.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/model_selection/plot_cv_indices.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_model_selection_plot_cv_indices.py: Visualizing cross-validation behavior in scikit-learn ===================================================== Choosing the right cross-validation object is a crucial part of fitting a model properly. There are many ways to split data into training and test sets in order to avoid model overfitting, to standardize the number of groups in test sets, etc. This example visualizes the behavior of several common scikit-learn objects for comparison. .. GENERATED FROM PYTHON SOURCE LINES 14-34 .. code-block:: default from sklearn.model_selection import ( TimeSeriesSplit, KFold, ShuffleSplit, StratifiedKFold, GroupShuffleSplit, GroupKFold, StratifiedShuffleSplit, StratifiedGroupKFold, ) import numpy as np import matplotlib.pyplot as plt from matplotlib.patches import Patch np.random.seed(1338) cmap_data = plt.cm.Paired cmap_cv = plt.cm.coolwarm n_splits = 4 .. GENERATED FROM PYTHON SOURCE LINES 35-47 Visualize our data ------------------ First, we must understand the structure of our data. It has 100 randomly generated input datapoints, 3 classes split unevenly across datapoints, and 10 "groups" split evenly across datapoints. As we'll see, some cross-validation objects do specific things with labeled data, others behave differently with grouped data, and others do not use this information. To begin, we'll visualize our data. .. GENERATED FROM PYTHON SOURCE LINES 47-88 .. code-block:: default # Generate the class/group data n_points = 100 X = np.random.randn(100, 10) percentiles_classes = [0.1, 0.3, 0.6] y = np.hstack([[ii] * int(100 * perc) for ii, perc in enumerate(percentiles_classes)]) # Evenly spaced groups repeated once groups = np.hstack([[ii] * 10 for ii in range(10)]) def visualize_groups(classes, groups, name): # Visualize dataset groups fig, ax = plt.subplots() ax.scatter( range(len(groups)), [0.5] * len(groups), c=groups, marker="_", lw=50, cmap=cmap_data, ) ax.scatter( range(len(groups)), [3.5] * len(groups), c=classes, marker="_", lw=50, cmap=cmap_data, ) ax.set( ylim=[-1, 5], yticks=[0.5, 3.5], yticklabels=["Data\ngroup", "Data\nclass"], xlabel="Sample index", ) visualize_groups(y, groups, "no groups") .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_001.png :alt: plot cv indices :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 89-96 Define a function to visualize cross-validation behavior -------------------------------------------------------- We'll define a function that lets us visualize the behavior of each cross-validation object. We'll perform 4 splits of the data. On each split, we'll visualize the indices chosen for the training set (in blue) and the test set (in red). .. GENERATED FROM PYTHON SOURCE LINES 96-143 .. code-block:: default def plot_cv_indices(cv, X, y, group, ax, n_splits, lw=10): """Create a sample plot for indices of a cross-validation object.""" # Generate the training/testing visualizations for each CV split for ii, (tr, tt) in enumerate(cv.split(X=X, y=y, groups=group)): # Fill in indices with the training/test groups indices = np.array([np.nan] * len(X)) indices[tt] = 1 indices[tr] = 0 # Visualize the results ax.scatter( range(len(indices)), [ii + 0.5] * len(indices), c=indices, marker="_", lw=lw, cmap=cmap_cv, vmin=-0.2, vmax=1.2, ) # Plot the data classes and groups at the end ax.scatter( range(len(X)), [ii + 1.5] * len(X), c=y, marker="_", lw=lw, cmap=cmap_data ) ax.scatter( range(len(X)), [ii + 2.5] * len(X), c=group, marker="_", lw=lw, cmap=cmap_data ) # Formatting yticklabels = list(range(n_splits)) + ["class", "group"] ax.set( yticks=np.arange(n_splits + 2) + 0.5, yticklabels=yticklabels, xlabel="Sample index", ylabel="CV iteration", ylim=[n_splits + 2.2, -0.2], xlim=[0, 100], ) ax.set_title("{}".format(type(cv).__name__), fontsize=15) return ax .. GENERATED FROM PYTHON SOURCE LINES 144-146 Let's see how it looks for the :class:`~sklearn.model_selection.KFold` cross-validation object: .. GENERATED FROM PYTHON SOURCE LINES 146-151 .. code-block:: default fig, ax = plt.subplots() cv = KFold(n_splits) plot_cv_indices(cv, X, y, groups, ax, n_splits) .