Coverage for biobb_ml/classification/logistic_regression.py: 83%
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« prev ^ index » next coverage.py v7.6.1, created at 2024-10-03 14:57 +0000
1#!/usr/bin/env python3
3"""Module containing the LogisticRegression class and the command line interface."""
4import argparse
5import joblib
6import pandas as pd
7import numpy as np
8from biobb_common.generic.biobb_object import BiobbObject
9from sklearn.preprocessing import StandardScaler
10from sklearn.model_selection import train_test_split
11from sklearn.metrics import confusion_matrix, classification_report, log_loss
12from sklearn import linear_model
13from biobb_common.configuration import settings
14from biobb_common.tools import file_utils as fu
15from biobb_common.tools.file_utils import launchlogger
16from biobb_ml.classification.common import check_input_path, check_output_path, getHeader, getIndependentVars, getIndependentVarsList, getTarget, getTargetValue, getWeight, plotMultipleCM, plotBinaryClassifier
19class LogisticRegression(BiobbObject):
20 """
21 | biobb_ml LogisticRegression
22 | Wrapper of the scikit-learn LogisticRegression method.
23 | Trains and tests a given dataset and saves the model and scaler. Visit the `LogisticRegression documentation page <https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html>`_ in the sklearn official website for further information.
25 Args:
26 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/classification/dataset_logistic_regression.csv>`_. Accepted formats: csv (edam:format_3752).
27 output_model_path (str): Path to the output model file. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_model_logistic_regression.pkl>`_. Accepted formats: pkl (edam:format_3653).
28 output_test_table_path (str) (Optional): Path to the test table file. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_test_logistic_regression.csv>`_. Accepted formats: csv (edam:format_3752).
29 output_plot_path (str) (Optional): Path to the statistics plot. If target is binary it shows confusion matrix, distributions of the predicted probabilities of both classes and ROC curve. If target is non-binary it shows confusion matrix. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_plot_logistic_regression.png>`_. Accepted formats: png (edam:format_3603).
30 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
31 * **independent_vars** (*dict*) - ({}) Independent variables you want to train from your dataset. You can specify either a list of columns names from your input dataset, a list of columns indexes or a range of columns indexes. Formats: { "columns": ["column1", "column2"] } or { "indexes": [0, 2, 3, 10, 11, 17] } or { "range": [[0, 20], [50, 102]] }. In case of mulitple formats, the first one will be picked.
32 * **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.
33 * **weight** (*dict*) - ({}) Weight variable 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.
34 * **solver** (*string*) - ("liblinear") Numerical optimizer to find parameters. Values: newton-cg (Recall the motivation for gradient descent step at x: we minimize the quadratic function), lbfgs (It's analogue of the Newton's Method but here the Hessian matrix is approximated using updates specified by gradient evaluations), liblinear (It's a linear classification that supports logistic regression and linear support vector machines), sag (SAG method optimizes the sum of a finite number of smooth convex functions), saga (It's a variant of SAG that also supports the non-smooth penalty=l1 option).
35 * **c_parameter** (*float*) - (0.01) [0~100|0.01] Inverse of regularization strength; must be a positive float. Smaller values specify stronger regularization.
36 * **normalize_cm** (*bool*) - (False) Whether or not to normalize the confusion matrix.
37 * **random_state_method** (*int*) - (5) [1~1000|1] Controls the randomness of the estimator.
38 * **random_state_train_test** (*int*) - (5) [1~1000|1] Controls the shuffling applied to the data before applying the split.
39 * **test_size** (*float*) - (0.2) [0~1|0.05] Represents the proportion of the dataset to include in the test split. It should be between 0.0 and 1.0.
40 * **scale** (*bool*) - (False) Whether or not to scale the input dataset.
