
.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/feature_selection/plot_feature_selection_pipeline.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_feature_selection_plot_feature_selection_pipeline.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_feature_selection_plot_feature_selection_pipeline.py:


==================
Pipeline ANOVA SVM
==================

This example shows how a feature selection can be easily integrated within
a machine learning pipeline.

We also show that you can easily inspect part of the pipeline.

.. GENERATED FROM PYTHON SOURCE LINES 14-16

We will start by generating a binary classification dataset. Subsequently, we
will divide the dataset into two subsets.

.. GENERATED FROM PYTHON SOURCE LINES 16-30

.. code-block:: Python


    from sklearn.datasets import make_classification
    from sklearn.model_selection import train_test_split

    X, y = make_classification(
        n_features=20,
        n_informative=3,
        n_redundant=0,
        n_classes=2,
        n_clusters_per_class=2,
        random_state=42,
    )
    X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=42)








.. GENERATED FROM PYTHON SOURCE LINES 31-43

A common mistake done with feature selection is to search a subset of
discriminative features on the full dataset, instead of only using the
training set. The usage of scikit-learn :func:`~sklearn.pipeline.Pipeline`
prevents to make such mistake.

Here, we will demonstrate how to build a pipeline where the first step will
be the feature selection.

When calling `fit` on the training data, a subset of feature will be selected
and the index of these selected features will be stored. The feature selector
will subsequently reduce the number of features, and pass this subset to the
classifier which will be trained.

.. GENERATED FROM PYTHON SOURCE LINES 43-53

.. code-block:: Python


    from sklearn.feature_selection import SelectKBest, f_classif
    from sklearn.pipeline import make_pipeline
    from sklearn.svm import LinearSVC

    anova_filter = SelectKBest(f_classif, k=3)
    clf = LinearSVC(dual="auto")
    anova_svm = make_pipeline(anova_filter, clf)
    anova_svm.fit(X_train, y_train)






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <style>#sk-container-id-15 {
      /* Definition of color scheme common for light and dark mode */
      --sklearn-color-text: black;
      --sklearn-color-line: gray;
      /* Definition of color scheme for unfitted estimators */
      --sklearn-color-unfitted-level-0: #fff5e6;
      --sklearn-color-unfitted-level-1: #f6e4d2;
      --sklearn-color-unfitted-level-2: #ffe0b3;
      --sklearn-color-unfitted-level-3: chocolate;
      /* Definition of color scheme for fitted estimators */
      --sklearn-color-fitted-level-0: #f0f8ff;
      --sklearn-color-fitted-level-1: #d4ebff;
      --sklearn-color-fitted-level-2: #b3dbfd;
      --sklearn-color-fitted-level-3: cornflowerblue;

      /* Specific color for light theme */
      --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));
      --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, white)));
      --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));
      --sklearn-color-icon: #696969;

      @media (prefers-color-scheme: dark) {
        /* Redefinition of color scheme for dark theme */
        --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));
        --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, #111)));
        --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));
        --sklearn-color-icon: #878787;
      }
    }

    #sk-container-id-15 {
      color: var(--sklearn-color-text);
    }

    #sk-container-id-15 pre {
      padding: 0;
    }

    #sk-container-id-15 input.sk-hidden--visually {
      border: 0;
      clip: rect(1px 1px 1px 1px);
      clip: rect(1px, 1px, 1px, 1px);
      height: 1px;
      margin: -1px;
      overflow: hidden;
      padding: 0;
      position: absolute;
      width: 1px;
    }

    #sk-container-id-15 div.sk-dashed-wrapped {
      border: 1px dashed var(--sklearn-color-line);
      margin: 0 0.4em 0.5em 0.4em;
      box-sizing: border-box;
      padding-bottom: 0.4em;
      background-color: var(--sklearn-color-background);
    }

    #sk-container-id-15 div.sk-container {
      /* jupyter's `normalize.less` sets `[hidden] { display: none; }`
         but bootstrap.min.css set `[hidden] { display: none !important; }`
         so we also need the `!important` here to be able to override the
         default hidden behavior on the sphinx rendered scikit-learn.org.
         See: https://github.com/scikit-learn/scikit-learn/issues/21755 */
      display: inline-block !important;
      position: relative;
    }

    #sk-container-id-15 div.sk-text-repr-fallback {
      display: none;
    }

    div.sk-parallel-item,
    div.sk-serial,
    div.sk-item {
      /* draw centered vertical line to link estimators */
      background-image: linear-gradient(var(--sklearn-color-text-on-default-background), var(--sklearn-color-text-on-default-background));
      background-size: 2px 100%;
      background-repeat: no-repeat;
      background-position: center center;
    }

