.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/classification/plot_lda_qda.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` 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_classification_plot_lda_qda.py: ==================================================================== Linear and Quadratic Discriminant Analysis with covariance ellipsoid ==================================================================== This example plots the covariance ellipsoids of each class and the decision boundary learned by :class:`~sklearn.discriminant_analysis.LinearDiscriminantAnalysis` (LDA) and :class:`~sklearn.discriminant_analysis.QuadraticDiscriminantAnalysis` (QDA). The ellipsoids display the double standard deviation for each class. With LDA, the standard deviation is the same for all the classes, while each class has its own standard deviation with QDA. .. GENERATED FROM PYTHON SOURCE LINES 13-17 .. code-block:: Python # Authors: The scikit-learn developers # SPDX-License-Identifier: BSD-3-Clause .. GENERATED FROM PYTHON SOURCE LINES 18-25 Data generation --------------- First, we define a function to generate synthetic data. It creates two blobs centered at `(0, 0)` and `(1, 1)`. Each blob is assigned a specific class. The dispersion of the blob is controlled by the parameters `cov_class_1` and `cov_class_2`, that are the covariance matrices used when generating the samples from the Gaussian distributions. .. GENERATED FROM PYTHON SOURCE LINES 25-40 .. code-block:: Python import numpy as np def make_data(n_samples, n_features, cov_class_1, cov_class_2, seed=0): rng = np.random.RandomState(seed) X = np.concatenate( [ rng.randn(n_samples, n_features) @ cov_class_1, rng.randn(n_samples, n_features) @ cov_class_2 + np.array([1, 1]), ] ) y = np.concatenate([np.zeros(n_samples), np.ones(n_samples)]) return X, y .. GENERATED FROM PYTHON SOURCE LINES 41-46 We generate three datasets. In the first dataset, the two classes share the same covariance matrix, and this covariance matrix has the specificity of being spherical (isotropic). The second dataset is similar to the first one but does not enforce the covariance to be spherical. Finally, the third dataset has a non-spherical covariance matrix for each class. .. GENERATED FROM PYTHON SOURCE LINES 46-73 .. code-block:: Python covariance = np.array([[1, 0], [0, 1]]) X_isotropic_covariance, y_isotropic_covariance = make_data( n_samples=1_000, n_features=2, cov_class_1=covariance, cov_class_2=covariance, seed=0, ) covariance = np.array([[0.0, -0.23], [0.83, 0.23]]) X_shared_covariance, y_shared_covariance = make_data( n_samples=300, n_features=2, cov_class_1=covariance, cov_class_2=covariance, seed=0, ) cov_class_1 = np.array([[0.0, -1.0], [2.5, 0.7]]) * 2.0 cov_class_2 = cov_class_1.T X_different_covariance, y_different_covariance = make_data( n_samples=300, n_features=2, cov_class_1=cov_class_1, cov_class_2=cov_class_2, seed=0, ) .. GENERATED FROM PYTHON SOURCE LINES 74-88 Plotting Functions ------------------ The code below is used to plot several pieces of information from the estimators used, i.e., :class:`~sklearn.discriminant_analysis.LinearDiscriminantAnalysis` (LDA) and :class:`~sklearn.discriminant_analysis.QuadraticDiscriminantAnalysis` (QDA). The displayed information includes: - the decision boundary based on the probability estimate of the estimator; - a scatter plot with circles representing the well-classified samples; - a scatter plot with crosses representing the misclassified samples; - the mean of each class, estimated by the estimator, marked with a star; - the estimated covariance represented by an ellipse at 2 standard deviations from the mean. .. GENERATED FROM PYTHON SOURCE LINES 88-171 .. code-block:: Python import matplotlib as mpl from matplotlib import colors from sklearn.inspection import DecisionBoundaryDisplay def plot_ellipse(mean, cov, color, ax): v, w = np.linalg.eigh(cov) u = w[0] / np.linalg.norm(w[0]) angle = np.arctan(u[1] / u[0]) angle = 180 * angle / np.pi # convert to degrees # filled Gaussian at 2 standard deviation ell = mpl.patches.Ellipse( mean, 2 * v[0] ** 0.5, 2 * v[1] ** 0.5, angle=180 + angle, facecolor=color, edgecolor="black", linewidth=2, ) ell.set_clip_box(ax.bbox) ell.set_alpha(0.4) ax.add_artist(ell) def plot_result(estimator, X, y, ax): cmap = colors.ListedColormap(["tab:red", "tab:blue"]) DecisionBoundaryDisplay.from_estimator( estimator, X, response_method="predict_proba", plot_method="pcolormesh", ax=ax, cmap="RdBu", alpha=0.3, ) DecisionBoundaryDisplay.from_estimator( estimator, X, response_method="predict_proba", plot_method="contour", ax=ax, alpha=1.0, levels=[0.5], ) y_pred = estimator.predict(X) X_right, y_right = X[y == y_pred], y[y == y_pred] X_wrong, y_wrong = X[y != y_pred], y[y != y_pred] ax.scatter(X_right[:, 0], X_right[:, 1], c=y_right, s=20, cmap=cmap, alpha=0.5) ax.scatter( X_wrong[:, 0], X_wrong[:, 1], c=y_wrong, s=30, cmap=cmap, alpha=0.9, marker="x", ) ax.scatter( estimator.means_[:, 0], estimator.means_[:, 1], c="yellow", s=200, marker="*", edgecolor="black", ) if isinstance(estimator, LinearDiscriminantAnalysis): covariance = [estimator.covariance_] * 2 else: covariance = estimator.covariance_ plot_ellipse(estimator.means_[0], covariance[0], "tab:red", ax) plot_ellipse(estimator.means_[1], covariance[1], "tab:blue", ax) ax.set_box_aspect(1) ax.spines["top"].set_visible(False) ax.spines["bottom"].set_visible(False) ax.spines["left"].set_visible(False) ax.spines["right"].set_visible(False) ax.set(xticks=[], yticks=[]) .. GENERATED FROM PYTHON SOURCE LINES 172-176 Comparison of LDA and QDA ------------------------- We compare the two estimators LDA and QDA on all three datasets. .. GENERATED FROM PYTHON SOURCE LINES 176-210 .. code-block:: Python import matplotlib.pyplot as plt from sklearn.discriminant_analysis import ( LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis, ) fig, axs = plt.subplots(nrows=3, ncols=2, sharex="row", sharey="row", figsize=(8, 12)) lda = LinearDiscriminantAnalysis(solver="svd", store_covariance=True) qda = QuadraticDiscriminantAnalysis(store_covariance=True) for ax_row, X, y in zip( axs, (X_isotropic_covariance, X_shared_covariance, X_different_covariance), (y_isotropic_covariance, y_shared_covariance, y_different_covariance), ): lda.fit(X, y) plot_result(lda, X, y, ax_row[0]) qda.fit(X, y) plot_result(qda, X, y, ax_row[1]) axs[0, 0].set_title("Linear Discriminant Analysis") axs[0, 0].set_ylabel("Data with fixed and spherical covariance") axs[1, 0].set_ylabel("Data with fixed covariance") axs[0, 1].set_title("Quadratic Discriminant Analysis") axs[2, 0].set_ylabel("Data with varying covariances") fig.suptitle( "Linear Discriminant Analysis vs Quadratic Discriminant Analysis", y=0.94, fontsize=15, ) plt.show() .. image-sg:: /auto_examples/classification/images/sphx_glr_plot_lda_qda_001.png :alt: Linear Discriminant Analysis vs Quadratic Discriminant Analysis, Linear Discriminant Analysis, Quadratic Discriminant Analysis :srcset: /auto_examples/classification/images/sphx_glr_plot_lda_qda_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 211-229 The first important thing to notice is that LDA and QDA are equivalent for the first and second datasets. Indeed, the major difference is that LDA assumes that the covariance matrix of each class is equal, while QDA estimates a covariance matrix per class. Since in these cases the data generative process has the same covariance matrix for both classes, QDA estimates two covariance matrices that are (almost) equal and therefore equivalent to the covariance matrix estimated by LDA. In the first dataset the covariance matrix used to generate the dataset is spherical, which results in a discriminant boundary that aligns with the perpendicular bisector between the two means. This is no longer the case for the second dataset. The discriminant boundary only passes through the middle of the two means. Finally, in the third dataset, we observe the real difference between LDA and QDA. QDA fits two covariance matrices and provides a non-linear discriminant boundary, whereas LDA underfits since it assumes that both classes share a single covariance matrix. .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.337 seconds) .. _sphx_glr_download_auto_examples_classification_plot_lda_qda.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-learn/scikit-learn/main?urlpath=lab/tree/notebooks/auto_examples/classification/plot_lda_qda.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_lda_qda.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_lda_qda.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_lda_qda.zip ` .. include:: plot_lda_qda.recommendations .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_