41 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
42 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
43 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
45 Examples:
46 This is a use example of how to use the building block from Python::
48 from biobb_ml.classification.logistic_regression import logistic_regression
49 prop = {
50 'independent_vars': {
51 'columns': [ 'column1', 'column2', 'column3' ]
52 },
53 'target': {
54 'column': 'target'
55 },
56 'solver': 'liblinear',
57 'c_parameter': 0.01,
58 'test_size': 0.2
59 }
60 logistic_regression(input_dataset_path='/path/to/myDataset.csv',
61 output_model_path='/path/to/newModel.pkl',
62 output_test_table_path='/path/to/newTable.csv',
63 output_plot_path='/path/to/newPlot.png',
64 properties=prop)
66 Info:
67 * wrapped_software:
68 * name: scikit-learn LogisticRegression
69 * version: >=0.24.2
70 * license: BSD 3-Clause
71 * ontology:
72 * name: EDAM
73 * schema: http://edamontology.org/EDAM.owl
75 """
77 def __init__(self, input_dataset_path, output_model_path,
78 output_test_table_path=None, output_plot_path=None, properties=None, **kwargs) -> None:
79 properties = properties or {}
81 # Call parent class constructor
82 super().__init__(properties)
83 self.locals_var_dict = locals().copy()
85 # Input/Output files
86 self.io_dict = {
87 "in": {"input_dataset_path": input_dataset_path},
88 "out": {"output_model_path": output_model_path, "output_test_table_path": output_test_table_path, "output_plot_path": output_plot_path}
89 }
91 # Properties specific for BB
92 self.independent_vars = properties.get('independent_vars', {})
93 self.target = properties.get('target', {})
94 self.weight = properties.get('weight', {})
95 self.solver = properties.get('solver', 'liblinear')
96 self.c_parameter = properties.get('c_parameter', 0.01)
97 self.normalize_cm = properties.get('normalize_cm', False)
98 self.random_state_method = properties.get('random_state_method', 5)
99 self.random_state_train_test = properties.get('random_state_train_test', 5)
100 self.test_size = properties.get('test_size', 0.2)
101 self.scale = properties.get('scale', False)
102 self.properties = properties
104 # Check the properties
105 self.check_properties(properties)
106 self.check_arguments()
108 def check_data_params(self, out_log, err_log):
109 """ Checks all the input/output paths and parameters """
110 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__)
111 self.io_dict["out"]["output_model_path"] = check_output_path(self.io_dict["out"]["output_model_path"], "output_model_path", False, out_log, self.__class__.__name__)
112 if self.io_dict["out"]["output_test_table_path"]:
113 self.io_dict["out"]["output_test_table_path"] = check_output_path(self.io_dict["out"]["output_test_table_path"], "output_test_table_path", True, out_log, self.__class__.__name__)
114 if self.io_dict["out"]["output_plot_path"]:
115 self.io_dict["out"]["output_plot_path"] = check_output_path(self.io_dict["out"]["output_plot_path"], "output_plot_path", True, out_log, self.__class__.__name__)
117 @launchlogger
118 def launch(self) -> int:
119 """Execute the :class:`LogisticRegression <classification.logistic_regression.LogisticRegression>` classification.logistic_regression.LogisticRegression object."""
121 # check input/output paths and parameters
122 self.check_data_params(self.out_log, self.err_log)
124 # Setup Biobb
125 if self.check_restart():
126 return 0
127 self.stage_files()
129 # load dataset
130 fu.log('Getting dataset from %s' % self.io_dict["in"]["input_dataset_path"], self.out_log, self.global_log)
131 if 'columns' in self.independent_vars:
132 labels = getHeader(self.io_dict["in"]["input_dataset_path"])
133 skiprows = 1
134 else:
135 labels = None
136 skiprows = None
137 data = pd.read_csv(self.io_dict["in"]["input_dataset_path"], header=None, sep="\\s+|;|:|,|\t", engine="python", skiprows=skiprows, names=labels)
139 # declare inputs, targets and weights
