91 lines
2.7 KiB
Python
91 lines
2.7 KiB
Python
"""
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===================================================
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Recursive feature elimination with cross-validation
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===================================================
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A Recursive Feature Elimination (RFE) example with automatic tuning of the
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number of features selected with cross-validation.
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"""
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# %%
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# Data generation
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# ---------------
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#
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# We build a classification task using 3 informative features. The introduction
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# of 2 additional redundant (i.e. correlated) features has the effect that the
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# selected features vary depending on the cross-validation fold. The remaining
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# features are non-informative as they are drawn at random.
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from sklearn.datasets import make_classification
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X, y = make_classification(
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n_samples=500,
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n_features=15,
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n_informative=3,
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n_redundant=2,
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n_repeated=0,
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n_classes=8,
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n_clusters_per_class=1,
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class_sep=0.8,
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random_state=0,
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)
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# %%
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# Model training and selection
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# ----------------------------
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#
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# We create the RFE object and compute the cross-validated scores. The scoring
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# strategy "accuracy" optimizes the proportion of correctly classified samples.
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from sklearn.feature_selection import RFECV
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from sklearn.linear_model import LogisticRegression
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from sklearn.model_selection import StratifiedKFold
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min_features_to_select = 1 # Minimum number of features to consider
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clf = LogisticRegression()
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cv = StratifiedKFold(5)
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rfecv = RFECV(
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estimator=clf,
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step=1,
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cv=cv,
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scoring="accuracy",
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min_features_to_select=min_features_to_select,
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n_jobs=2,
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)
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rfecv.fit(X, y)
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print(f"Optimal number of features: {rfecv.n_features_}")
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# %%
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# In the present case, the model with 3 features (which corresponds to the true
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# generative model) is found to be the most optimal.
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#
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# Plot number of features VS. cross-validation scores
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# ---------------------------------------------------
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import matplotlib.pyplot as plt
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import pandas as pd
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cv_results = pd.DataFrame(rfecv.cv_results_)
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plt.figure()
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plt.xlabel("Number of features selected")
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plt.ylabel("Mean test accuracy")
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plt.errorbar(
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x=cv_results["n_features"],
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y=cv_results["mean_test_score"],
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yerr=cv_results["std_test_score"],
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)
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plt.title("Recursive Feature Elimination \nwith correlated features")
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plt.show()
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# %%
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# From the plot above one can further notice a plateau of equivalent scores
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# (similar mean value and overlapping errorbars) for 3 to 5 selected features.
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# This is the result of introducing correlated features. Indeed, the optimal
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# model selected by the RFE can lie within this range, depending on the
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# cross-validation technique. The test accuracy decreases above 5 selected
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# features, this is, keeping non-informative features leads to over-fitting and
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# is therefore detrimental for the statistical performance of the models.
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