from model.splitters import * from model.featurizers import * from model.predictors import * from model.proposers import * from model.utils import * from pathlib import Path # dataset directory project_root = Path(__file__).resolve().parents[3] main_dir = project_root / 'data' / 'benchmark' seq_dir = main_dir / 'sequences' datasets_dir = main_dir / 'datasets' summary = pd.read_csv(main_dir / 'dataset_summary.csv') for index, row in summary.iterrows(): # default variables dataset_name, dataset_fname, sequence = receive_dataset_vars(row) # get dataset vars wt_file = retrieve_wt_file(dataset_name, seq_dir, sequence) # generate fasta file of sequence working_df_head, working_df_head_valid = preprocess_dataset(dataset_fname, datasets_dir, stringency='singles') # variables for training models protein_name = os.path.join(f"benchmark/", dataset_name) train_df = working_df_head_valid[['mutant','DMS_score','DMS_score_bin']].copy() # get feature feature = select_feature('onehot', protein_name) featurizers = [feature] # get splitters # generate split based on mutational load and do k-fold cross-validation splitters = [] for max_train_mut_load in range(1,4,1): splitter = MutLoadProteinSplitter(protein_name, train_df, wt_file, use_cache=True, y_scaling=True, val_split=0.15) splitter.split_data(max_train_muts=max_train_mut_load, min_test_muts=4, k_folds=5) splitters = splitters + splitter.folds models = [Fcn] run_nn_model_experiments(splitters, featurizers, models, experiment_name=dataset_name, use_cache=True, sweep_depth='custom', search_method='grid', count=1 )