| { | |
| "id": "xgb_rank_paired_meta", | |
| "kind": "xgb", | |
| "view": "paired_meta", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "rank:pairwise", | |
| "depth": 3 | |
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| { | |
| "id": "xgb_rank_paired", | |
| "kind": "xgb", | |
| "view": "paired", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "rank:pairwise", | |
| "depth": 5 | |
| }, | |
| { | |
| "id": "xgb_reg_raw", | |
| "kind": "xgb", | |
| "view": "raw", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "reg:squarederror", | |
| "depth": 3 | |
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| { | |
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| "kind": "xgb", | |
| "view": "paired_meta", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "reg:squarederror", | |
| "depth": 3 | |
| } | |
| ], | |
| "neural_epochs": 40, | |
| "xgb_max_rounds": 300, | |
| "xgb_patience": 30, | |
| "ridge": { | |
| "views": [ | |
| "original", | |
| "alpha", | |
| "raw", | |
| "paired", | |
| "paired_meta", | |
| "metadata" | |
| ], | |
| "normalizations": [ | |
| "total", | |
| "within_protein" | |
| ], | |
| "targets": [ | |
| "zscore", | |
| "gaussian_rank" | |
| ], | |
| "lambdas": [ | |
| 1e-05, | |
| 0.0001, | |
| 0.001, | |
| 0.01, | |
| 0.1, | |
| 1.0, | |
| 10.0 | |
| ], | |
| "group_weights": "equal training proteins", | |
| "selection": "six inner leave-one-training-protein-out folds within original six training proteins; select equal-protein mean inner SCC, refit on original six training proteins", | |
| "scaler_fitting": "every inner fit uses only its five training proteins; outer refit uses only original six", | |
| "deterministic": true, | |
| "no_duplicate_seed_fits": true | |
| } | |
| }, | |
| "local": { | |
| "folds": [ | |
| { | |
| "fold": 0, | |
| "train": [ | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "HEM3_HUMAN_Loggerenberg_2023", | |
| "test": "AMIE_PSEAE_Wrenbeck_2017" | |
| }, | |
| { | |
| "fold": 1, | |
| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "LGK_LIPST_Klesmith_2015", | |
| "test": "HEM3_HUMAN_Loggerenberg_2023" | |
| }, | |
| { | |
| "fold": 2, | |
| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "OTC_HUMAN_Lo_2023", | |
| "test": "LGK_LIPST_Klesmith_2015" | |
| }, | |
| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "OXDA_RHOTO_Vanella_2023_activity", | |
| "test": "OTC_HUMAN_Lo_2023" | |
| }, | |
| { | |
| "fold": 4, | |
| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "Q59976_STRSQ_Romero_2015", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "PTEN_HUMAN_Mighell_2018", | |
| "test": "OXDA_RHOTO_Vanella_2023_activity" | |
| }, | |
| { | |
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| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "RASH_HUMAN_Bandaru_2017" | |
| ], | |
| "valid": "Q59976_STRSQ_Romero_2015", | |
| "test": "PTEN_HUMAN_Mighell_2018" | |
| }, | |
| { | |
| "fold": 6, | |
| "train": [ | |
| "AMIE_PSEAE_Wrenbeck_2017", | |
| "HEM3_HUMAN_Loggerenberg_2023", | |
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| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018" | |
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| { | |
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| "LGK_LIPST_Klesmith_2015", | |
| "OTC_HUMAN_Lo_2023", | |
| "OXDA_RHOTO_Vanella_2023_activity", | |
| "PTEN_HUMAN_Mighell_2018", | |
| "Q59976_STRSQ_Romero_2015" | |
| ], | |
| "valid": "AMIE_PSEAE_Wrenbeck_2017", | |
| "test": "RASH_HUMAN_Bandaru_2017" | |
| } | |
| ], | |
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| "global_site_meta": [ | |
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| }, | |
| "feature_contract": "WT mutation-site Protenix single/pair-summary tokens (384+128), mutant-minus-WT same-site difference, optional global paired Alpha features and 62D sequence descriptors", | |
| "mapping": "protein token indices selected by is_ligand<0.5 and single_mask>0.5; protein token count equals full-length sequence in every WT and mutant; mutation positions are one-based full-length positions", | |
| "neural_and_tree_configs": [ | |
| { | |
| "id": "nn_site_pair", | |
| "kind": "nn", | |
| "view": "site_pair", | |
| "normalization": "within_protein", | |
| "target": "gaussian_rank", | |
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| "balanced": true | |
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| { | |
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| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "rank_weight": 0.2, | |
| "balanced": true | |
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| { | |
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| "kind": "xgb", | |
| "view": "site_meta", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "rank:pairwise", | |
| "depth": 3 | |
| }, | |
| { | |
| "id": "xgb_global_site_reg", | |
| "kind": "xgb", | |
| "view": "global_site_meta", | |
| "normalization": "total", | |
| "target": "gaussian_rank", | |
| "objective": "reg:squarederror", | |
| "depth": 3 | |
| } | |
| ], | |
| "neural_epochs": 40, | |
| "xgb_max_rounds": 300, | |
| "xgb_patience": 30, | |
| "ridge": { | |
| "views": [ | |
| "site_wt", | |
| "site_delta", | |
| "site_pair", | |
| "site_meta", | |
| "global_site_meta" | |
| ], | |
| "normalizations": [ | |
| "total", | |
| "within_protein" | |
| ], | |
| "targets": [ | |
| "zscore", | |
| "gaussian_rank" | |
| ], | |
| "lambdas": [ | |
| 1e-05, | |
| 0.0001, | |
| 0.001, | |
| 0.01, | |
| 0.1, | |
| 1.0, | |
| 10.0 | |
| ], | |
| "selection": "six inner leave-one-training-protein-out folds inside the original six outer training proteins; select macro inner SCC and refit all original six", | |
| "deterministic": true | |
| } | |
| } | |
| } | |