Classification of text documents using sparse features

This is an example showing how scikit-learn can be used to classify documents by topics using a bag-of-words approach. This example uses a scipy.sparse matrix to store the features and demonstrates various classifiers that can efficiently handle sparse matrices.

The dataset used in this example is the 20 newsgroups dataset. It will be automatically downloaded, then cached.

# Author: Peter Prettenhofer <peter.prettenhofer@gmail.com>
#         Olivier Grisel <olivier.grisel@ensta.org>
#         Mathieu Blondel <mathieu@mblondel.org>
#         Lars Buitinck
# License: BSD 3 clause

import logging
import numpy as np
from optparse import OptionParser
import sys
from time import time
import matplotlib.pyplot as plt

from sklearn.datasets import fetch_20newsgroups
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.feature_extraction.text import HashingVectorizer
from sklearn.feature_selection import SelectFromModel
from sklearn.feature_selection import SelectKBest, chi2
from sklearn.linear_model import RidgeClassifier
from sklearn.pipeline import Pipeline
from sklearn.svm import LinearSVC
from sklearn.linear_model import SGDClassifier
from sklearn.linear_model import Perceptron
from sklearn.linear_model import PassiveAggressiveClassifier
from sklearn.naive_bayes import BernoulliNB, ComplementNB, MultinomialNB
from sklearn.neighbors import KNeighborsClassifier
from sklearn.neighbors import NearestCentroid
from sklearn.ensemble import RandomForestClassifier
from sklearn.utils.extmath import density
from sklearn import metrics


# Display progress logs on stdout
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")

op = OptionParser()
op.add_option(
    "--report",
    action="store_true",
    dest="print_report",
    help="Print a detailed classification report.",
)
op.add_option(
    "--chi2_select",
    action="store",
    type="int",
    dest="select_chi2",
    help="Select some number of features using a chi-squared test",
)
op.add_option(
    "--confusion_matrix",
    action="store_true",
    dest="print_cm",
    help="Print the confusion matrix.",
)
op.add_option(
    "--top10",
    action="store_true",
    dest="print_top10",
    help="Print ten most discriminative terms per class for every classifier.",
)
op.add_option(
    "--all_categories",
    action="store_true",
    dest="all_categories",
    help="Whether to use all categories or not.",
)
op.add_option("--use_hashing", action="store_true", help="Use a hashing vectorizer.")
op.add_option(
    "--n_features",
    action="store",
    type=int,
    default=2 ** 16,
    help="n_features when using the hashing vectorizer.",
)
op.add_option(
    "--filtered",
    action="store_true",
    help=(
        "Remove newsgroup information that is easily overfit: "
        "headers, signatures, and quoting."
    ),
)


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)

print(__doc__)
op.print_help()
print()

Out:

Usage: plot_document_classification_20newsgroups.py [options]

Options:
  -h, --help            show this help message and exit
  --report              Print a detailed classification report.
  --chi2_select=SELECT_CHI2
                        Select some number of features using a chi-squared
                        test
  --confusion_matrix    Print the confusion matrix.
  --top10               Print ten most discriminative terms per class for
                        every classifier.
  --all_categories      Whether to use all categories or not.
  --use_hashing         Use a hashing vectorizer.
  --n_features=N_FEATURES
                        n_features when using the hashing vectorizer.
  --filtered            Remove newsgroup information that is easily overfit:
                        headers, signatures, and quoting.

