File size: 5,964 Bytes
3b99abb | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | {
"framework": "PyTorch",
"task": "protein-language-modeling",
"model": "SaProt",
"description": "Structure-aware protein language modeling with amino-acid and Foldseek 3Di tokens for representation extraction, mutation-effect prediction, inverse folding, pretraining, downstream fine-tuning, and benchmark evaluation.",
"subtasks": [
"structure-aware-sequence-encoding",
"masked-language-model-inference",
"protein-embedding-extraction",
"zero-shot-mutation-effect-prediction",
"protein-inverse-folding",
"saprot-pretraining",
"downstream-finetuning",
"benchmark-evaluation",
"esm2-baseline-evaluation"
],
"entrypoints": {
"train": "scripts/training.py",
"pretrain_config": "conf/pretrain/saprot.yaml",
"thermos_finetune_config": "conf/Thermostability/saprot.yaml",
"scnet_thermos_finetune_config": "conf/scnet/Thermostability_saprot_1gpu.yaml",
"mutation_zeroshot": "scripts/mutation_zeroshot.py",
"proteingym_config": "conf/ProteinGym/saprot.yaml",
"clinvar_config": "conf/ClinVar/saprot.yaml",
"scnet_clinvar_config": "conf/scnet/ClinVar_saprot.yaml",
"clinvar_auc": "scripts/compute_clinvar_auc.py",
"environment_setup": "scripts/environment.sh"
},
"packages": [
"model",
"scripts.dataset",
"scripts.utils"
],
"configs": {
"root": "conf",
"saprot_tasks": [
"conf/Thermostability/saprot.yaml",
"conf/EC/saprot.yaml",
"conf/GO/MF/saprot.yaml",
"conf/GO/BP/saprot.yaml",
"conf/GO/CC/saprot.yaml",
"conf/MetalIonBinding/saprot.yaml",
"conf/HumanPPI/saprot.yaml",
"conf/Contact/saprot.yaml",
"conf/DeepLoc/cls2/saprot.yaml",
"conf/DeepLoc/cls10/saprot.yaml",
"conf/ProteinGym/saprot.yaml",
"conf/ClinVar/saprot.yaml"
],
"esm2_baselines": [
"conf/Thermostability/esm2.yaml",
"conf/EC/esm2.yaml",
"conf/GO/MF/esm2.yaml",
"conf/GO/BP/esm2.yaml",
"conf/GO/CC/esm2.yaml",
"conf/MetalIonBinding/esm2.yaml",
"conf/HumanPPI/esm2.yaml",
"conf/Contact/esm2.yaml",
"conf/DeepLoc/cls2/esm2.yaml",
"conf/DeepLoc/cls10/esm2.yaml",
"conf/ProteinGym/esm2.yaml",
"conf/ClinVar/esm2.yaml"
],
"scnet": [
"conf/scnet/Thermostability_saprot_1gpu.yaml",
"conf/scnet/ClinVar_saprot.yaml"
]
},
"example_data": [
"scripts/example/8ac8.cif"
],
"data_roots": {
"downstream_lmdb": "scripts/LMDB",
"pretrain_lmdb": "scripts/LMDB/AF2_Uniref50/foldseek",
"proteingym": "scripts/LMDB/ProteinGym/substitutions",
"clinvar": "scripts/LMDB/ClinVar",
"thermos": "scripts/LMDB/Thermostability/foldseek"
},
"model_cache": "weight/PLMs",
"default_model": "weight/PLMs/SaProt_650M_AF2",
"optional_models": {
"esm2_650m": "weight/PLMs/esm2_t33_650M_UR50D",
"saprot_inverse_folding": "weight/PLMs/SaProt_650M_AF2_inverse_folding"
},
"external_tools": {
"foldseek": "scripts/bin/foldseek"
},
"outputs": {
"finetuned_checkpoints": "weight/{task}/*.pt",
"proteingym_scores": "output/ProteinGym/SaProt_650M_AF2.tsv",
"clinvar_predictions": "output/ClinVar/SaProt_650M_AF2",
"scnet_clinvar_predictions": "output/ClinVar/SaProt_650M_AF2_scnet"
},
"quick_commands": {
"setup": "bash scripts/environment.sh",
"train_thermostability": "python scripts/training.py -c conf/Thermostability/saprot.yaml",
"train_thermostability_scnet_1gpu": "python scripts/training.py -c conf/scnet/Thermostability_saprot_1gpu.yaml",
"zeroshot_proteingym": "python scripts/mutation_zeroshot.py -c conf/ProteinGym/saprot.yaml",
"zeroshot_clinvar": "python scripts/mutation_zeroshot.py -c conf/ClinVar/saprot.yaml",
"compute_clinvar_auc": "python scripts/compute_clinvar_auc.py -c conf/ClinVar/saprot.yaml"
}
}
|