.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/applications/plot_digits_denoising.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_applications_plot_digits_denoising.py: ================================ Image denoising using kernel PCA ================================ This example shows how to use :class:`~sklearn.decomposition.KernelPCA` to denoise images. In short, we take advantage of the approximation function learned during `fit` to reconstruct the original image. We will compare the results with an exact reconstruction using :class:`~sklearn.decomposition.PCA`. We will use USPS digits dataset to reproduce presented in Sect. 4 of [1]_. .. topic:: References .. [1] `Bakır, Gökhan H., Jason Weston, and Bernhard Schölkopf. "Learning to find pre-images." Advances in neural information processing systems 16 (2004): 449-456. `_ .. GENERATED FROM PYTHON SOURCE LINES 23-27 .. code-block:: default # Authors: Guillaume Lemaitre # Licence: BSD 3 clause .. GENERATED FROM PYTHON SOURCE LINES 28-34 Load the dataset via OpenML --------------------------- The USPS digits datasets is available in OpenML. We use :func:`~sklearn.datasets.fetch_openml` to get this dataset. In addition, we normalize the dataset such that all pixel values are in the range (0, 1). .. GENERATED FROM PYTHON SOURCE LINES 34-42 .. code-block:: default import numpy as np from sklearn.datasets import fetch_openml from sklearn.preprocessing import MinMaxScaler from sklearn.model_selection import train_test_split X, y = fetch_openml(data_id=41082, as_frame=False, return_X_y=True) X = MinMaxScaler().fit_transform(X) .. GENERATED FROM PYTHON SOURCE LINES 43-56 The idea will be to learn a PCA basis (with and without a kernel) on noisy images and then use these models to reconstruct and denoise these images. Thus, we split our dataset into a training and testing set composed of 1,000 samples for the training and 100 samples for testing. These images are noise-free and we will use them to evaluate the efficiency of the denoising approaches. In addition, we create a copy of the original dataset and add a Gaussian noise. The idea of this application, is to show that we can denoise corrupted images by learning a PCA basis on some uncorrupted images. We will use both a PCA and a kernel-based PCA to solve this problem. .. GENERATED FROM PYTHON SOURCE LINES 56-67 .. code-block:: default X_train, X_test, y_train, y_test = train_test_split( X, y, stratify=y, random_state=0, train_size=1_000, test_size=100 ) rng = np.random.RandomState(0) noise = rng.normal(scale=0.25, size=X_test.shape) X_test_noisy = X_test + noise noise = rng.normal(scale=0.25, size=X_train.shape) X_train_noisy = X_train + noise .. GENERATED FROM PYTHON SOURCE LINES 68-70 In addition, we will create a helper function to qualitatively assess the image reconstruction by plotting the test images. .. GENERATED FROM PYTHON SOURCE LINES 70-82 .. code-block:: default import matplotlib.pyplot as plt def plot_digits(X, title): """Small helper function to plot 100 digits.""" fig, axs = plt.subplots(nrows=10, ncols=10, figsize=(8, 8)) for img, ax in zip(X, axs.ravel()): ax.imshow(img.reshape((16, 16)), cmap="Greys") ax.axis("off") fig.suptitle(title, fontsize=24) .. GENERATED FROM PYTHON SOURCE LINES 83-88 In addition, we will use the mean squared error (MSE) to quantitatively assess the image reconstruction. Let's first have a look to see the difference between noise-free and noisy images. We will check the test set in this regard. .. GENERATED FROM PYTHON SOURCE LINES 88-93 .. code-block:: default plot_digits(X_test, "Uncorrupted test images") plot_digits( X_test_noisy, f"Noisy test images\nMSE: {np.mean((X_test - X_test_noisy) ** 2):.2f}" ) .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_001.png :alt: Uncorrupted test images :srcset: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_001.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_002.png :alt: Noisy test images MSE: 0.06 :srcset: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_002.png :class: sphx-glr-multi-img .. GENERATED FROM PYTHON SOURCE LINES 94-99 Learn the `PCA` basis --------------------- We can now learn our PCA basis using both a linear PCA and a kernel PCA that uses a radial basis function (RBF) kernel. .. GENERATED FROM PYTHON SOURCE LINES 99-109 .. code-block:: default from sklearn.decomposition import PCA, KernelPCA pca = PCA(n_components=32) kernel_pca = KernelPCA( n_components=400, kernel="rbf", gamma=1e-3, fit_inverse_transform=True, alpha=5e-3 ) pca.fit(X_train_noisy) _ = kernel_pca.fit(X_train_noisy) .. GENERATED FROM PYTHON SOURCE LINES 110-120 Reconstruct and denoise test images ----------------------------------- Now, we can transform and reconstruct the noisy test set. Since we used less components than the number of original features, we will get an approximation of the original set. Indeed, by dropping the components explaining variance in PCA the least, we hope to remove noise. Similar thinking happens in kernel PCA; however, we expect a better reconstruction because we use a non-linear kernel to learn the PCA basis and a kernel ridge to learn the mapping function. .. GENERATED FROM PYTHON SOURCE LINES 120-125 .. code-block:: default X_reconstructed_kernel_pca = kernel_pca.inverse_transform( kernel_pca.transform(X_test_noisy) ) X_reconstructed_pca = pca.inverse_transform(pca.transform(X_test_noisy)) .. GENERATED FROM PYTHON SOURCE LINES 126-137 .. code-block:: default plot_digits(X_test, "Uncorrupted test images") plot_digits( X_reconstructed_pca, f"PCA reconstruction\nMSE: {np.mean((X_test - X_reconstructed_pca) ** 2):.2f}", ) plot_digits( X_reconstructed_kernel_pca, "Kernel PCA reconstruction\n" f"MSE: {np.mean((X_test - X_reconstructed_kernel_pca) ** 2):.2f}", ) .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_003.png :alt: Uncorrupted test images :srcset: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_003.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_004.png :alt: PCA reconstruction MSE: 0.02 :srcset: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_004.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_005.png :alt: Kernel PCA reconstruction MSE: 0.03 :srcset: /auto_examples/applications/images/sphx_glr_plot_digits_denoising_005.png :class: sphx-glr-multi-img .. GENERATED FROM PYTHON SOURCE LINES 138-144 PCA has a lower MSE than kernel PCA. However, the qualitative analysis might not favor PCA instead of kernel PCA. We observe that kernel PCA is able to remove background noise and provide a smoother image. However, it should be noted that the results of the denoising with kernel PCA will depend of the parameters `n_components`, `gamma`, and `alpha`. .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 9.857 seconds) .. _sphx_glr_download_auto_examples_applications_plot_digits_denoising.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/applications/plot_digits_denoising.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_digits_denoising.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_digits_denoising.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_