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.

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sphinx_gallery/gen_rst.py", line 440, in _memory_usage
    out = func()
  File "/usr/lib/python3/dist-packages/sphinx_gallery/gen_rst.py", line 425, in __call__
    exec(self.code, self.globals)
  File "/build/scikit-learn-WWYjTV/scikit-learn-0.22.2.post1+dfsg/examples/text/plot_document_clustering.py", line 129, in <module>
    dataset = fetch_20newsgroups(subset='all', categories=categories,
  File "/build/scikit-learn-WWYjTV/scikit-learn-0.22.2.post1+dfsg/.pybuild/cpython3_3.8/build/sklearn/datasets/_twenty_newsgroups.py", line 250, in fetch_20newsgroups
    cache = _download_20newsgroups(target_dir=twenty_home,
  File "/build/scikit-learn-WWYjTV/scikit-learn-0.22.2.post1+dfsg/.pybuild/cpython3_3.8/build/sklearn/datasets/_twenty_newsgroups.py", line 73, in _download_20newsgroups
    archive_path = _fetch_remote(ARCHIVE, dirname=target_dir)
  File "/build/scikit-learn-WWYjTV/scikit-learn-0.22.2.post1+dfsg/.pybuild/cpython3_3.8/build/sklearn/datasets/_base.py", line 902, in _fetch_remote
    urlretrieve(remote.url, file_path)
  File "/usr/lib/python3.8/urllib/request.py", line 247, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/lib/python3.8/urllib/request.py", line 525, in open
    response = self._open(req, data)
  File "/usr/lib/python3.8/urllib/request.py", line 542, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain
    result = func(*args)
  File "/usr/lib/python3.8/urllib/request.py", line 1393, in https_open
    return self.do_open(http.client.HTTPSConnection, req,
  File "/usr/lib/python3.8/urllib/request.py", line 1353, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>
# Author: Peter Prettenhofer <peter.prettenhofer@gmail.com>
#         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)
        vectorizer = make_pipeline(hasher, TfidfTransformer())
    else:
        vectorizer = HashingVectorizer(n_features=opts.n_features,
                                       stop_words='english',
                                       alternate_sign=False, norm='l2')
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 0.010 seconds)

Gallery generated by Sphinx-Gallery