7 files changed, 2176 insertions, 0 deletions
diff --git a/datasets/newsgroups/README b/datasets/newsgroups/README
new file mode 100644
index 0000000..78e92ee
--- /dev/null
+++ b/datasets/newsgroups/README
@@ -0,0 +1,7 @@
+For running the script newsgroups_extract.py we used N = 500 and topics are
+'comp.graphics', 'misc.forsale', and 'sci.med'.
+
+The randomly generated ids in our case are in the file 'newsgroups-500-3.ids'.
+
+Before running the script, be sure to generate the stopwords file using
+'stop.sh'.
diff --git a/datasets/newsgroups/newsgroups-500-3.ids b/datasets/newsgroups/newsgroups-500-3.ids
new file mode 100644
index 0000000..9b468bd
--- /dev/null
+++ b/datasets/newsgroups/newsgroups-500-3.ids
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diff --git a/datasets/newsgroups/newsgroups_extract.py b/datasets/newsgroups/newsgroups_extract.py
new file mode 100644
index 0000000..51c5030
--- /dev/null
+++ b/datasets/newsgroups/newsgroups_extract.py
@@ -0,0 +1,137 @@
+from sklearn.decomposition import PCA
+from sklearn.feature_extraction.text import TfidfVectorizer
+
+import hashlib
+import logging
+import numpy as np
+import os
+import os.path
+import sys
+import tarfile
+import wget
+
+
+DATA_URL = "http://kdd.ics.uci.edu/databases/20newsgroups/20_newsgroups.tar.gz"
+DATA_FILE = "20_newsgroups.tar.gz"
+DATA_SHA256 = "b7bbf82b7831f7dbb1a09d9312f66fa78565c8de25526999b0d66f69d37e414"
+
+
+def build_topic_corpus(corpus_file, n, topic):
+    logging.info("Extracting corpus for topic '{}'".format(topic))
+    topic_items = []
+    names = corpus_file.getnames()
+    for name in names:
+        if topic in name:
+            ti = corpus_file.getmember(name)
+            if ti.isfile():
+                topic_items.append(name)
+    if len(topic_items) == 0:
+        # Topic does not exist (no items fetched)
+        raise ValueError(topic)
+
+    topic_ids = []
+    topic_corpus = []
+    indices = np.arange(len(topic_items))
+    np.random.shuffle(indices)
+    indices = indices[:n]
+    for i in indices:
+        ti = corpus_file.getmember(topic_items[i])
+        with corpus_file.extractfile(ti) as f:
+            try:
+                contents = str(f.read(), encoding="utf8")
+            except ValueError as e:
+                logging.warn("Encoding error in '{}': {}".format(ti.name, e))
+                continue
+            _, item_id = os.path.split(ti.name)
+            topic_ids.append(item_id)
+            topic_corpus.append(contents)
+
+    return topic_ids, topic_corpus
+
+
+def build_corpus(n, topics):
+    """
+    Builds a corpus with each topic, with N items each.
+    Returns a list of document IDs and a corpus which is a dict where each topic
+    is a key mapped to a list of document contents.
+    """
+    ids = []
+    corpus = dict()
+    with tarfile.open(DATA_FILE, "r:gz") as f:
+        for topic in topics:
+            topic_ids, topic_corpus = build_topic_corpus(f, n, topic)
+            corpus[topic] = topic_corpus
+            ids.extend(topic_ids)
+    return ids, corpus
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 4:
+        print("usage: {} STOP_WORDS N TOPIC [ TOPIC [ ... ] ]".format(sys.argv[0]))
+        print("The program reads the file STOP_WORDS for stop words, extracts"
+            + " and generates a BoW model from N random articles of each TOPIC")
+        exit(1)
+
+    logging.basicConfig(filename="newsgroups_extract.log",
+                        format="%(levelname)s:%(message)s",
+                        level=logging.INFO)
+
+    if not os.path.exists(DATA_FILE):
+        logging.info("Downloading data from '{}'".format(DATA_URL))
+        wget.download(DATA_URL, DATA_FILE)
+        with open(DATA_FILE, "rb") as f:
