.. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_text_plot_document_clustering.py: ======================================= Clustering text documents using k-means ======================================= This is an example showing how the scikit-learn can be used to cluster documents by topics using a bag-of-words approach. This example uses a scipy.sparse matrix to store the features instead of standard numpy arrays. Two feature extraction methods can be used in this example: - TfidfVectorizer uses a in-memory vocabulary (a python dict) to map the most frequent words to features indices and hence compute a word occurrence frequency (sparse) matrix. The word frequencies are then reweighted using the Inverse Document Frequency (IDF) vector collected feature-wise over the corpus. - HashingVectorizer hashes word occurrences to a fixed dimensional space, possibly with collisions. The word count vectors are then normalized to each have l2-norm equal to one (projected to the euclidean unit-ball) which seems to be important for k-means to work in high dimensional space. HashingVectorizer does not provide IDF weighting as this is a stateless model (the fit method does nothing). When IDF weighting is needed it can be added by pipelining its output to a TfidfTransformer instance. Two algorithms are demoed: ordinary k-means and its more scalable cousin minibatch k-means. Additionally, latent semantic analysis can also be used to reduce dimensionality and discover latent patterns in the data. It can be noted that k-means (and minibatch k-means) are very sensitive to feature scaling and that in this case the IDF weighting helps improve the quality of the clustering by quite a lot as measured against the "ground truth" provided by the class label assignments of the 20 newsgroups dataset. This improvement is not visible in the Silhouette Coefficient which is small for both as this measure seem to suffer from the phenomenon called "Concentration of Measure" or "Curse of Dimensionality" for high dimensional datasets such as text data. Other measures such as V-measure and Adjusted Rand Index are information theoretic based evaluation scores: as they are only based on cluster assignments rather than distances, hence not affected by the curse of dimensionality. Note: as k-means is optimizing a non-convex objective function, it will likely end up in a local optimum. Several runs with independent random init might be necessary to get a good convergence. .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Usage: plot_document_clustering.py [options] Options: -h, --help show this help message and exit --lsa=N_COMPONENTS Preprocess documents with latent semantic analysis. --no-minibatch Use ordinary k-means algorithm (in batch mode). --no-idf Disable Inverse Document Frequency feature weighting. --use-hashing Use a hashing feature vectorizer --n-features=N_FEATURES Maximum number of features (dimensions) to extract from text. --verbose Print progress reports inside k-means algorithm. Loading 20 newsgroups dataset for categories: ['alt.atheism', 'talk.religion.misc', 'comp.graphics', 'sci.space'] 3387 documents 4 categories Extracting features from the training dataset using a sparse vectorizer done in 0.691398s n_samples: 3387, n_features: 10000 Clustering sparse data with MiniBatchKMeans(batch_size=1000, init_size=1000, n_clusters=4, n_init=1, verbose=False) done in 0.057s Homogeneity: 0.359 Completeness: 0.440 V-measure: 0.396 Adjusted Rand-Index: 0.253 Silhouette Coefficient: 0.007 Top terms per cluster: Cluster 0: henry alaska toronto moon zoo spencer aurora space nsmca zoology Cluster 1: com graphics university posting host nntp know uk article cs Cluster 2: god com sandvik people keith morality sgi kent livesey jesus Cluster 3: space nasa access gov digex pat shuttle hst orbit net | .. code-block:: python # Author: Peter Prettenhofer # Lars Buitinck # License: BSD 3 clause from sklearn.datasets import fetch_20newsgroups from sklearn.decomposition import TruncatedSVD from sklearn.feature_extraction.text import TfidfVectorizer from sklearn.feature_extraction.text import HashingVectorizer from sklearn.feature_extraction.text import TfidfTransformer from sklearn.pipeline import make_pipeline from sklearn.preprocessing import Normalizer from sklearn import metrics from sklearn.cluster import KMeans, MiniBatchKMeans import logging from optparse import OptionParser import sys from time import time import numpy as np # Display progress logs on stdout logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s') # parse commandline arguments op = OptionParser() op.add_option("--lsa", dest="n_components", type="int", help="Preprocess documents with latent semantic