    /* Parallel-specific style estimator block */

    #sk-container-id-15 div.sk-parallel-item::after {
      content: "";
      width: 100%;
      border-bottom: 2px solid var(--sklearn-color-text-on-default-background);
      flex-grow: 1;
    }

    #sk-container-id-15 div.sk-parallel {
      display: flex;
      align-items: stretch;
      justify-content: center;
      background-color: var(--sklearn-color-background);
      position: relative;
    }

    #sk-container-id-15 div.sk-parallel-item {
      display: flex;
      flex-direction: column;
    }

    #sk-container-id-15 div.sk-parallel-item:first-child::after {
      align-self: flex-end;
      width: 50%;
    }

    #sk-container-id-15 div.sk-parallel-item:last-child::after {
      align-self: flex-start;
      width: 50%;
    }

    #sk-container-id-15 div.sk-parallel-item:only-child::after {
      width: 0;
    }

    /* Serial-specific style estimator block */

    #sk-container-id-15 div.sk-serial {
      display: flex;
      flex-direction: column;
      align-items: center;
      background-color: var(--sklearn-color-background);
      padding-right: 1em;
      padding-left: 1em;
    }


    /* Toggleable style: style used for estimator/Pipeline/ColumnTransformer box that is
    clickable and can be expanded/collapsed.
    - Pipeline and ColumnTransformer use this feature and define the default style
    - Estimators will overwrite some part of the style using the `sk-estimator` class
    */

    /* Pipeline and ColumnTransformer style (default) */

    #sk-container-id-15 div.sk-toggleable {
      /* Default theme specific background. It is overwritten whether we have a
      specific estimator or a Pipeline/ColumnTransformer */
      background-color: var(--sklearn-color-background);
    }

    /* Toggleable label */
    #sk-container-id-15 label.sk-toggleable__label {
      cursor: pointer;
      display: block;
      width: 100%;
      margin-bottom: 0;
      padding: 0.5em;
      box-sizing: border-box;
      text-align: center;
    }

    #sk-container-id-15 label.sk-toggleable__label-arrow:before {
      /* Arrow on the left of the label */
      content: "▸";
      float: left;
      margin-right: 0.25em;
      color: var(--sklearn-color-icon);
    }

    #sk-container-id-15 label.sk-toggleable__label-arrow:hover:before {
      color: var(--sklearn-color-text);
    }

    /* Toggleable content - dropdown */

    #sk-container-id-15 div.sk-toggleable__content {
      max-height: 0;
      max-width: 0;
      overflow: hidden;
      text-align: left;
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-0);
    }

    #sk-container-id-15 div.sk-toggleable__content.fitted {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-0);
    }

    #sk-container-id-15 div.sk-toggleable__content pre {
      margin: 0.2em;
      border-radius: 0.25em;
      color: var(--sklearn-color-text);
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-0);
    }

    #sk-container-id-15 div.sk-toggleable__content.fitted pre {
      /* unfitted */
      background-color: var(--sklearn-color-fitted-level-0);
    }

    #sk-container-id-15 input.sk-toggleable__control:checked~div.sk-toggleable__content {
      /* Expand drop-down */
      max-height: 200px;
      max-width: 100%;
      overflow: auto;
    }

    #sk-container-id-15 input.sk-toggleable__control:checked~label.sk-toggleable__label-arrow:before {
      content: "▾";
    }

    /* Pipeline/ColumnTransformer-specific style */

    #sk-container-id-15 div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {
      color: var(--sklearn-color-text);
      background-color: var(--sklearn-color-unfitted-level-2);
    }

    #sk-container-id-15 div.sk-label.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {
      background-color: var(--sklearn-color-fitted-level-2);
    }

    /* Estimator-specific style */

    /* Colorize estimator box */
    #sk-container-id-15 div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-2);
    }

    #sk-container-id-15 div.sk-estimator.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-2);
    }

    #sk-container-id-15 div.sk-label label.sk-toggleable__label,
    #sk-container-id-15 div.sk-label label {
      /* The background is the default theme color */
      color: var(--sklearn-color-text-on-default-background);
    }

    /* On hover, darken the color of the background */
    #sk-container-id-15 div.sk-label:hover label.sk-toggleable__label {
      color: var(--sklearn-color-text);
      background-color: var(--sklearn-color-unfitted-level-2);
    }

    /* Label box, darken color on hover, fitted */
    #sk-container-id-15 div.sk-label.fitted:hover label.sk-toggleable__label.fitted {
      color: var(--sklearn-color-text);
      background-color: var(--sklearn-color-fitted-level-2);
    }

    /* Estimator label */

    #sk-container-id-15 div.sk-label label {
      font-family: monospace;
      font-weight: bold;
      display: inline-block;
      line-height: 1.2em;
    }