+            if not hashlib.sha256(f.read()).hexdigest() != DATA_SHA256:
+                logging.error("'{}' is corrupted; aborting".format(DATA_FILE))
+                exit(1)
+
+    # Read stop words list
+    try:
+        with open(sys.argv[1]) as stop_words_file:
+            stop_words = stop_words_file.read().split()
+    except Exception as e:
+        logging.error("Could not read stop words: {}".format(e))
+        exit(1)
+
+    try:
+        n = int(sys.argv[2])
+        if (n < 2) or (n > 1000):
+            raise ValueError("N must be between 2 and 1000")
+    except ValueError as e:
+        logging.error("Invalid argument: {}".format(e))
+        exit(1)
+
+    # Extract text corpus from tarball
+    logging.info("Building corpus")
+    topics = sys.argv[3:]
+    try:
+        ids, corpus = build_corpus(n, topics)
+    except ValueError as e:
+        logging.error("Invalid topic: {}".format(e))
+        exit(1)
+
+    corpus_text = []
+    for topic_items in corpus.values():
+        corpus_text.extend(topic_items)
+
+    # Compute the TF-IDF matrix
+    logging.info("Computing TF-IDF matrix")
+    vectorizer = TfidfVectorizer(min_df=0.01, stop_words=stop_words)
+    X = vectorizer.fit_transform(corpus_text)
+
+    # Reduce data dimensionality using PCA
+    logging.info("Computing PCA and reducing to 512 dimensions")
+    X = PCA(n_components=512, whiten=True).fit_transform(X.toarray())
+
+    # Save all extracted features and related data
+    logging.info("Writing IDs file")
+    ids_fname = "newsgroups-{}-{}.ids".format(n, len(topics))
+    np.savetxt(ids_fname, ids, fmt="%s")
+
+    logging.info("Writing table file")
+    tbl_fname = "newsgroups-{}-{}.tbl".format(n, len(topics))
+    np.savetxt(tbl_fname, X.todense(), fmt="%f")
+
+    logging.info("Writing labels file")
+    labels_fname = "newsgroups-{}-{}.labels".format(n, len(topics))
+    counts = [len(topic_items) for topic_items in corpus.values()]
+    np.savetxt(labels_fname, np.repeat(topics, counts), fmt="%s")
diff --git a/datasets/newsgroups/source b/datasets/newsgroups/source
new file mode 100644
index 0000000..764f792
--- /dev/null
+++ b/datasets/newsgroups/source
@@ -0,0 +1 @@
+http://kdd.ics.uci.edu/databases/20newsgroups/20newsgroups.html
diff --git a/datasets/newsgroups/stop.sh b/datasets/newsgroups/stop.sh
new file mode 100644
index 0000000..36a5f74
--- /dev/null
+++ b/datasets/newsgroups/stop.sh
@@ -0,0 +1,12 @@
+# stop.sh
+#
+# Generate proper stop words list from the 'stop.txt' file.
+
+
+# Original source: http://snowball.tartarus.org/algorithms/english/stop.txt
+# NOTE: in our experiments, stop.txt has been modified to include the last stop
+# words (stop.txt is included).
+
+sed 's/|.*//g' <stop.txt \
+    | sed 's/ \+//g' \
+    | sed '/^$/d' >words.txt
diff --git a/datasets/newsgroups/stop.txt b/datasets/newsgroups/stop.txt
new file mode 100644
index 0000000..5d0a34b
--- /dev/null
+++ b/datasets/newsgroups/stop.txt
@@ -0,0 +1,310 @@
+
+ | An English stop word list. Comments begin with vertical bar. Each stop
+ | word is at the start of a line.
+
+ | Many of the forms below are quite rare (e.g. "yourselves") but included for
+ |  completeness.
+
+           | PRONOUNS FORMS
+             | 1st person sing
+
+i              | subject, always in upper case of course
+
+me             | object
+my             | possessive adjective
+               | the possessive pronoun `mine' is best suppressed, because of the
+               | sense of coal-mine etc.
+myself         | reflexive
+             | 1st person plural
+we             | subject
+
+| us           | object
+               | care is required here because US = United States. It is usually
+               | safe to remove it if it is in lower case.
