#!/usr/bin/env python3
"""Module containing the Resampling class and the command line interface."""
import argparse
import pandas as pd
import numpy as np
from collections import Counter
from biobb_common.generic.biobb_object import BiobbObject
from sklearn import preprocessing
from sklearn.model_selection import cross_val_score
from sklearn.model_selection import RepeatedStratifiedKFold
from sklearn.ensemble import RandomForestClassifier
from biobb_ml.resampling.reg_resampler import resampler
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_ml.resampling.common import check_input_path, check_output_path, getCombinedMethod, checkResamplingType, getSamplingStrategy, getHeader, getTargetValue, getTarget, resampling_methods
[docs]class Resampling(BiobbObject):
"""
| biobb_ml Resampling
| Wrapper of the imblearn.combine methods.
| Combine over- and under-sampling methods to remove samples and supplement the dataset. If regression is specified as type, the data will be resampled to classes in order to apply the resampling model. Visit the imbalanced-learn official website for the different methods accepted in this wrapper: `SMOTETomek <https://imbalanced-learn.readthedocs.io/en/stable/generated/imblearn.combine.SMOTETomek.html>`_, `SMOTEENN <https://imbalanced-learn.readthedocs.io/en/stable/generated/imblearn.combine.SMOTEENN.html>`_.
Args:
input_dataset_path (str): Path to the input dataset. File type: input. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/data/resampling/dataset_resampling.csv>`_. Accepted formats: csv (edam:format_3752).
output_dataset_path (str): Path to the output dataset. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/resampling/ref_output_resampling.csv>`_. Accepted formats: csv (edam:format_3752).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **method** (*str*) - (None) Resampling method. It's a mandatory property. Values: smotetomek (`SMOTETomek <https://imbalanced-learn.readthedocs.io/en/stable/generated/imblearn.combine.SMOTETomek.html>`_: Class to perform over-sampling using SMOTE and cleaning using Tomek links), smotenn (`SMOTEENN <https://imbalanced-learn.readthedocs.io/en/stable/generated/imblearn.combine.SMOTEENN.html>`_: Class to perform over-sampling using SMOTE and cleaning using ENN).
* **type** (*str*) - (None) Type of oversampling. It's a mandatory property. Values: regression (the oversampling will be applied on a continuous dataset), classification (the oversampling will be applied on a classified dataset).
* **target** (*dict*) - ({}) Dependent variable you want to predict from your dataset. You can specify either a column name or a column index. Formats: { "column": "column3" } or { "index": 21 }. In case of mulitple formats, the first one will be picked.
* **evaluate** (*bool*) - (False) Whether or not to evaluate the dataset before and after applying the resampling.
* **evaluate_splits** (*int*) - (3) [2~100|1] Number of folds to be applied by the Repeated Stratified K-Fold evaluation method. Must be at least 2.
* **evaluate_repeats** (*int*) - (3) [2~100|1] Number of times Repeated Stratified K-Fold cross validator needs to be repeated.
* **n_bins** (*int*) - (5) [1~100|1] Only for regression resampling. The number of classes that the user wants to generate with the target data.
* **balanced_binning** (*bool*) - (False) Only for regression resampling. Decides whether samples are to be distributed roughly equally across all classes.
* **sampling_strategy_over** (*dict*) - ({ "target": "auto" }) Sampling information applied in the dataset oversampling process. Formats: { "target": "auto" }, { "ratio": 0.3 } or { "dict": { 0: 300, 1: 200, 2: 100 } }. When "target", specify the class targeted by the resampling; the number of samples in the different classes will be equalized; possible choices are: minority (resample only the minority class), not minority (resample all classes but the minority class), not majority (resample all classes but the majority class), all (resample all classes), auto (equivalent to 'not majority'). When "ratio", it corresponds to the desired ratio of the number of samples in the minority class over the number of samples in the majority class after resampling (ONLY IN CASE OF BINARY CLASSIFICATION). When "dict", the keys correspond to the targeted classes and the values correspond to the desired number of samples for each targeted class.
* **sampling_strategy_under** (*dict*) - ({ "target": "auto" }) Sampling information applied in the dataset cleaning process. Formats: { "target": "auto" } or { "list": [0, 2, 3] }. When "target", specify the class targeted by the resampling; the number of samples in the different classes will be equalized; possible choices are: majority (resample only the majority class), not minority (resample all classes but the minority class), not majority (resample all classes but the majority class), all (resample all classes), auto (equivalent to 'not minority'). When "list", the list contains the classes targeted by the resampling.