Load data from the training set

Let’s load data from the newsgroups dataset which comprises around 18000 newsgroups posts on 20 topics split in two subsets: one for training (or development) and the other one for testing (or for performance evaluation).

if opts.all_categories:
    categories = None
else:
    categories = [
        "alt.atheism",
        "talk.religion.misc",
        "comp.graphics",
        "sci.space",
    ]

if opts.filtered:
    remove = ("headers", "footers", "quotes")
else:
    remove = ()

print("Loading 20 newsgroups dataset for categories:")
print(categories if categories else "all")

data_train = fetch_20newsgroups(
    subset="train", categories=categories, shuffle=True, random_state=42, remove=remove
)

data_test = fetch_20newsgroups(
    subset="test", categories=categories, shuffle=True, random_state=42, remove=remove
)
print("data loaded")

# order of labels in `target_names` can be different from `categories`
target_names = data_train.target_names


def size_mb(docs):
    return sum(len(s.encode("utf-8")) for s in docs) / 1e6


data_train_size_mb = size_mb(data_train.data)
data_test_size_mb = size_mb(data_test.data)

print(
    "%d documents - %0.3fMB (training set)" % (len(data_train.data), data_train_size_mb)
)
print("%d documents - %0.3fMB (test set)" % (len(data_test.data), data_test_size_mb))
print("%d categories" % len(target_names))
print()

# split a training set and a test set
y_train, y_test = data_train.target, data_test.target

print("Extracting features from the training data using a sparse vectorizer")
t0 = time()
if opts.use_hashing:
    vectorizer = HashingVectorizer(
        stop_words="english", alternate_sign=False, n_features=opts.n_features
    )
    X_train = vectorizer.transform(data_train.data)
else:
    vectorizer = TfidfVectorizer(sublinear_tf=True, max_df=0.5, stop_words="english")
    X_train = vectorizer.fit_transform(data_train.data)
duration = time() - t0
print("done in %fs at %0.3fMB/s" % (duration, data_train_size_mb / duration))
print("n_samples: %d, n_features: %d" % X_train.shape)
print()

print("Extracting features from the test data using the same vectorizer")
t0 = time()
X_test = vectorizer.transform(data_test.data)
duration = time() - t0
print("done in %fs at %0.3fMB/s" % (duration, data_test_size_mb / duration))
print("n_samples: %d, n_features: %d" % X_test.shape)
print()

# mapping from integer feature name to original token string
if opts.use_hashing:
    feature_names = None
else:
    feature_names = vectorizer.get_feature_names_out()

if opts.select_chi2:
    print("Extracting %d best features by a chi-squared test" % opts.select_chi2)
    t0 = time()
    ch2 = SelectKBest(chi2, k=opts.select_chi2)
    X_train = ch2.fit_transform(X_train, y_train)
    X_test = ch2.transform(X_test)
    if feature_names is not None:
        # keep selected feature names
        feature_names = feature_names[ch2.get_support()]
    print("done in %fs" % (time() - t0))
    print()


def trim(s):
    """Trim string to fit on terminal (assuming 80-column display)"""
    return s if len(s) <= 80 else s[:77] + "..."

Out:

Loading 20 newsgroups dataset for categories:
['alt.atheism', 'talk.religion.misc', 'comp.graphics', 'sci.space']
data loaded
2034 documents - 3.980MB (training set)
1353 documents - 2.867MB (test set)
4 categories

Extracting features from the training data using a sparse vectorizer
done in 0.383082s at 10.388MB/s
n_samples: 2034, n_features: 33809

Extracting features from the test data using the same vectorizer
done in 0.236998s at 12.099MB/s
n_samples: 1353, n_features: 33809

Benchmark classifiers

We train and test the datasets with 15 different classification models and get performance results for each model.

def benchmark(clf):
    print("_" * 80)
    print("Training: ")
    print(clf)
    t0 = time()
    clf.fit(X_train, y_train)
    train_time = time() - t0
    print("train time: %0.3fs" % train_time)

    t0 = time()
    pred = clf.predict(X_test)
    test_time = time() - t0
    print("test time:  %0.3fs" % test_time)

    score = metrics.accuracy_score(y_test, pred)
    print("accuracy:   %0.3f" % score)

    if hasattr(clf, "coef_"):
        print("dimensionality: %d" % clf.coef_.shape[1])
        print("density: %f" % density(clf.coef_))