    #sk-container-id-15 div.sk-label-container {
      text-align: center;
    }

    /* Estimator-specific */
    #sk-container-id-15 div.sk-estimator {
      font-family: monospace;
      border: 1px dotted var(--sklearn-color-border-box);
      border-radius: 0.25em;
      box-sizing: border-box;
      margin-bottom: 0.5em;
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-0);
    }

    #sk-container-id-15 div.sk-estimator.fitted {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-0);
    }

    /* on hover */
    #sk-container-id-15 div.sk-estimator:hover {
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-2);
    }

    #sk-container-id-15 div.sk-estimator.fitted:hover {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-2);
    }

    /* Specification for estimator info (e.g. "i" and "?") */

    /* Common style for "i" and "?" */

    .sk-estimator-doc-link,
    a:link.sk-estimator-doc-link,
    a:visited.sk-estimator-doc-link {
      float: right;
      font-size: smaller;
      line-height: 1em;
      font-family: monospace;
      background-color: var(--sklearn-color-background);
      border-radius: 1em;
      height: 1em;
      width: 1em;
      text-decoration: none !important;
      margin-left: 1ex;
      /* unfitted */
      border: var(--sklearn-color-unfitted-level-1) 1pt solid;
      color: var(--sklearn-color-unfitted-level-1);
    }

    .sk-estimator-doc-link.fitted,
    a:link.sk-estimator-doc-link.fitted,
    a:visited.sk-estimator-doc-link.fitted {
      /* fitted */
      border: var(--sklearn-color-fitted-level-1) 1pt solid;
      color: var(--sklearn-color-fitted-level-1);
    }

    /* On hover */
    div.sk-estimator:hover .sk-estimator-doc-link:hover,
    .sk-estimator-doc-link:hover,
    div.sk-label-container:hover .sk-estimator-doc-link:hover,
    .sk-estimator-doc-link:hover {
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-3);
      color: var(--sklearn-color-background);
      text-decoration: none;
    }

    div.sk-estimator.fitted:hover .sk-estimator-doc-link.fitted:hover,
    .sk-estimator-doc-link.fitted:hover,
    div.sk-label-container:hover .sk-estimator-doc-link.fitted:hover,
    .sk-estimator-doc-link.fitted:hover {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-3);
      color: var(--sklearn-color-background);
      text-decoration: none;
    }

    /* Span, style for the box shown on hovering the info icon */
    .sk-estimator-doc-link span {
      display: none;
      z-index: 9999;
      position: relative;
      font-weight: normal;
      right: .2ex;
      padding: .5ex;
      margin: .5ex;
      width: min-content;
      min-width: 20ex;
      max-width: 50ex;
      color: var(--sklearn-color-text);
      box-shadow: 2pt 2pt 4pt #999;
      /* unfitted */
      background: var(--sklearn-color-unfitted-level-0);
      border: .5pt solid var(--sklearn-color-unfitted-level-3);
    }

    .sk-estimator-doc-link.fitted span {
      /* fitted */
      background: var(--sklearn-color-fitted-level-0);
      border: var(--sklearn-color-fitted-level-3);
    }

    .sk-estimator-doc-link:hover span {
      display: block;
    }

    /* "?"-specific style due to the `<a>` HTML tag */

    #sk-container-id-15 a.estimator_doc_link {
      float: right;
      font-size: 1rem;
      line-height: 1em;
      font-family: monospace;
      background-color: var(--sklearn-color-background);
      border-radius: 1rem;
      height: 1rem;
      width: 1rem;
      text-decoration: none;
      /* unfitted */
      color: var(--sklearn-color-unfitted-level-1);
      border: var(--sklearn-color-unfitted-level-1) 1pt solid;
    }

    #sk-container-id-15 a.estimator_doc_link.fitted {
      /* fitted */
      border: var(--sklearn-color-fitted-level-1) 1pt solid;
      color: var(--sklearn-color-fitted-level-1);
    }

    /* On hover */
    #sk-container-id-15 a.estimator_doc_link:hover {
      /* unfitted */
      background-color: var(--sklearn-color-unfitted-level-3);
      color: var(--sklearn-color-background);
      text-decoration: none;
    }