+our            | possessive adjective
+ours           | possessive pronoun
+ourselves      | reflexive
+             | second person (archaic `thou' forms not included)
+you            | subject and object
+your           | possessive adjective
+yours          | possessive pronoun
+yourself       | reflexive (singular)
+yourselves     | reflexive (plural)
+             | third person singular
+he             | subject
+him            | object
+his            | possessive adjective and pronoun
+himself        | reflexive
+
+she            | subject
+her            | object and possessive adjective
+hers           | possessive pronoun
+herself        | reflexive
+
+it             | subject and object
+its            | possessive adjective
+itself         | reflexive
+             | third person plural
+they           | subject
+them           | object
+their          | possessive adjective
+theirs         | possessive pronoun
+themselves     | reflexive
+             | other forms (demonstratives, interrogatives)
+what
+which
+who
+whom
+this
+that
+these
+those
+
+           | VERB FORMS (using F.R. Palmer's nomenclature)
+             | BE
+am             | 1st person, present
+is             | -s form (3rd person, present)
+are            | present
+was            | 1st person, past
+were           | past
+be             | infinitive
+been           | past participle
+being          | -ing form
+             | HAVE
+have           | simple
+has            | -s form
+had            | past
+having         | -ing form
+             | DO
+do             | simple
+does           | -s form
+did            | past
+doing          | -ing form
+
+ | The forms below are, I believe, best omitted, because of the significant
+ | homonym forms:
+
+ |  He made a WILL
+ |  old tin CAN
+ |  merry month of MAY
+ |  a smell of MUST
+ |  fight the good fight with all thy MIGHT
+
+ | would, could, should, ought might however be included
+
+ |          | AUXILIARIES
+ |            | WILL
+ |will
+
+would
+
+ |            | SHALL
+ |shall
+
+should
+
+ |            | CAN
+ |can
+
+could
+
+ |            | MAY
+ |may
+ |might
+ |            | MUST
+ |must
+ |            | OUGHT
+
+ought
+
+           | COMPOUND FORMS, increasingly encountered nowadays in 'formal' writing
+              | pronoun + verb
+
+i'm
+you're
+he's
+she's
+it's
+we're
+they're
+i've
+you've
+we've
+they've
+i'd
+you'd
+he'd
+she'd
+we'd
+they'd
+i'll
+you'll
+he'll
+she'll
+we'll
+they'll
+
+              | verb + negation
+
+isn't
+aren't
+wasn't
+weren't
+hasn't
+haven't
+hadn't
+doesn't
+don't
+didn't
+
+              | auxiliary + negation
+
+won't
+wouldn't
+shan't
+shouldn't
+can't
+cannot
+couldn't
+mustn't
+
+             | miscellaneous forms
+
+let's
+that's
+who's
+what's
+here's
+there's
+when's
+where's
+why's
+how's
+
+              | rarer forms
+
+ | daren't needn't
+
+              | doubtful forms
+
+ | oughtn't mightn't
+
+           | ARTICLES
+a
+an
+the
+
+           | THE REST (Overlap among prepositions, conjunctions, adverbs etc is so
+           | high, that classification is pointless.)
+and
+but
+if
+or
+because
+as
+until
+while
+
+of
+at
+by
+for
+with
+about
+against
+between
+into
+through
+during
+before
+after
+above
+below
+to
+from
+up
+down
+in
+out
+on
+off
+over
+under
+
+again
+further
+then
+once
+
+here
+there
+when
+where
+why
+how
+
+all
+any
+both
+each
+few
+more
+most
+other
+some
+such
+
+no
+nor
+not
+only
+own
+same
+so
+than
+too
+very
+
+one
+every
+least
+less
+many
+now
+ever
+never
+say
+says
+said
+also
+get
+go
+goes
+just
+made
+make
+put
+see
+seen
+whether
+like
+well
+back
+even
+still
+way
+take
+since
+another
+however
+two
+three
+four
+five
+first
+second
+new
+old
+high
+long
+
diff --git a/datasets/newsgroups/words.txt b/datasets/newsgroups/words.txt
new file mode 100644
index 0000000..0d11300
--- /dev/null
+++ b/datasets/newsgroups/words.txt
@@ -0,0 +1,216 @@
+i
+me
+my
+myself
+we
+our
+ours
+ourselves
+you
+your
+yours
+yourself
+yourselves
+he
+him
+his
+himself
+she
+her
+hers
+herself
+it
+its
+itself
+they
+them
+their
+theirs
+themselves
+what
+which
+who
+whom
+this
+that
+these
+those
+am
+is
+are
+was
+were
+be
+been
+being
+have
+has
+had
+having
+do
+does
+did
+doing
+would
+should
+could
+ought
+i'm
+you're
+he's
+she's
+it's
+we're
+they're
+i've
+you've
+we've
+they've
+i'd
+you'd
+he'd
+she'd
+we'd
+they'd
+i'll
+you'll
+he'll
+she'll
+we'll
+they'll
+isn't
+aren't
+wasn't
+weren't
+hasn't
+haven't
+hadn't
+doesn't
+don't
+didn't
+won't
+wouldn't
+shan't
+shouldn't
+can't
+cannot
+couldn't
+mustn't
+let's
+that's
+who's
+what's
+here's
+there's
+when's
+where's
+why's
+how's
+a
+an
+the
+and
+but
+if
+or
+because
+as
+until
+while
+of
+at
+by
+for
+with
+about
+against
+between
+into
+through
+during
+before
+after
+above
+below
+to
+from
+up
+down
+in
+out
+on
+off
+over
+under
+again
+further
+then
+once
+here
+there
+when
+where
+why
+how
+all
+any
+both
+each
+few
+more
+most
+other
+some
+such
+no
+nor
+not
+only
+own
+same
+so
+than
+too
+very
+one
+every
+least
+less
+many
+now
+ever
+never
+say
+says
+said
+also
+get
+go
+goes
+just
+made
+make
+put
+see
+seen
+whether
+like
+well
+back
+even
+still
+way
+take
+since
+another
+however
+two
+three
+four
+five
+first
+second
+new
+old
+high
+long