        if opts.print_top10 and feature_names is not None:
            print("top 10 keywords per class:")
            for i, label in enumerate(target_names):
                top10 = np.argsort(clf.coef_[i])[-10:]
                print(trim("%s: %s" % (label, " ".join(feature_names[top10]))))
        print()

    if opts.print_report:
        print("classification report:")
        print(metrics.classification_report(y_test, pred, target_names=target_names))

    if opts.print_cm:
        print("confusion matrix:")
        print(metrics.confusion_matrix(y_test, pred))

    print()
    clf_descr = str(clf).split("(")[0]
    return clf_descr, score, train_time, test_time


results = []
for clf, name in (
    (RidgeClassifier(tol=1e-2, solver="sag"), "Ridge Classifier"),
    (Perceptron(max_iter=50), "Perceptron"),
    (PassiveAggressiveClassifier(max_iter=50), "Passive-Aggressive"),
    (KNeighborsClassifier(n_neighbors=10), "kNN"),
    (RandomForestClassifier(), "Random forest"),
):
    print("=" * 80)
    print(name)
    results.append(benchmark(clf))

for penalty in ["l2", "l1"]:
    print("=" * 80)
    print("%s penalty" % penalty.upper())
    # Train Liblinear model
    results.append(benchmark(LinearSVC(penalty=penalty, dual=False, tol=1e-3)))

    # Train SGD model
    results.append(benchmark(SGDClassifier(alpha=0.0001, max_iter=50, penalty=penalty)))

# Train SGD with Elastic Net penalty
print("=" * 80)
print("Elastic-Net penalty")
results.append(
    benchmark(SGDClassifier(alpha=0.0001, max_iter=50, penalty="elasticnet"))
)

# Train NearestCentroid without threshold
print("=" * 80)
print("NearestCentroid (aka Rocchio classifier)")
results.append(benchmark(NearestCentroid()))

# Train sparse Naive Bayes classifiers
print("=" * 80)
print("Naive Bayes")
results.append(benchmark(MultinomialNB(alpha=0.01)))
results.append(benchmark(BernoulliNB(alpha=0.01)))
results.append(benchmark(ComplementNB(alpha=0.1)))

print("=" * 80)
print("LinearSVC with L1-based feature selection")
# The smaller C, the stronger the regularization.
# The more regularization, the more sparsity.
results.append(
    benchmark(
        Pipeline(
            [
                (
                    "feature_selection",
                    SelectFromModel(LinearSVC(penalty="l1", dual=False, tol=1e-3)),
                ),
                ("classification", LinearSVC(penalty="l2")),
            ]
        )
    )
)

Out:

================================================================================
Ridge Classifier
________________________________________________________________________________
Training:
RidgeClassifier(solver='sag', tol=0.01)
/home/circleci/project/sklearn/linear_model/_ridge.py:729: UserWarning: "sag" solver requires many iterations to fit an intercept with sparse inputs. Either set the solver to "auto" or "sparse_cg", or set a low "tol" and a high "max_iter" (especially if inputs are not standardized).
  warnings.warn(
train time: 0.167s
test time:  0.001s
accuracy:   0.898
dimensionality: 33809
density: 1.000000


================================================================================
Perceptron
________________________________________________________________________________
Training:
Perceptron(max_iter=50)
train time: 0.015s
test time:  0.001s
accuracy:   0.888
dimensionality: 33809
density: 0.255302


================================================================================
Passive-Aggressive
________________________________________________________________________________
Training:
PassiveAggressiveClassifier(max_iter=50)
train time: 0.027s
test time:  0.001s
accuracy:   0.902
dimensionality: 33809
density: 0.711867


================================================================================
kNN
________________________________________________________________________________
Training:
KNeighborsClassifier(n_neighbors=10)
train time: 0.001s
test time:  0.148s
accuracy:   0.858

================================================================================
Random forest
________________________________________________________________________________
Training:
RandomForestClassifier()
train time: 1.258s
test time:  0.079s
accuracy:   0.826