* **random_state_method** (*int*) - (5) [1~1000|1] Controls the randomization of the algorithm.
* **random_state_evaluate** (*int*) - (5) [1~1000|1] Controls the shuffling applied to the Repeated Stratified K-Fold evaluation method.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_ml.resampling.resampling import resampling
prop = {
'method': 'smotenn',
'type': 'regression',
'target': {
'column': 'target'
},
'evaluate': true,
'n_bins': 10,
'sampling_strategy_over': {
'dict': { '4': 1000, '5': 1000, '6': 1000, '7': 1000 }
},
'sampling_strategy_under': {
'list': [0,1]
}
}
resampling(input_dataset_path='/path/to/myDataset.csv',
output_dataset_path='/path/to/newDataset.csv',
properties=prop)
Info:
* wrapped_software:
* name: imbalanced-learn combine
* version: >0.7.0
* license: MIT
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_dataset_path, output_dataset_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_dataset_path": input_dataset_path},
"out": {"output_dataset_path": output_dataset_path}
}
# Properties specific for BB
self.method = properties.get('method', None)
self.type = properties.get('type', None)
self.target = properties.get('target', {})
self.evaluate = properties.get('evaluate', False)
self.evaluate_splits = properties.get('evaluate_splits', 3)
self.evaluate_repeats = properties.get('evaluate_repeats', 3)
self.n_bins = properties.get('n_bins', 5)
self.balanced_binning = properties.get('balanced_binning', False)
self.sampling_strategy_over = properties.get('sampling_strategy_over', {'target': 'auto'})
self.sampling_strategy_under = properties.get('sampling_strategy_under', {'target': 'auto'})
self.random_state_method = properties.get('random_state_method', 5)
self.random_state_evaluate = properties.get('random_state_evaluate', 5)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_dataset_path"] = check_input_path(self.io_dict["in"]["input_dataset_path"], "input_dataset_path", out_log, self.__class__.__name__)
self.io_dict["out"]["output_dataset_path"] = check_output_path(self.io_dict["out"]["output_dataset_path"], "output_dataset_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Resampling <resampling.resampling.Resampling>` resampling.resampling.Resampling object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# check mandatory properties
method, over, under = getCombinedMethod(self.method, self.out_log, self.__class__.__name__)
checkResamplingType(self.type, self.out_log, self.__class__.__name__)
sampling_strategy_over = getSamplingStrategy(self.sampling_strategy_over, self.out_log, self.__class__.__name__)
sampling_strategy_under = getSamplingStrategy(self.sampling_strategy_under, self.out_log, self.__class__.__name__)
# load dataset
fu.log('Getting dataset from %s' % self.io_dict["in"]["input_dataset_path"], self.out_log, self.global_log)
if 'column' in self.target:
labels = getHeader(self.io_dict["in"]["input_dataset_path"])
skiprows = 1
header = 0
else:
labels = None
skiprows = None
header = None
data = pd.read_csv(self.io_dict["in"]["input_dataset_path"], header=None, sep="\\s+|;|:|,|\t", engine="python", skiprows=skiprows, names=labels)
train_df = data
ranges = None
le = preprocessing.LabelEncoder()
cols_encoded = []
for column in train_df:
# if type object, LabelEncoder.fit_transform
if train_df[column].dtypes == 'object':
cols_encoded.append(column)
train_df[column] = le.fit_transform(train_df[column])
# defining X
X = train_df.loc[:, train_df.columns != getTargetValue(self.target, self.out_log, self.__class__.__name__)]
# calling resample method
if self.method == 'smotetomek':
method = method(smote=over(sampling_strategy=sampling_strategy_over), tomek=under(sampling_strategy=sampling_strategy_under), random_state=self.random_state_method)
elif self.method == 'smotenn':
method = method(smote=over(sampling_strategy=sampling_strategy_over), enn=under(sampling_strategy=sampling_strategy_under), random_state=self.random_state_method)
fu.log('Target: %s' % (getTargetValue(self.target, self.out_log, self.__class__.__name__)), self.out_log, self.global_log)
# resampling
if self.type == 'regression':
fu.log('Resampling regression dataset, continuous data will be classified', self.out_log, self.global_log)
# call resampler class for Regression ReSampling
rs = resampler()
