From 434eed65b4b2eb5f0f8814467576cd808742ccfd Mon Sep 17 00:00:00 2001
From: Olivier Grisel <olivier.grisel@ensta.org>
Date: Sun, 4 Jul 2010 22:40:27 +0200
Subject: [PATCH] example usage of MLComp document classification datasets
---
doc/tutorial.rst | 23 +++--
examples/mlcomp_document_classification.py | 99 ++++++++++++++++++++++
scikits/learn/datasets/mlcomp.py | 9 +-
scikits/learn/features/text.py | 11 ++-
4 files changed, 130 insertions(+), 12 deletions(-)
create mode 100644 examples/mlcomp_document_classification.py
diff --git a/doc/tutorial.rst b/doc/tutorial.rst
index d15496c79b..565069b16b 100644
--- a/doc/tutorial.rst
+++ b/doc/tutorial.rst
@@ -16,11 +16,11 @@ single number, and for instance a multi-dimensional entry (aka
*multivariate* data), is it said to have several attributes, or
*features*.
-We can separate learning problems in a few large categories:
+We can separate learning problems in a few large categories:
* **supervised learning**, in which the data comes with additional
attributes that we want to predict. This problem can be either:
-
+
* **classification**: samples belong to two or more classes and we
want to learn from already labeled data how to predict the class
of un-labeled data. An example of classification problem would
@@ -45,7 +45,7 @@ We can separate learning problems in a few large categories:
.. topic:: Training set and testing set
Machine learning is about learning some properties of a data set and
- applying them to new data. This is why a common practice in machine
+ applying them to new data. This is why a common practice in machine
learning to evaluate an algorithm is to split the data at hand in two
sets, one that we call a *training set* on which we learn data
properties, and one that we call a *testing set*, on which we test
@@ -76,7 +76,7 @@ access to the features that can be used to classify the digits samples::
array([[ 0., 0., 5., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 10., 0., 0.],
[ 0., 0., 0., ..., 16., 9., 0.],
- ...,
+ ...,
[ 0., 0., 1., ..., 6., 0., 0.],
[ 0., 0., 2., ..., 12., 0., 0.],
[ 0., 0., 10., ..., 12., 1., 0.]])
@@ -89,7 +89,7 @@ learn:
array([0, 1, 2, ..., 8, 9, 8])
.. topic:: Shape of the data arrays
-
+
The data is always a 2D array, `n_samples, n_features`, although
the original data may have had a different shape. In the case of the
digits, each original sample is an image of shape `8, 8` and can be
@@ -106,10 +106,19 @@ array([0, 1, 2, ..., 8, 9, 8])
[ 0., 0., 6., 13., 10., 0., 0., 0.]])
The :ref:`simple example on this dataset <example_plot_digits_classification.py>`
- illustrates how starting from the original problem one can shape the
+ illustrates how starting from the original problem one can shape the
data for consumption in the `scikit.learn`.
+``scikits.learn`` also offers the possibility to reuse external datasets coming
+from the http://mlcomp.org online service that provides a repository of public
+datasets for various tasks (binary & multi label classification, regression,
+document classification, ...) along with a runtime environment to compare
+program performance on those datasets. Please refer to the following example for
+for instructions on the ``mlcomp`` dataset loader:
+:ref:`example_mlcomp_document_classification.py`.
+
+
Learning and Predicting
------------------------
@@ -158,4 +167,4 @@ resolution. Do you agree with the classifier?
A complete example of this classification problem is available as an
example that you can run and study:
-:ref:`example_plot_digits_classification.py`.
+:ref:`example_plot_digits_classification.py`.
diff --git a/examples/mlcomp_document_classification.py b/examples/mlcomp_document_classification.py
new file mode 100644
index 0000000000..2782a393b8
--- /dev/null
+++ b/examples/mlcomp_document_classification.py
@@ -0,0 +1,99 @@
+"""
+================================
+Classification of text documents
+================================
+
+This is an example showing how the scikit-learn can be used to classify
+documents by topics using a bag-of-words approach.
+
+The dataset used in this example is the 20 newsgroups dataset and should be
+downloaded from the http://mlcomp.org (free registration required):
+
+ http://mlcomp.org/datasets/379
+
+Once downloaded unzip the arhive somewhere on your filesystem. For instance in::
+
+ % mkdir -p ~/data/mlcomp
+ % cd ~/data/mlcomp
+ % unzip /path/to/dataset-379-20news-18828_XXXXX.zip
+
+You should get a folder ``~/data/mlcomp/379`` with a file named ``metadata`` and
+subfolders ``raw``, ``train`` and ``test`` holding the text documents organized by
+newsgroups.
