Biclustering documents with the Spectral Co-clustering algorithm¶

from collections import defaultdict
import operator
from time import time

import numpy as np

from sklearn.cluster.bicluster import SpectralCoclustering
from sklearn.cluster import MiniBatchKMeans
from sklearn.datasets.twenty_newsgroups import fetch_20newsgroups
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.metrics.cluster import v_measure_score

print(__doc__)


def number_normalizer(tokens):
    """ Map all numeric tokens to a placeholder.

    For many applications, tokens that begin with a number are not directly
    useful, but the fact that such a token exists can be relevant.  By applying
    this form of dimensionality reduction, some methods may perform better.
    """
    return ("#NUMBER" if token[0].isdigit() else token for token in tokens)


class NumberNormalizingVectorizer(TfidfVectorizer):
    def build_tokenizer(self):
        tokenize = super().build_tokenizer()
        return lambda doc: list(number_normalizer(tokenize(doc)))


# exclude 'comp.os.ms-windows.misc'
categories = ['alt.atheism', 'comp.graphics',
              'comp.sys.ibm.pc.hardware', 'comp.sys.mac.hardware',
              'comp.windows.x', 'misc.forsale', 'rec.autos',
              'rec.motorcycles', 'rec.sport.baseball',
              'rec.sport.hockey', 'sci.crypt', 'sci.electronics',
              'sci.med', 'sci.space', 'soc.religion.christian',
              'talk.politics.guns', 'talk.politics.mideast',
              'talk.politics.misc', 'talk.religion.misc']
newsgroups = fetch_20newsgroups(categories=categories)
y_true = newsgroups.target

vectorizer = NumberNormalizingVectorizer(stop_words='english', min_df=5)
cocluster = SpectralCoclustering(n_clusters=len(categories),
                                 svd_method='arpack', random_state=0)
kmeans = MiniBatchKMeans(n_clusters=len(categories), batch_size=20000,
                         random_state=0)

print("Vectorizing...")
X = vectorizer.fit_transform(newsgroups.data)

print("Coclustering...")
start_time = time()
cocluster.fit(X)
y_cocluster = cocluster.row_labels_
print("Done in {:.2f}s. V-measure: {:.4f}".format(
    time() - start_time,
    v_measure_score(y_cocluster, y_true)))

print("MiniBatchKMeans...")
start_time = time()
y_kmeans = kmeans.fit_predict(X)
print("Done in {:.2f}s. V-measure: {:.4f}".format(
    time() - start_time,
    v_measure_score(y_kmeans, y_true)))

feature_names = vectorizer.get_feature_names()
document_names = list(newsgroups.target_names[i] for i in newsgroups.target)


def bicluster_ncut(i):
    rows, cols = cocluster.get_indices(i)
    if not (np.any(rows) and np.any(cols)):
        import sys
        return sys.float_info.max
    row_complement = np.nonzero(np.logical_not(cocluster.rows_[i]))[0]
    col_complement = np.nonzero(np.logical_not(cocluster.columns_[i]))[0]
    # Note: the following is identical to X[rows[:, np.newaxis],
    # cols].sum() but much faster in scipy <= 0.16
    weight = X[rows][:, cols].sum()
    cut = (X[row_complement][:, cols].sum() +
           X[rows][:, col_complement].sum())
    return cut / weight


def most_common(d):
    """Items of a defaultdict(int) with the highest values.

    Like Counter.most_common in Python >=2.7.
    """
    return sorted(d.items(), key=operator.itemgetter(1), reverse=True)


bicluster_ncuts = list(bicluster_ncut(i)
                       for i in range(len(newsgroups.target_names)))
best_idx = np.argsort(bicluster_ncuts)[:5]

print()
print("Best biclusters:")
print("----------------")
for idx, cluster in enumerate(best_idx):
    n_rows, n_cols = cocluster.get_shape(cluster)
    cluster_docs, cluster_words = cocluster.get_indices(cluster)
    if not len(cluster_docs) or not len(cluster_words):
        continue

    # categories
    counter = defaultdict(int)
    for i in cluster_docs:
        counter[document_names[i]] += 1
    cat_string = ", ".join("{:.0f}% {}".format(float(c) / n_rows * 100, name)
                           for name, c in most_common(counter)[:3])

    # words
    out_of_cluster_docs = cocluster.row_labels_ != cluster
    out_of_cluster_docs = np.where(out_of_cluster_docs)[0]
    word_col = X[:, cluster_words]
    word_scores = np.array(word_col[cluster_docs, :].sum(axis=0) -
                           word_col[out_of_cluster_docs, :].sum(axis=0))
    word_scores = word_scores.ravel()
    important_words = list(feature_names[cluster_words[i]]
                           for i in word_scores.argsort()[:-11:-1])

    print("bicluster {} : {} documents, {} words".format(
        idx, n_rows, n_cols))
    print("categories   : {}".format(cat_string))
    print("words        : {}\n".format(', '.join(important_words)))