# Create n_bins classes for the dataset
ranges, y, target_pos = rs.fit(train_df, target=getTargetValue(self.target, self.out_log, self.__class__.__name__), bins=self.n_bins, balanced_binning=self.balanced_binning, verbose=0)
# Get the re-sampled data
final_X, final_y = rs.resample(method, train_df, y)
elif self.type == 'classification':
# get X and y
y = getTarget(self.target, train_df, self.out_log, self.__class__.__name__)
# fit and resample
final_X, final_y = method.fit_resample(X, y)
target_pos = None
# evaluate resampling
if self.evaluate:
fu.log('Evaluating data before resampling with RandomForestClassifier', self.out_log, self.global_log)
cv = RepeatedStratifiedKFold(n_splits=self.evaluate_splits, n_repeats=self.evaluate_repeats, random_state=self.random_state_evaluate)
# evaluate model
scores = cross_val_score(RandomForestClassifier(class_weight='balanced'), X, y, scoring='accuracy', cv=cv, n_jobs=-1)
if not np.isnan(np.mean(scores)):
fu.log('Mean Accuracy before resampling: %.3f' % (np.mean(scores)), self.out_log, self.global_log)
else:
fu.log('Unable to calculate cross validation score, NaN was returned.', self.out_log, self.global_log)
# log distribution before resampling
dist = ''
for k, v in Counter(y).items():
per = v / len(y) * 100
rng = ''
if ranges:
rng = str(ranges[k])
dist = dist + 'Class=%d, n=%d (%.3f%%) %s\n' % (k, v, per, rng)
fu.log('Classes distribution before resampling:\n\n%s' % dist, self.out_log, self.global_log)
# join final_X and final_y in the output dataframe
if header is None:
# numpy
out_df = np.column_stack((final_X, final_y))
else:
# pandas
out_df = final_X.join(final_y)
# if no header, convert np to pd
if header is None:
out_df = pd.DataFrame(data=out_df)
# if cols encoded, decode them
if cols_encoded:
for column in cols_encoded:
if header is None:
out_df = out_df.astype({column: int})
out_df[column] = le.inverse_transform(out_df[column].values.ravel())
# if no header, target is in a different column
if target_pos:
t = target_pos
else:
t = getTargetValue(self.target, self.out_log, self.__class__.__name__)
# log distribution after resampling
if self.type == 'regression':
ranges, y_out, _ = rs.fit(out_df, target=t, bins=self.n_bins, balanced_binning=self.balanced_binning, verbose=0)
elif self.type == 'classification':
y_out = getTarget(self.target, out_df, self.out_log, self.__class__.__name__)
dist = ''
for k, v in Counter(y_out).items():
per = v / len(y_out) * 100
rng = ''
if ranges:
rng = str(ranges[k])
dist = dist + 'Class=%d, n=%d (%.3f%%) %s\n' % (k, v, per, rng)
fu.log('Classes distribution after resampling:\n\n%s' % dist, self.out_log, self.global_log)
# evaluate resampling
if self.evaluate:
fu.log('Evaluating data after resampling with RandomForestClassifier', self.out_log, self.global_log)
cv = RepeatedStratifiedKFold(n_splits=3, n_repeats=3, random_state=42)
# evaluate model
scores = cross_val_score(RandomForestClassifier(class_weight='balanced'), final_X, y_out, scoring='accuracy', cv=cv, n_jobs=-1)
if not np.isnan(np.mean(scores)):
fu.log('Mean Accuracy after resampling a %s dataset with %s method: %.3f' % (self.type, resampling_methods[self.method]['method'], np.mean(scores)), self.out_log, self.global_log)
else:
fu.log('Unable to calculate cross validation score, NaN was returned.', self.out_log, self.global_log)
# save output
hdr = False
if header == 0:
hdr = True
fu.log('Saving resampled dataset to %s' % self.io_dict["out"]["output_dataset_path"], self.out_log, self.global_log)
out_df.to_csv(self.io_dict["out"]["output_dataset_path"], index=False, header=hdr)
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def resampling(input_dataset_path: str, output_dataset_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Resampling <resampling.resampling.Resampling>` class and
execute the :meth:`launch() <resampling.resampling.Resampling.launch>` method."""
return Resampling(input_dataset_path=input_dataset_path,
output_dataset_path=output_dataset_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Wrapper of the imblearn.combine methods.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.')
required_args.add_argument('--output_dataset_path', required=True, help='Path to the output dataset. Accepted formats: csv.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
resampling(input_dataset_path=args.input_dataset_path,
output_dataset_path=args.output_dataset_path,
properties=properties)
if __name__ == '__main__':
main()