    #sk-container-id-15 a.estimator_doc_link.fitted:hover {
      /* fitted */
      background-color: var(--sklearn-color-fitted-level-3);
    }
    </style><div id="sk-container-id-15" class="sk-top-container"><div class="sk-text-repr-fallback"><pre>Pipeline(steps=[(&#x27;selectkbest&#x27;, SelectKBest(k=3)),
                    (&#x27;linearsvc&#x27;, LinearSVC(dual=&#x27;auto&#x27;))])</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class="sk-container" hidden><div class="sk-item sk-dashed-wrapped"><div class="sk-label-container"><div class="sk-label fitted sk-toggleable"><input class="sk-toggleable__control sk-hidden--visually" id="sk-estimator-id-38" type="checkbox" ><label for="sk-estimator-id-38" class="sk-toggleable__label fitted sk-toggleable__label-arrow fitted">&nbsp;&nbsp;Pipeline<a class="sk-estimator-doc-link fitted" rel="noreferrer" target="_blank" href="https://scikit-learn.org/1.4/modules/generated/sklearn.pipeline.Pipeline.html">?<span>Documentation for Pipeline</span></a><span class="sk-estimator-doc-link fitted">i<span>Fitted</span></span></label><div class="sk-toggleable__content fitted"><pre>Pipeline(steps=[(&#x27;selectkbest&#x27;, SelectKBest(k=3)),
                    (&#x27;linearsvc&#x27;, LinearSVC(dual=&#x27;auto&#x27;))])</pre></div> </div></div><div class="sk-serial"><div class="sk-item"><div class="sk-estimator fitted sk-toggleable"><input class="sk-toggleable__control sk-hidden--visually" id="sk-estimator-id-39" type="checkbox" ><label for="sk-estimator-id-39" class="sk-toggleable__label fitted sk-toggleable__label-arrow fitted">&nbsp;SelectKBest<a class="sk-estimator-doc-link fitted" rel="noreferrer" target="_blank" href="https://scikit-learn.org/1.4/modules/generated/sklearn.feature_selection.SelectKBest.html">?<span>Documentation for SelectKBest</span></a></label><div class="sk-toggleable__content fitted"><pre>SelectKBest(k=3)</pre></div> </div></div><div class="sk-item"><div class="sk-estimator fitted sk-toggleable"><input class="sk-toggleable__control sk-hidden--visually" id="sk-estimator-id-40" type="checkbox" ><label for="sk-estimator-id-40" class="sk-toggleable__label fitted sk-toggleable__label-arrow fitted">&nbsp;LinearSVC<a class="sk-estimator-doc-link fitted" rel="noreferrer" target="_blank" href="https://scikit-learn.org/1.4/modules/generated/sklearn.svm.LinearSVC.html">?<span>Documentation for LinearSVC</span></a></label><div class="sk-toggleable__content fitted"><pre>LinearSVC(dual=&#x27;auto&#x27;)</pre></div> </div></div></div></div></div></div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 54-60

Once the training is complete, we can predict on new unseen samples. In this
case, the feature selector will only select the most discriminative features
based on the information stored during training. Then, the data will be
passed to the classifier which will make the prediction.

Here, we show the final metrics via a classification report.

.. GENERATED FROM PYTHON SOURCE LINES 60-66

.. code-block:: Python


    from sklearn.metrics import classification_report

    y_pred = anova_svm.predict(X_test)
    print(classification_report(y_test, y_pred))





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

                  precision    recall  f1-score   support

               0       0.92      0.80      0.86        15
               1       0.75      0.90      0.82        10

        accuracy                           0.84        25
       macro avg       0.84      0.85      0.84        25
    weighted avg       0.85      0.84      0.84        25





.. GENERATED FROM PYTHON SOURCE LINES 67-70

Be aware that you can inspect a step in the pipeline. For instance, we might
be interested about the parameters of the classifier. Since we selected
three features, we expect to have three coefficients.

.. GENERATED FROM PYTHON SOURCE LINES 70-73

.. code-block:: Python


    anova_svm[-1].coef_





.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    array([[0.75788833, 0.27161955, 0.26113448]])



.. GENERATED FROM PYTHON SOURCE LINES 74-78

However, we do not know which features were selected from the original
dataset. We could proceed by several manners. Here, we will invert the
transformation of these coefficients to get information about the original
space.

.. GENERATED FROM PYTHON SOURCE LINES 78-81

.. code-block:: Python


    anova_svm[:-1].inverse_transform(anova_svm[-1].coef_)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    array([[0.        , 0.        , 0.75788833, 0.        , 0.        ,
            0.        , 0.        , 0.        , 0.        , 0.27161955,
            0.        , 0.        , 0.        , 0.        , 0.        ,
            0.        , 0.        , 0.        , 0.        , 0.26113448]])



.. GENERATED FROM PYTHON SOURCE LINES 82-84

We can see that the features with non-zero coefficients are the selected
features by the first step.


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.011 seconds)


.. _sphx_glr_download_auto_examples_feature_selection_plot_feature_selection_pipeline.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_feature_selection_pipeline.ipynb <plot_feature_selection_pipeline.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_feature_selection_pipeline.py <plot_feature_selection_pipeline.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_feature_selection_pipeline.zip <plot_feature_selection_pipeline.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_
