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These 10 scikit-learn patterns cover variance filters, supervised ranking, model-based selection and recursive elimination. They are not 10 interchangeable algorithms: choose one that fits your target and feature assumptions, then evaluate it inside a pipeline so selection does not leak information from validation data.

Set up the examples

Each snippet assumes X contains the feature columns and y contains the target. The snippets show the relevant scikit-learn imports beside each pattern; install scikit-learn and ensure your data is in a format accepted by the selected estimator and score function. For supervised selectors, fit only on training data or put the selector in a pipeline as shown below.

10 feature-selection one-liners

1. Remove constant features

VarianceThreshold is unsupervised: it looks at X, not y. Its default threshold of zero removes features that do not vary.

from sklearn.feature_selection import VarianceThreshold

X_var = VarianceThreshold().fit_transform(X)

2. Remove features below a variance floor

A positive threshold removes low-variance features as well. The example uses 0.01 only as an illustration; variance depends on feature scale, so choose a threshold appropriate to your data rather than treating this value as universal.

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from sklearn.feature_selection import VarianceThreshold

X_var = VarianceThreshold(threshold=0.01).fit_transform(X)

3. Keep the top features by ANOVA F-score for classification

f_classif scores each feature individually against a classification target. SelectKBest retains the requested number of highest-scoring features.

from sklearn.feature_selection import SelectKBest, f_classif

X_top = SelectKBest(f_classif, k=10).fit_transform(X, y)

4. Keep the top features by F-score for regression

For a regression target, use f_regression instead of the classification score.

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from sklearn.feature_selection import SelectKBest, f_regression

X_top = SelectKBest(f_regression, k=10).fit_transform(X, y)

5. Rank non-negative features with chi-squared scoring

chi2 is a univariate score for classification, and its input features must be non-negative. If your data includes negative values, do not apply this snippet without an appropriate transformation.

from sklearn.feature_selection import SelectKBest, chi2

X_top = SelectKBest(chi2, k=10).fit_transform(X, y)

6. Rank features by mutual information for classification

Mutual information can detect statistical dependence beyond the relationships captured by an F-test. It estimates dependence nonparametrically, so results require enough data for a useful estimate and correct treatment of discrete versus continuous features.

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from sklearn.feature_selection import SelectKBest, mutual_info_classif

X_top = SelectKBest(mutual_info_classif, k=10).fit_transform(X, y)

7. Select features using model importance

SelectFromModel relies on an estimator that exposes feature importances or coefficients after fitting. This random-forest example uses the selector’s default threshold, which is estimator-dependent; for reproducible choices, set a threshold deliberately and validate it.

from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import SelectFromModel

X_model = SelectFromModel(estimator=RandomForestClassifier()).fit_transform(X, y)

8. Use L1-regularized logistic regression as a selector

L1 regularization can drive some logistic-regression coefficients to zero, giving SelectFromModel a sparse set of weights to use. This is a classification pattern, and coefficient-based selection can be affected by feature scaling.

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from sklearn.feature_selection import SelectFromModel
from sklearn.linear_model import LogisticRegression

X_l1 = SelectFromModel(
    LogisticRegression(penalty="l1", solver="liblinear")
).fit_transform(X, y)

9. Recursively eliminate features to a chosen count

Recursive Feature Elimination (RFE) repeatedly fits an estimator and removes features according to its feature weights. The estimator must expose coefficients or feature importances.

from sklearn.feature_selection import RFE
from sklearn.linear_model import LogisticRegression

X_rfe = RFE(
    estimator=LogisticRegression(), n_features_to_select=10
).fit_transform(X, y)

10. Put selection and prediction in one pipeline

A pipeline lets cross-validation fit the selector using each training fold and then apply it to that fold’s held-out data. This is the safe pattern for evaluating selection with cross-validation.

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from sklearn.feature_selection import SelectKBest, f_classif
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import cross_val_score
from sklearn.pipeline import make_pipeline

pipe = make_pipeline(SelectKBest(f_classif, k=10), LogisticRegression())
scores = cross_val_score(pipe, X, y, cv=5)
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Which selection family should you use?

Family What it uses Useful distinction Watch out for
Variance filter Features in X only Removes constant or low-variance columns without using the target Threshold is scale-sensitive and says nothing about target relevance
Univariate filter A per-feature score against y Simple feature ranking; SelectKBest keeps a chosen count Each feature is scored individually; match the score to target type and assumptions
Mutual information Estimated feature-target dependence Can represent broader statistical dependence than an F-test Nonparametric estimates need enough data and suitable discrete-feature declarations
Model-based Estimator coefficients or importances Selection reflects a chosen model’s weights Results depend on estimator, threshold and, for coefficient models, feature scales
Recursive or sequential Repeated model fits or feature-subset evaluation Can account for model performance as features are selected Usually costs more fitting work; selection must remain inside validation folds

These examples are one-line patterns, not 10 distinct algorithms: several use the same selector with a different score or configuration. Other scikit-learn options include SelectPercentile, SelectFdr, RFECV and SequentialFeatureSelector. Sequential approaches can require substantially more model fitting than a simple filter, so consider computation as well as assumptions and validation results.

Prevent feature-selection leakage

The scikit-learn Common pitfalls and recommended practices guide says: “As with any other type of preprocessing, feature selection should only use the training data.” If a selector is fit on the full dataset before a split, information from the eventual validation or test set can influence which features are chosen, making an evaluation misleading.

Scikit-learn’s current Common pitfalls documentation, shown as version 1.9.1, illustrates the problem with 200 samples and 10,000 random features: selecting before splitting reports 0.76 accuracy, while splitting first and fitting selection on training data reports 0.5. These are outputs from a synthetic leakage demonstration with random targets, not general benchmarks or expected performance figures.

  1. Choose the selector and prediction estimator for the task.
  2. Place both in a scikit-learn Pipeline or make_pipeline.
  3. Pass the complete pipeline—not a preselected matrix—to cross_val_score or a model-selection routine.
  4. For a final holdout evaluation, split first, fit the pipeline on training data, and score it on the untouched test data.

Choose and evaluate a selector

  • Use a variance filter when the aim is to remove constant or near-constant columns, not to identify features predictive of y.
  • For supervised filters, match the score to classification or regression; use chi2 only with non-negative features.
  • Use mutual information when broader dependence is useful and the sample size and feature-type settings support a meaningful estimate.
  • Use model-based or recursive selection when the chosen estimator’s weights or repeated evaluation are relevant to the modeling objective; account for scaling and extra fit cost.
  • Compare selectors through the same leakage-safe validation procedure. A selected feature count or a high training score alone does not establish that a selector will generalize.

For release-specific behavior, check the installed version’s VarianceThreshold, SelectKBest, feature-selection API and SelectFromModel documentation. The SelectFromModel link is the development documentation, so verify defaults against your installed release before relying on them.

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