.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/cluster/plot_cluster_comparison.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_cluster_plot_cluster_comparison.py: ========================================================= Comparing different clustering algorithms on toy datasets ========================================================= This example shows characteristics of different clustering algorithms on datasets that are "interesting" but still in 2D. With the exception of the last dataset, the parameters of each of these dataset-algorithm pairs has been tuned to produce good clustering results. Some algorithms are more sensitive to parameter values than others. The last dataset is an example of a 'null' situation for clustering: the data is homogeneous, and there is no good clustering. For this example, the null dataset uses the same parameters as the dataset in the row above it, which represents a mismatch in the parameter values and the data structure. While these examples give some intuition about the algorithms, this intuition might not apply to very high dimensional data. .. GENERATED FROM PYTHON SOURCE LINES 26-288 .. image-sg:: /auto_examples/cluster/images/sphx_glr_plot_cluster_comparison_001.png :alt: MiniBatch KMeans, Affinity Propagation, MeanShift, Spectral Clustering, Ward, Agglomerative Clustering, DBSCAN, HDBSCAN, OPTICS, BIRCH, Gaussian Mixture :srcset: /auto_examples/cluster/images/sphx_glr_plot_cluster_comparison_001.png :class: sphx-glr-single-img .. code-block:: Python # Authors: The scikit-learn developers # SPDX-License-Identifier: BSD-3-Clause import time import warnings from itertools import cycle, islice import matplotlib.pyplot as plt import numpy as np from sklearn import cluster, datasets, mixture from sklearn.neighbors import kneighbors_graph from sklearn.preprocessing import StandardScaler # ============ # Generate datasets. We choose the size big enough to see the scalability # of the algorithms, but not too big to avoid too long running times # ============ n_samples = 500 seed = 30 noisy_circles = datasets.make_circles( n_samples=n_samples, factor=0.5, noise=0.05, random_state=seed ) noisy_moons = datasets.make_moons(n_samples=n_samples, noise=0.05, random_state=seed) blobs = datasets.make_blobs(n_samples=n_samples, random_state=seed) rng = np.random.RandomState(seed) no_structure = rng.rand(n_samples, 2), None # Anisotropicly distributed data random_state = 170 X, y = datasets.make_blobs(n_samples=n_samples, random_state=random_state) transformation = [[0.6, -0.6], [-0.4, 0.8]] X_aniso = np.dot(X, transformation) aniso = (X_aniso, y) # blobs with varied variances varied = datasets.make_blobs( n_samples=n_samples, cluster_std=[1.0, 2.5, 0.5], random_state=random_state ) # ============ # Set up cluster parameters # ============ plt.figure(figsize=(9 * 2 + 3, 13)) plt.subplots_adjust( left=0.02, right=0.98, bottom=0.001, top=0.95, wspace=0.05, hspace=0.01 ) plot_num = 1 default_base = { "quantile": 0.3, "eps": 0.3, "damping": 0.9, "preference": -200, "n_neighbors": 3, "n_clusters": 3, "min_samples": 7, "xi": 0.05, "min_cluster_size": 0.1, "allow_single_cluster": True, "hdbscan_min_cluster_size": 15, "hdbscan_min_samples": 3, "random_state": 42, } datasets = [ ( noisy_circles, { "damping": 0.77, "preference": -240, "quantile": 0.2, "n_clusters": 2, "min_samples": 7, "xi": 0.08, }, ), ( noisy_moons, { "damping": 0.75, "preference": -220, "n_clusters": 2, "min_samples": 7, "xi": 0.1, }, ), ( varied, { "eps": 0.18, "n_neighbors": 2, "min_samples": 7, "xi": 0.01, "min_cluster_size": 0.2, }, ), ( aniso, { "eps": 0.15, "n_neighbors": 2, "min_samples": 7, "xi": 0.1, "min_cluster_size": 0.2, }, ), (blobs, {"min_samples": 7, "xi": 0.1, "min_cluster_size": 0.2}), (no_structure, {}), ] for i_dataset, (dataset, algo_params) in enumerate(datasets): # update parameters with dataset-specific values params = default_base.copy() params.update(algo_params) X, y = dataset # normalize dataset for easier parameter selection X = StandardScaler().fit_transform(X) # estimate bandwidth for mean shift bandwidth = cluster.estimate_bandwidth(X, quantile=params["quantile"]) # connectivity matrix for structured Ward connectivity = kneighbors_graph( X, n_neighbors=params["n_neighbors"], include_self=False ) # make connectivity symmetric connectivity = 0.5 * (connectivity + connectivity.T) # ============ # Create cluster objects # ============ ms = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True) two_means = cluster.MiniBatchKMeans( n_clusters=params["n_clusters"], random_state=params["random_state"], ) ward = cluster.AgglomerativeClustering( n_clusters=params["n_clusters"], linkage="ward", connectivity=connectivity ) spectral = cluster.SpectralClustering( n_clusters=params["n_clusters"], eigen_solver="arpack", affinity="nearest_neighbors", random_state=params["random_state"], ) dbscan = cluster.DBSCAN(eps=params["eps"]) hdbscan = cluster.HDBSCAN( min_samples=params["hdbscan_min_samples"], min_cluster_size=params["hdbscan_min_cluster_size"], allow_single_cluster=params["allow_single_cluster"], ) optics = cluster.OPTICS( min_samples=params["min_samples"], xi=params["xi"], min_cluster_size=params["min_cluster_size"], ) affinity_propagation = cluster.AffinityPropagation( damping=params["damping"], preference=params["preference"], random_state=params["random_state"], ) average_linkage = cluster.AgglomerativeClustering( linkage="average", metric="cityblock", n_clusters=params["n_clusters"], connectivity=connectivity, ) birch = cluster.Birch(n_clusters=params["n_clusters"]) gmm = mixture.GaussianMixture( n_components=params["n_clusters"], covariance_type="full", random_state=params["random_state"], ) clustering_algorithms = ( ("MiniBatch\nKMeans", two_means), ("Affinity\nPropagation", affinity_propagation), ("MeanShift", ms), ("Spectral\nClustering", spectral), ("Ward", ward), ("Agglomerative\nClustering", average_linkage), ("DBSCAN", dbscan), ("HDBSCAN", hdbscan), ("OPTICS", optics), ("BIRCH", birch), ("Gaussian\nMixture", gmm), ) for name, algorithm in clustering_algorithms: t0 = time.time() # catch warnings related to kneighbors_graph with warnings.catch_warnings(): warnings.filterwarnings( "ignore", message="the number of connected components of the " + "connectivity matrix is [0-9]{1,2}" + " > 1. Completing it to avoid stopping the tree early.", category=UserWarning, ) warnings.filterwarnings( "ignore", message="Graph is not fully connected, spectral embedding" + " may not work as expected.", category=UserWarning, ) algorithm.fit(X) t1 = time.time() if hasattr(algorithm, "labels_"): y_pred = algorithm.labels_.astype(int) else: y_pred = algorithm.predict(X) plt.subplot(len(datasets), len(clustering_algorithms), plot_num) if i_dataset == 0: plt.title(name, size=18) colors = np.array( list( islice( cycle( [ "#377eb8", "#ff7f00", "#4daf4a", "#f781bf", "#a65628", "#984ea3", "#999999", "#e41a1c", "#dede00", ] ), int(max(y_pred) + 1), ) ) ) # add black color for outliers (if any) colors = np.append(colors, ["#000000"]) plt.scatter(X[:, 0], X[:, 1], s=10, color=colors[y_pred]) plt.xlim(-2.5, 2.5) plt.ylim(-2.5, 2.5) plt.xticks(()) plt.yticks(()) plt.text( 0.99, 0.01, ("%.2fs" % (t1 - t0)).lstrip("0"), transform=plt.gca().transAxes, size=15, horizontalalignment="right", ) plot_num += 1 plt.show() .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 5.719 seconds) .. _sphx_glr_download_auto_examples_cluster_plot_cluster_comparison.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/cluster/plot_cluster_comparison.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_cluster_comparison.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_cluster_comparison.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_cluster_comparison.zip ` .. include:: plot_cluster_comparison.recommendations .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_