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_002.png :alt: KFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 152-161 As you can see, by default the KFold cross-validation iterator does not take either datapoint class or group into consideration. We can change this by using either: - ``StratifiedKFold`` to preserve the percentage of samples for each class. - ``GroupKFold`` to ensure that the same group will not appear in two different folds. - ``StratifiedGroupKFold`` to keep the constraint of ``GroupKFold`` while attempting to return stratified folds. .. GENERATED FROM PYTHON SOURCE LINES 161-181 .. code-block:: default # To better demonstrate the difference, we will assign samples to groups # unevenly: uneven_groups = np.sort(np.random.randint(0, 10, n_points)) cvs = [StratifiedKFold, GroupKFold, StratifiedGroupKFold] for cv in cvs: fig, ax = plt.subplots(figsize=(6, 3)) plot_cv_indices(cv(n_splits), X, y, uneven_groups, ax, n_splits) ax.legend( [Patch(color=cmap_cv(0.8)), Patch(color=cmap_cv(0.02))], ["Testing set", "Training set"], loc=(1.02, 0.8), ) # Make the legend fit plt.tight_layout() fig.subplots_adjust(right=0.7) .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_003.png :alt: StratifiedKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_003.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_004.png :alt: GroupKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_004.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_005.png :alt: StratifiedGroupKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_005.png :class: sphx-glr-multi-img .. GENERATED FROM PYTHON SOURCE LINES 182-192 Next we'll visualize this behavior for a number of CV iterators. Visualize cross-validation indices for many CV objects ------------------------------------------------------ Let's visually compare the cross validation behavior for many scikit-learn cross-validation objects. Below we will loop through several common cross-validation objects, visualizing the behavior of each. Note how some use the group/class information while others do not. .. GENERATED FROM PYTHON SOURCE LINES 192-219 .. code-block:: default cvs = [ KFold, GroupKFold, ShuffleSplit, StratifiedKFold, StratifiedGroupKFold, GroupShuffleSplit, StratifiedShuffleSplit, TimeSeriesSplit, ] for cv in cvs: this_cv = cv(n_splits=n_splits) fig, ax = plt.subplots(figsize=(6, 3)) plot_cv_indices(this_cv, X, y, groups, ax, n_splits) ax.legend( [Patch(color=cmap_cv(0.8)), Patch(color=cmap_cv(0.02))], ["Testing set", "Training set"], loc=(1.02, 0.8), ) # Make the legend fit plt.tight_layout() fig.subplots_adjust(right=0.7) plt.show() .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_006.png :alt: KFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_006.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_007.png :alt: GroupKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_007.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_008.png :alt: ShuffleSplit :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_008.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_009.png :alt: StratifiedKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_009.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_010.png :alt: StratifiedGroupKFold :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_010.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_011.png :alt: GroupShuffleSplit :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_011.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_012.png :alt: StratifiedShuffleSplit :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_012.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_013.png :alt: TimeSeriesSplit :srcset: /auto_examples/model_selection/images/sphx_glr_plot_cv_indices_013.png :class: sphx-glr-multi-img .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 0.946 seconds) .. _sphx_glr_download_auto_examples_model_selection_plot_cv_indices.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-learn/scikit-learn/1.0.X?urlpath=lab/tree/notebooks/auto_examples/model_selection/plot_cv_indices.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_cv_indices.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_cv_indices.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_