+
+Then set the ``MLCOMP_DATASETS_HOME`` environment variable pointing to
+the root folder holding the uncompressed archive::
+
+ % export MLCOMP_DATASETS_HOME="~/data/mlcomp"
+
+Then you are ready to run this example using your favorite python shell::
+
+ % ipython examples/mlcomp_document_classification.py
+
+"""
+# Author: Olivier Grisel <olivier.grisel@ensta.org>
+# License: Simplified BSD
+
+from time import time
+import sys
+import os
+import numpy as np
+import pylab as pl
+from scikits.learn.datasets import load_mlcomp
+from scikits.learn.logistic import LogisticRegression
+from scikits.learn.svm import LinearSVC
+from scikits.learn.metrics import confusion_matrix
+
+if 'MLCOMP_DATASETS_HOME' not in os.environ:
+ print "Please follow those instructions to get started:"
+ print __doc__
+ sys.exit(0)
+
+# Load the training set
+print "Loading 20 newsgroups training set... "
+t0 = time()
+news_train = load_mlcomp('20news-18828', 'train')
+print "done in %fs" % (time() - t0)
+
+# The documents have been hashed into TF-IDF (Term Frequencies times Inverse
+# Document Frequencies) vectors of a fixed dimension.
+# Currently most scikits.learn wrappers or algorithm implementations are unable
+# to leverage efficiently a sparse datastracture; hence we use of a this dense
+# representation of a text dataset. Efficient handling of sparse data
+# structures should be expected for in an upcoming version of scikits.learn
+print "n_samples: %d, n_features: %d" % news_train.data.shape
+
+print "Training a linear classification model with L1 penalty... "
+parameters = {
+ 'loss': 'l2',
+ 'penalty': 'l1',
+ 'C': 10,
+ 'dual': False,
+ 'eps': 1e-4,
+}
+print "parameters:", parameters
+t0 = time()
+clf = LinearSVC(**parameters).fit(news_train.data, news_train.target)
+print "done in %fs" % (time() - t0)
+print "Percentage of non zeros coef: %f" % (np.mean(clf.coef_ != 0) * 100)
+
+print "Loading 20 newsgroups test set... "
+t0 = time()
+news_test = load_mlcomp('20news-18828', 'test')
+print "done in %fs" % (time() - t0)
+
+print "Predicting the labels of the test set..."
+t0 = time()
+pred = clf.predict(news_test.data)
+print "done in %fs" % (time() - t0)
+print "Classification accuracy: %f" % (np.mean(pred == news_test.target) * 100)
+
+cm = confusion_matrix(news_test.target, pred)
+print "Confusion matrix:"
+print cm
+
+# Show confusion matrix
+pl.matshow(cm)
+pl.title('Confusion matrix')
+pl.colorbar()
+pl.show()
diff --git a/scikits/learn/datasets/mlcomp.py b/scikits/learn/datasets/mlcomp.py
index 42a0deb8eb..f6678dbe32 100644
--- a/scikits/learn/datasets/mlcomp.py
+++ b/scikits/learn/datasets/mlcomp.py
@@ -3,6 +3,7 @@
"""Glue code to load http://mlcomp.org data as a scikit.learn dataset"""
import os
+import numpy as np
from scikits.learn.datasets.base import Bunch
from scikits.learn.features.text import HashingVectorizer
@@ -14,6 +15,12 @@ def load_document_classification(dataset_path, metadata, set_, **kw):
filenames = []
vectorizer = kw.get('vectorizer', HashingVectorizer())
+ # TODO: make it possible to plug a several pass system to filter-out tokens
+ # that occur in more than 30% of the documents for instance.
+
+ # TODO: use joblib.Parallel or multiprocessing to parallelize the following
+ # (provided this is not IO bound)
+
dataset_path = os.path.join(dataset_path, set_)
folders = [f for f in sorted(os.listdir(dataset_path))
if os.path.isdir(os.path.join(dataset_path, f))]
@@ -26,7 +33,7 @@ def load_document_classification(dataset_path, metadata, set_, **kw):
target.extend(len(documents) * [label])
filenames.extend(documents)
- return Bunch(data=vectorizer.get_vectors(), target=target,
+ return Bunch(data=vectorizer.get_vectors(), target=np.array(target),
target_names=target_names, filenames=filenames,
DESCR=metadata.get('description'))
diff --git a/scikits/learn/features/text.py b/scikits/learn/features/text.py
index 9835401388..e77a5f842a 100644
--- a/scikits/learn/features/text.py
+++ b/scikits/learn/features/text.py
@@ -26,6 +26,8 @@ class SimpleAnalyzer(object):
token_pattern = re.compile(r"\b\w\w+\b", re.U)
+ # TODO: make it possible to pass stop words list here
+
def __init__(self, default_charset='utf-8'):
self.charset = default_charset
@@ -58,7 +60,11 @@ class HashingVectorizer(object):
# TODO: implement me using the murmurhash that might be faster: but profile
# me first :)
- def __init__(self, dim=1000, probes=3, analyzer=SimpleAnalyzer(),
+ # TODO: make it possible to select between the current dense representation
+ # and sparse alternatives from scipy.sparse once the liblinear and libsvm
+ # wrappers have been updated to be able to handle it efficiently
+
+ def __init__(self, dim=5000, probes=3, analyzer=SimpleAnalyzer(),
use_idf=True):
self.dim = dim
self.probes = probes
@@ -121,7 +127,6 @@ class HashingVectorizer(object):
else:
self.tf_vectors = np.vstack((self.tf_vectors, tf_vectors))
-
def get_vectors(self):
if self.use_idf:
return self.get_tfidf()
@@ -129,5 +134,3 @@ class HashingVectorizer(object):
return self.tf_vectors
-
-
--
GitLab