Preprocess API

IMPROVE general preprocess parameters

log_level
Type: str
Default: “DEBUG”
Help: Set log levels. Default is WARNING. Levels are: DEBUG, INFO, WARNING, ERROR, CRITICAL, NOTSET.
input_dir
Type: str
Default: “./”
Help: Base directory for input data. All additional input pathes will be relative to the base input directory.
output_dir
Type: str
Default: “./”
Help: Base directory for output data. All additional relative output pathes will be placed into the base output directory.
config_file
Type: str
Default: None
Help: Config file in INI format.
param_log_file
Type: str
Default: “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: str
Default: “.parquet”
Help: File format to save the ML data file (e.g., ‘.pt’, ‘.tfrecords’).
input_supp_data_dir
Type: str
Default: None
Help: Dir containing supplementary data in addition to benchmark data (usually model-specific data).
x_data_dir
Type: str
Default: “x_data”
Help: Dir name that contains the files with features data (x data).
y_data_dir
Type: str
Default: “y_data”
Help: Dir name that contains the files with target data (y data).
splits_dir
Type: str
Default: “splits”
Help: Dir name that contains files that store split ids of the y data file.
train_split_file
Type: str
Default: “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: str
Default: “fake”
Help: The path to the file that contains the val split ids (e.g., ‘split_0_val_id’).
test_split_file
Type: str
Default: “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: str
Default: “fake”
Help: List of files that contain the y (prediction variable) data. Example: [[‘response.tsv’]].
x_data_canc_files
Type: str
Default: “fake”
Help: List of feature files including gene_system_identifer. Example: [[‘cancer_gene_expression.tsv’, [‘Gene_Symbol’]]].
x_data_drug_files
Type: str
Default: “fake”
Help: List of feature files. Example: [[‘drug_SMILES.tsv’]].
canc_col_name
Type: str
Default: “improve_sample_id”
Help: Column name in the y (response) data file that contains the cancer sample ids.
drug_col_name
Type: str
Default: “improve_chem_id”
Help: Column name in the y (response) data file that contains the drug ids.
y_col_name
Type: str
Default: “auc”
Help: Column name in the y data file (e.g., response.tsv), that represents the target variable that the model predicts.