analysis.") op.add_option("--no-minibatch", action="store_false", dest="minibatch", default=True, help="Use ordinary k-means algorithm (in batch mode).") op.add_option("--no-idf", action="store_false", dest="use_idf", default=True, help="Disable Inverse Document Frequency feature weighting.") op.add_option("--use-hashing", action="store_true", default=False, help="Use a hashing feature vectorizer") op.add_option("--n-features", type=int, default=10000, help="Maximum number of features (dimensions)" " to extract from text.") op.add_option("--verbose", action="store_true", dest="verbose", default=False, help="Print progress reports inside k-means algorithm.") print(__doc__) op.print_help() def is_interactive(): return not hasattr(sys.modules['__main__'], '__file__') # work-around for Jupyter notebook and IPython console argv = [] if is_interactive() else sys.argv[1:] (opts, args) = op.parse_args(argv) if len(args) > 0: op.error("this script takes no arguments.") sys.exit(1) # ############################################################################# # Load some categories from the training set categories = [ 'alt.atheism', 'talk.religion.misc', 'comp.graphics', 'sci.space', ] # Uncomment the following to do the analysis on all the categories # categories = None print("Loading 20 newsgroups dataset for categories:") print(categories) dataset = fetch_20newsgroups(subset='all', categories=categories, shuffle=True, random_state=42) print("%d documents" % len(dataset.data)) print("%d categories" % len(dataset.target_names)) print() labels = dataset.target true_k = np.unique(labels).shape[0] print("Extracting features from the training dataset " "using a sparse vectorizer") t0 = time() if opts.use_hashing: if opts.use_idf: # Perform an IDF normalization on the output of HashingVectorizer hasher = HashingVectorizer(n_features=opts.n_features, stop_words='english', alternate_sign=False, norm=None, binary=False) vectorizer = make_pipeline(hasher, TfidfTransformer()) else: vectorizer = HashingVectorizer(n_features=opts.n_features, stop_words='english', alternate_sign=False, norm='l2', binary=False) else: vectorizer = TfidfVectorizer(max_df=0.5, max_features=opts.n_features, min_df=2, stop_words='english', use_idf=opts.use_idf) X = vectorizer.fit_transform(dataset.data) print("done in %fs" % (time() - t0)) print("n_samples: %d, n_features: %d" % X.shape) print() if opts.n_components: print("Performing dimensionality reduction using LSA") t0 = time() # Vectorizer results are normalized, which makes KMeans behave as # spherical k-means for better results. Since LSA/SVD results are # not normalized, we have to redo the normalization. svd = TruncatedSVD(opts.n_components) normalizer = Normalizer(copy=False) lsa = make_pipeline(svd, normalizer) X = lsa.fit_transform(X) print("done in %fs" % (time() - t0)) explained_variance = svd.explained_variance_ratio_.sum() print("Explained variance of the SVD step: {}%".format( int(explained_variance * 100))) print() # ############################################################################# # Do the actual clustering if opts.minibatch: km = MiniBatchKMeans(n_clusters=true_k, init='k-means++', n_init=1, init_size=1000, batch_size=1000, verbose=opts.verbose) else: km = KMeans(n_clusters=true_k, init='k-means++', max_iter=100, n_init=1, verbose=opts.verbose) print("Clustering sparse data with %s" % km) t0 = time() km.fit(X) print("done in %0.3fs" % (time() - t0)) print() print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels, km.labels_)) print("Completeness: %0.3f" % metrics.completeness_score(labels, km.labels_)) print("V-measure: %0.3f" % metrics.v_measure_score(labels, km.labels_)) print("Adjusted Rand-Index: %.3f" % metrics.adjusted_rand_score(labels, km.labels_)) print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, km.labels_, sample_size=1000)) print() if not opts.use_hashing: print("Top terms per cluster:") if opts.n_components: original_space_centroids = svd.inverse_transform(km.cluster_centers_) order_centroids = original_space_centroids.argsort()[:, ::-1] else: order_centroids = km.cluster_centers_.argsort()[:, ::-1] terms = vectorizer.get_feature_names() for i in range(true_k): print("Cluster %d:" % i, end='') for ind in order_centroids[i, :10]: print(' %s' % terms[ind], end='') print() **Total running time of the script:** ( 0 minutes 1.137 seconds) .. _sphx_glr_download_auto_examples_text_plot_document_clustering.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: sphx-glr-download :download:`Download Python source code: plot_document_clustering.py ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: plot_document_clustering.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_