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config.json
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config.json
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{
"EMBEDDING_MODELS" : {
"ESM2_T6_8M_UR50D": false,
"ESM2_T12_35M_UR50D": false,
"ESM2_T30_150M_UR50D": false,
"ESM2_T33_650M_UR50D": true,
"ESM2_T36_3B_UR50D": false,
"ESM2_T48_15B_UR50D": false,
"ESMFold": false,
"AMPLIFY_120M": false,
"AMPLIFY_120M_base": false,
"AMPLIFY_350M": false,
"AMPLIFY_350M_base": false
},
"EMBEDDING_LAYERS": [-1],
"EMBEDDING_TYPES": ["MEAN"],
"NORMALISE_EMBEDDINGS": false,
"DOWNSTREAM_MODELS": {
"FFNN": true,
"LSTM_UNIDIRECTIONAL": false,
"LSTM_BIDIRECTIONAL": false,
"GRU_UNIDIRECTIONAL": false,
"GRU_BIDIRECTIONAL": false
},
"DATASETS_FOR_TRAINING": ["ROCKLIN_INDELS"],
"DATASETS_FOR_INFERENCE": ["ROCKLIN_INDELS"],
"AMINO_ACIDS": "ACDEFGHIKLMNPQRSTVWY",
"SPLITS": {
"TRAINING_SIZE": 0.8,
"VALIDATION_SIZE": 0.00,
"TESTING_SIZE": 0.2
},
"MODEL_ARCHITECTURE": {
"HIDDEN_LAYERS": [256, 2],
"DROPOUT_LAYERS": [0, 0, 0, 0],
"WEIGHT_DECAY": 0.0007,
"ACTIVATION_FUNCTIONS": {
"RELU": false,
"LEAKYRELU": false,
"ELU": false,
"GELU": true,
"SELU": false
},
"LOSS_FUNCTIONS": {
"MSELOSS": false,
"MAELOSS": true,
"HUBERLOSS": false
},
"OPTIMISERS": {
"ADAM": true,
"SGD": false,
"RMSPROP": false,
"ADAMW": false
}
},
"TRAINING_PARAMETERS": {
"BATCH_SIZE": 128,
"LEARNING_RATE": 0.005,
"MIN_EPOCHS": 30,
"MAX_EPOCHS": 100,
"PATIENCE": 3,
"RANDOM_STATE": 1,
"N_WORKERS": 0
},
"HYPERPARAMETER_TUNING": {
"SEARCH_ITERATIONS": 10,
"MIN_BATCH_SIZE": 4,
"MAX_BATCH_SIZE": 256,
"MIN_HIDDEN_LAYERS": 1,
"MAX_HIDDEN_LAYERS": 4,
"MIN_HIDDEN_LAYER_SIZE": 2,
"MAX_HIDDEN_LAYER_SIZE": 16,
"MIN_DROPOUT": 0.0,
"MAX_DROPOUT": 0.5,
"MIN_LEARNING_RATE": 0.001,
"MAX_LEARNING_RATE": 0.01,
"MIN_WEIGHT_DECAY": 0,
"MAX_WEIGHT_DECAY": 0.001
},
"DATASETS" : {
"MAGDA" : {
"PATH" : "magda/data_main_magda.csv",
"DOMAIN_NAME_COLUMN" : "domain",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq",
"ENERGY_COLUMN": "",
"FITNESS_COLUMN" : "scaled_fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
},
"TONI" : {
"PATH" : "toni/data_main_toni.tsv",
"DOMAIN_NAME_COLUMN" : "domain_ID",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq",
"ENERGY_COLUMN": "",
"FITNESS_COLUMN" : "normalized_fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
},
"SMALL_TONI": {
"PATH": "toni/data_small_toni.tsv",
"DOMAIN_NAME_COLUMN": "domain_ID",
"VARIANT_AA_SEQ_COLUMN": "aa_seq",
"ENERGY_COLUMN": "",
"FITNESS_COLUMN" : "normalized_fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
},
"ROCKLIN" : {
"PATH" : "rocklin/data_with_fitness_rocklin.csv",
"DOMAIN_NAME_COLUMN" : "name",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq_full",
"ENERGY_COLUMN": "ddG_ML",
"FITNESS_COLUMN" : "fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": "."
},
"SMALL_ROCKLIN" : {
"PATH" : "rocklin/small_subset_with_fitness_rocklin.csv",
"DOMAIN_NAME_COLUMN" : "name",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq_full",
"ENERGY_COLUMN": "ddG_ML",
"FITNESS_COLUMN" : "fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": "."
},
"ROCKLIN_INDELS" : {
"PATH" : "rocklin/indels_with_fitness_rocklin.csv",
"DOMAIN_NAME_COLUMN" : "name",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq_full",
"ENERGY_COLUMN": "ddG_ML",
"FITNESS_COLUMN" : "fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": "."
},
"SMALL_ROCKLIN_INDELS" : {
"PATH" : "rocklin/indels_small_subset_with_fitness_rocklin.csv",
"DOMAIN_NAME_COLUMN" : "name",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq_full",
"ENERGY_COLUMN": "ddG_ML",
"FITNESS_COLUMN" : "fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": "."
},
"SMALL_ROCKLIN_SUBSTITUTIONS" : {
"PATH" : "rocklin/substitutions_small_subset_with_fitness_rocklin.csv",
"DOMAIN_NAME_COLUMN" : "name",
"VARIANT_AA_SEQ_COLUMN" : "aa_seq_full",
"ENERGY_COLUMN": "ddG_ML",
"FITNESS_COLUMN" : "fitness",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": "."
},
"FIREPROT" : {
"PATH" : "fireprot/",
"DOMAIN_NAME_COLUMN" : "",
"VARIANT_AA_SEQ_COLUMN" : "",
"ENERGY_COLUMN": "ddG",
"FITNESS_COLUMN" : "",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
},
"VAMP_SEQ": {
"PATH":"vamp_seq/data_main_vamp_seq.csv",
"DOMAIN_NAME_COLUMN":"mutant",
"VARIANT_AA_SEQ_COLUMN":"mutated_sequence",
"ENERGY_COLUMN": "",
"FITNESS_COLUMN":"DMS_score",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
},
"CUSTOM": {
"PATH":"",
"DOMAIN_NAME_COLUMN":"",
"VARIANT_AA_SEQ_COLUMN":"",
"ENERGY_COLUMN": "",
"FITNESS_COLUMN":"",
"IS_ENERGY_REVERSED": false,
"IS_FITNESS_REVERSED": false,
"DROP_DOMAIN_NAME_EXTENSION": null
}
}
}