Preprocess API
IMPROVE general preprocess parameters
- log_level
- Type: strDefault: “DEBUG”Help: Set log levels. Default is WARNING. Levels are: DEBUG, INFO, WARNING, ERROR, CRITICAL, NOTSET.
- input_dir
- Type: strDefault: “./”Help: Base directory for input data. All additional input pathes will be relative to the base input directory.
- output_dir
- Type: strDefault: “./”Help: Base directory for output data. All additional relative output pathes will be placed into the base output directory.
- config_file
- Type: strDefault: NoneHelp: Config file in INI format.
- param_log_file
- Type: strDefault: “param_log_file.txt”Help: Log of final parameters used for run. Saved in output_dir if file name, can be an absolute path.
- data_format
- Type: strDefault: “.parquet”Help: File format to save the ML data file (e.g., ‘.pt’, ‘.tfrecords’).
- input_supp_data_dir
- Type: strDefault: NoneHelp: Dir containing supplementary data in addition to benchmark data (usually model-specific data).
- x_data_dir
- Type: strDefault: “x_data”Help: Dir name that contains the files with features data (x data).
- y_data_dir
- Type: strDefault: “y_data”Help: Dir name that contains the files with target data (y data).
- splits_dir
- Type: strDefault: “splits”Help: Dir name that contains files that store split ids of the y data file.
- train_split_file
- Type: strDefault: “fake”Help: The path to the file that contains the train split ids (e.g., ‘split_0_train_id’, ‘split_0_train_size_1024’).
- val_split_file
- Type: strDefault: “fake”Help: The path to the file that contains the val split ids (e.g., ‘split_0_val_id’).
- test_split_file
- Type: strDefault: “fake”Help: The path to the file that contains the test split ids (e.g., ‘split_0_test_id’).
Drug Response Prediction preprocess parameters
- y_data_files
- Type: strDefault: “fake”Help: List of files that contain the y (prediction variable) data. Example: [[‘response.tsv’]].
- x_data_canc_files
- Type: strDefault: “fake”Help: List of feature files including gene_system_identifer. Example: [[‘cancer_gene_expression.tsv’, [‘Gene_Symbol’]]].
- x_data_drug_files
- Type: strDefault: “fake”Help: List of feature files. Example: [[‘drug_SMILES.tsv’]].
- canc_col_name
- Type: strDefault: “improve_sample_id”Help: Column name in the y (response) data file that contains the cancer sample ids.
- drug_col_name
- Type: strDefault: “improve_chem_id”Help: Column name in the y (response) data file that contains the drug ids.
- y_col_name
- Type: strDefault: “auc”Help: Column name in the y data file (e.g., response.tsv), that represents the target variable that the model predicts.