140 # the inputs are all the independent variables
141 X = getIndependentVars(self.independent_vars, data, self.out_log, self.__class__.__name__)
142 fu.log('Independent variables: [%s]' % (getIndependentVarsList(self.independent_vars)), self.out_log, self.global_log)
143 # target
144 y = getTarget(self.target, data, self.out_log, self.__class__.__name__)
145 fu.log('Target: %s' % (getTargetValue(self.target)), self.out_log, self.global_log)
146 # weights
147 if self.weight:
148 w = getWeight(self.weight, data, self.out_log, self.__class__.__name__)
149 fu.log('Weight column provided', self.out_log, self.global_log)
151 # train / test split
152 fu.log('Creating train and test sets', self.out_log, self.global_log)
153 arrays_sets = (X, y)
154 # if user provide weights
155 if self.weight:
156 arrays_sets = arrays_sets + (w,)
157 X_train, X_test, y_train, y_test, w_train, w_test = train_test_split(*arrays_sets, test_size=self.test_size, random_state=self.random_state_train_test)
158 else:
159 X_train, X_test, y_train, y_test = train_test_split(*arrays_sets, test_size=self.test_size, random_state=self.random_state_train_test)
161 # scale dataset
162 if self.scale:
163 fu.log('Scaling dataset', self.out_log, self.global_log)
164 scaler = StandardScaler()
165 X_train = scaler.fit_transform(X_train)
167 # classification
168 fu.log('Training dataset applying logistic regression', self.out_log, self.global_log)
169 model = linear_model.LogisticRegression(C=self.c_parameter, solver=self.solver, random_state=self.random_state_method)
171 arrays_fit = (X_train, y_train)
172 # if user provide weights
173 if self.weight:
174 arrays_fit = arrays_fit + (w_train,)
176 model.fit(*arrays_fit)
178 y_hat_train = model.predict(X_train)
179 # classification report
180 cr_train = classification_report(y_train, y_hat_train)
181 # log loss
182 yhat_prob_train = model.predict_proba(X_train)
183 l_loss_train = log_loss(y_train, yhat_prob_train)
184 fu.log('Calculating scores and report for training dataset\n\nCLASSIFICATION REPORT\n\n%s\nLog loss: %.3f\n' % (cr_train, l_loss_train), self.out_log, self.global_log)
186 # compute confusion matrix
187 cnf_matrix_train = confusion_matrix(y_train, y_hat_train)
188 np.set_printoptions(precision=2)
189 if self.normalize_cm:
190 cnf_matrix_train = cnf_matrix_train.astype('float') / cnf_matrix_train.sum(axis=1)[:, np.newaxis]
191 cm_type = 'NORMALIZED CONFUSION MATRIX'
192 else:
193 cm_type = 'CONFUSION MATRIX, WITHOUT NORMALIZATION'
195 fu.log('Calculating confusion matrix for training dataset\n\n%s\n\n%s\n' % (cm_type, cnf_matrix_train), self.out_log, self.global_log)
197 # testing
198 # predict data from x_test
199 if self.scale:
200 X_test = scaler.transform(X_test)
201 y_hat_test = model.predict(X_test)
202 test_table = pd.DataFrame()
203 y_hat_prob = model.predict_proba(X_test)
204 y_hat_prob = np.around(y_hat_prob, decimals=2)
205 y_hat_prob = tuple(map(tuple, y_hat_prob))
206 test_table['P' + np.array2string(np.unique(y_test))] = y_hat_prob
207 y_test = y_test.reset_index(drop=True)
208 test_table['target'] = y_test
210 fu.log('Testing\n\nTEST DATA\n\n%s\n' % test_table, self.out_log, self.global_log)
212 # classification report
213 cr = classification_report(y_test, y_hat_test)
214 # log loss
215 yhat_prob = model.predict_proba(X_test)
216 l_loss = log_loss(y_test, yhat_prob)
217 fu.log('Calculating scores and report for testing dataset\n\nCLASSIFICATION REPORT\n\n%s\nLog loss: %.3f\n' % (cr, l_loss), self.out_log, self.global_log)
219 # compute confusion matrix
220 cnf_matrix = confusion_matrix(y_test, y_hat_test)
221 np.set_printoptions(precision=2)
222 if self.normalize_cm:
223 cnf_matrix = cnf_matrix.astype('float') / cnf_matrix.sum(axis=1)[:, np.newaxis]
224 cm_type = 'NORMALIZED CONFUSION MATRIX'
225 else:
226 cm_type = 'CONFUSION MATRIX, WITHOUT NORMALIZATION'
228 fu.log('Calculating confusion matrix for testing dataset\n\n%s\n\n%s\n' % (cm_type, cnf_matrix), self.out_log, self.global_log)
