felimination 0.5.0

This library contains some useful scikit-learn compatible classes for feature selection.

Felimination

This library contains some useful scikit-learn compatible classes for feature selection.

Features

• Recursive Feature Elimination with Cross Validation using Permutation Importance
• Hybrid Genetic Algorithms x Feature Importance selection

Requirements

• Python 3.10+
• NumPy
• Scikit-learn
• Pandas

Installation

In a terminal shell run the following command

pip install felimination

Usage

Recursive Feature Elimination

In this section it will be illustrated how to use the PermutationImportanceRFECV class.

import numpy as np
from sklearn.datasets import make_classification
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import StratifiedKFold, cross_validate

from felimination.callbacks import plot_progress_callback
from felimination.rfe import PermutationImportanceRFECV


X, y = make_classification(
    n_samples=1000,
    n_features=200,
    n_informative=6,
    n_redundant=10,
    n_clusters_per_class=1,
    random_state=42,
    shuffle=False
)

model = LogisticRegression(random_state=42)

selector = PermutationImportanceRFECV(
    model,
    step=0.2,
    callbacks=[plot_progress_callback],
    scoring="roc_auc",
    cv=StratifiedKFold(random_state=42, shuffle=True),
    best_iteration_selection_criteria="mean_test_score"
)

selector.fit(X, y)

selector.support_
# array([False,  True,  True,  True, False,  True,  True,  True,  True,
#         True,  True, False, False, False, False,  True, False,  True,
#        False,  True, False, False, False, False, False, False, False,
#         True, False, False, False, False, False, False, False, False,
#         True, False, False, False, False, False,  True, False, False,
#         True, False,  True, False, False, False, False, False, False,
#        False, False, False, False, False, False, False, False, False,
#        False, False,  True,  True, False, False,  True, False,  True,
#        False,  True, False, False,  True, False, False, False,  True,
#        False,  True, False, False, False,  True, False,  True, False,
#        False, False, False,  True, False,  True, False, False, False,
#        False, False, False,  True, False, False,  True,  True,  True,
#        False, False, False, False, False,  True, False, False, False,
#        False, False, False, False, False, False, False, False, False,
#        False, False, False, False, False, False, False, False, False,
#        False, False, False, False, False, False, False, False, False,
#        False,  True, False, False, False, False, False, False, False,
#        False, False,  True,  True, False, False, False,  True, False,
#        False, False, False, False, False, False,  True, False, False,
#        False, False, False, False, False,  True, False, False, False,
#         True, False,  True, False, False, False,  True, False, False,
#        False, False, False, False, False, False, False, False,  True,
#        False, False])

selector.ranking_
# array([23,  5, 12,  2, 24, 15, 16,  1,  3,  6,  4, 24, 23, 19, 24, 14, 19,
#        17, 21, 16, 24, 20, 24, 21, 24, 18, 22, 16, 22, 23, 24, 21, 22, 22,
#        21, 22, 16, 20, 23, 23, 24, 20, 13, 24, 23, 13, 23, 14, 23, 22, 22,
#        24, 19, 19, 23, 19, 23, 20, 23, 23, 22, 23, 23, 23, 24, 17, 11, 20,
#        23, 10, 22, 14, 18, 13, 24, 21, 12, 23, 24, 18,  9, 21, 13, 21, 24,
#        21, 16, 18, 15, 21, 24, 22, 20, 17, 20, 17, 22, 21, 24, 19, 19, 24,
#        16, 20, 24, 15, 17, 17, 24, 24, 24, 22, 21, 14, 21, 22, 23, 24, 21,
#        21, 22, 20, 23, 23, 24, 20, 23, 23, 24, 24, 18, 19, 20, 22, 23, 24,
#        22, 18, 21, 24, 24, 23, 22, 24, 22, 15, 20, 21, 23, 23, 22, 19, 22,
#        20, 22,  8, 12, 20, 23, 22, 17, 18, 23, 24, 24, 22, 21, 24, 11, 19,
#        20, 24, 21, 24, 18, 21, 16, 21, 19, 24, 17, 18, 15, 24, 22, 24, 10,
#        19, 22, 24, 23, 24, 23, 20, 24, 23, 19,  7, 18, 23])
selector.plot()

Genetic Algorithms

In this section it will be illustrated how to use the HybridImportanceGACVFeatureSelector class.

import numpy as np
from sklearn.datasets import make_classification
from sklearn.linear_model import LogisticRegression

from felimination.ga import HybridImportanceGACVFeatureSelector


# Create dummy dataset
X, y = make_classification(
    n_samples=1000,
    n_features=20,
    n_informative=6,
    n_redundant=10,
    n_clusters_per_class=1,
    random_state=42,
)

# Initialize selector
selector = HybridImportanceGACVFeatureSelector(
    LogisticRegression(random_state=42),
    random_state=42,
    pool_size=5,
    patience=5
)

# Run optimisation
selector.fit(X, y)

# Show selected features
selector.support_
#array([False,  True, False,  True,  True, False, False, False,  True,
#       False, False, False,  True,  True,  True,  True, False,  True,
#        True, False])

# Show best solution
selector.best_solution_
# {'features': [1, 12, 13, 8, 17, 15, 18, 4, 3, 14],
#  'train_scores_per_fold': [0.88625, 0.89, 0.8825, 0.8925, 0.88625],
#  'test_scores_per_fold': [0.895, 0.885, 0.885, 0.89, 0.89],
#  'cv_importances': [array([[ 1.09135972,  1.13502636,  1.12100231,  0.38285736,  0.28944072,
#            0.04688614,  0.44259813,  0.09832365,  0.10190421, -0.48101593]]),
#   array([[ 1.17345812,  1.29375208,  1.2065342 ,  0.40418709,  0.41839714,
#            0.00447802,  0.466717  ,  0.21733829, -0.00842075, -0.50078996]]),
#   array([[ 1.15416104,  1.18458564,  1.18083266,  0.37071253,  0.22842685,
#            0.1087814 ,  0.44446793,  0.12740545,  0.00621562, -0.54064287]]),
#   array([[ 1.26011643,  1.36996058,  1.30481424,  0.48183549,  0.40589887,
#           -0.01849671,  0.45606913,  0.18330816,  0.03667055, -0.50869557]]),
#   array([[ 1.18227123,  1.28988253,  1.2496398 ,  0.50754295,  0.38942303,
#           -0.01725074,  0.4481891 ,  0.19472963,  0.10034316, -0.50131192]])],
#  'mean_train_score': 0.8875,
#  'mean_test_score': 0.889,
#  'mean_cv_importances': array([ 1.17227331,  1.25464144,  1.21256464,  0.42942709,  0.34631732,
#          0.02487962,  0.45160826,  0.16422104,  0.04734256, -0.50649125])}

# Show progress as a plot
selector.plot()

Looks like that the optimisation process converged after 2 steps, since the best score did not improve for 5(=patience) consecutive steps, the optimisation process stopped early.

License

This project is licensed under the BSD 3-Clause License - see the LICENSE.md file for details

Acknowledgments

• scikit-learn