================================================================================
L2 penalty
________________________________________________________________________________
Training:
LinearSVC(dual=False, tol=0.001)
train time: 0.072s
test time:  0.001s
accuracy:   0.900
dimensionality: 33809
density: 1.000000


________________________________________________________________________________
Training:
SGDClassifier(max_iter=50)
train time: 0.024s
test time:  0.001s
accuracy:   0.903
dimensionality: 33809
density: 0.579424


================================================================================
L1 penalty
________________________________________________________________________________
Training:
LinearSVC(dual=False, penalty='l1', tol=0.001)
train time: 0.176s
test time:  0.001s
accuracy:   0.873
dimensionality: 33809
density: 0.005553


________________________________________________________________________________
Training:
SGDClassifier(max_iter=50, penalty='l1')
train time: 0.092s
test time:  0.002s
accuracy:   0.880
dimensionality: 33809
density: 0.022509


================================================================================
Elastic-Net penalty
________________________________________________________________________________
Training:
SGDClassifier(max_iter=50, penalty='elasticnet')
train time: 0.134s
test time:  0.001s
accuracy:   0.901
dimensionality: 33809
density: 0.184685


================================================================================
NearestCentroid (aka Rocchio classifier)
________________________________________________________________________________
Training:
NearestCentroid()
train time: 0.004s
test time:  0.002s
accuracy:   0.855

================================================================================
Naive Bayes
________________________________________________________________________________
Training:
MultinomialNB(alpha=0.01)
train time: 0.003s
test time:  0.001s
accuracy:   0.899
/home/circleci/project/sklearn/utils/deprecation.py:103: FutureWarning: Attribute `coef_` was deprecated in version 0.24 and will be removed in 1.1 (renaming of 0.26).
  warnings.warn(msg, category=FutureWarning)
dimensionality: 33809
density: 1.000000


________________________________________________________________________________
Training:
BernoulliNB(alpha=0.01)
train time: 0.005s
test time:  0.004s
accuracy:   0.884
/home/circleci/project/sklearn/utils/deprecation.py:103: FutureWarning: Attribute `coef_` was deprecated in version 0.24 and will be removed in 1.1 (renaming of 0.26).
  warnings.warn(msg, category=FutureWarning)
dimensionality: 33809
density: 1.000000


________________________________________________________________________________
Training:
ComplementNB(alpha=0.1)
train time: 0.003s
test time:  0.001s
accuracy:   0.911
/home/circleci/project/sklearn/utils/deprecation.py:103: FutureWarning: Attribute `coef_` was deprecated in version 0.24 and will be removed in 1.1 (renaming of 0.26).
  warnings.warn(msg, category=FutureWarning)
dimensionality: 33809
density: 1.000000


================================================================================
LinearSVC with L1-based feature selection
________________________________________________________________________________
Training:
Pipeline(steps=[('feature_selection',
                 SelectFromModel(estimator=LinearSVC(dual=False, penalty='l1',
                                                     tol=0.001))),
                ('classification', LinearSVC())])
train time: 0.192s
test time:  0.002s
accuracy:   0.879

Add plots

The bar plot indicates the accuracy, training time (normalized) and test time (normalized) of each classifier.

indices = np.arange(len(results))

results = [[x[i] for x in results] for i in range(4)]

clf_names, score, training_time, test_time = results
training_time = np.array(training_time) / np.max(training_time)
test_time = np.array(test_time) / np.max(test_time)

plt.figure(figsize=(12, 8))
plt.title("Score")
plt.barh(indices, score, 0.2, label="score", color="navy")
plt.barh(indices + 0.3, training_time, 0.2, label="training time", color="c")
plt.barh(indices + 0.6, test_time, 0.2, label="test time", color="darkorange")
plt.yticks(())
plt.legend(loc="best")
plt.subplots_adjust(left=0.25)
plt.subplots_adjust(top=0.95)
plt.subplots_adjust(bottom=0.05)

for i, c in zip(indices, clf_names):
    plt.text(-0.3, i, c)

plt.show()