230 if (self.io_dict["out"]["output_test_table_path"]):
231 fu.log('Saving testing data to %s' % self.io_dict["out"]["output_test_table_path"], self.out_log, self.global_log)
232 test_table.to_csv(self.io_dict["out"]["output_test_table_path"], index=False, header=True)
234 # plot
235 if self.io_dict["out"]["output_plot_path"]:
236 vs = y.unique().tolist()
237 vs.sort()
238 if len(vs) > 2:
239 plot = plotMultipleCM(cnf_matrix_train, cnf_matrix, self.normalize_cm, vs)
240 fu.log('Saving confusion matrix plot to %s' % self.io_dict["out"]["output_plot_path"], self.out_log, self.global_log)
241 else:
242 plot = plotBinaryClassifier(model, yhat_prob_train, yhat_prob, cnf_matrix_train, cnf_matrix, y_train, y_test, normalize=self.normalize_cm)
243 fu.log('Saving binary classifier evaluator plot to %s' % self.io_dict["out"]["output_plot_path"], self.out_log, self.global_log)
244 plot.savefig(self.io_dict["out"]["output_plot_path"], dpi=150)
246 # save model, scaler and parameters
247 tv = y.unique().tolist()
248 tv.sort()
249 variables = {
250 'target': self.target,
251 'independent_vars': self.independent_vars,
252 'scale': self.scale,
253 'target_values': tv
254 }
255 fu.log('Saving model to %s' % self.io_dict["out"]["output_model_path"], self.out_log, self.global_log)
256 with open(self.io_dict["out"]["output_model_path"], "wb") as f:
257 joblib.dump(model, f)
258 if self.scale:
259 joblib.dump(scaler, f)
260 joblib.dump(variables, f)
262 # Copy files to host
263 self.copy_to_host()
265 self.tmp_files.extend([
266 self.stage_io_dict.get("unique_dir")
267 ])
268 self.remove_tmp_files()
270 self.check_arguments(output_files_created=True, raise_exception=False)
272 return 0
275def logistic_regression(input_dataset_path: str, output_model_path: str, output_test_table_path: str = None, output_plot_path: str = None, properties: dict = None, **kwargs) -> int:
276 """Execute the :class:`LogisticRegression <classification.logistic_regression.LogisticRegression>` class and
277 execute the :meth:`launch() <classification.logistic_regression.LogisticRegression.launch>` method."""
279 return LogisticRegression(input_dataset_path=input_dataset_path,
280 output_model_path=output_model_path,
281 output_test_table_path=output_test_table_path,
282 output_plot_path=output_plot_path,
283 properties=properties, **kwargs).launch()
286def main():
287 """Command line execution of this building block. Please check the command line documentation."""
288 parser = argparse.ArgumentParser(description="Wrapper of the scikit-learn LogisticRegression method.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
289 parser.add_argument('--config', required=False, help='Configuration file')
291 # Specific args of each building block
292 required_args = parser.add_argument_group('required arguments')
293 required_args.add_argument('--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.')
294 required_args.add_argument('--output_model_path', required=True, help='Path to the output model file. Accepted formats: pkl.')
295 parser.add_argument('--output_test_table_path', required=False, help='Path to the test table file. Accepted formats: csv.')
296 parser.add_argument('--output_plot_path', required=False, help='Path to the statistics plot. If target is binary it shows confusion matrix, distributions of the predicted probabilities of both classes and ROC curve. If target is non-binary it shows confusion matrix. Accepted formats: png.')
298 args = parser.parse_args()
299 args.config = args.config or "{}"
300 properties = settings.ConfReader(config=args.config).get_prop_dic()
302 # Specific call of each building block
303 logistic_regression(input_dataset_path=args.input_dataset_path,
304 output_model_path=args.output_model_path,
305 output_test_table_path=args.output_test_table_path,
306 output_plot_path=args.output_plot_path,
307 properties=properties)
310if __name__ == '__main__':
311 main()