def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.k is not None and options.k < 2:
raise ValueError('cluster number must be >= 2')
if options.method == MINIBATCH_KMEANS and not with_sklearn:
logging.warning('minibatch kmeans not available, using kmeans (slow)')
options.method = KMEANS
if options.jobs != 1 and (options.method != KMEANS or not with_sklearn):
logging.warning('jobs > 1 only supported scikit-learn %s' % KMEANS)
options.jobs = 1
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.k is None:
options.k = int(math.ceil((len(wv.words())/2)**0.5))
logging.info('set k=%d (%d words)' % (options.k, len(wv.words())))
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
logging.info('normalize features to unit variance')
vectors = scipy.cluster.vq.whiten(vectors)
return words, vectors, options
def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.k is not None and options.k < 2:
raise ValueError('cluster number must be >= 2')
if options.method == MINIBATCH_KMEANS and not with_sklearn:
logging.warning('minibatch kmeans not available, using kmeans (slow)')
options.method = KMEANS
if options.jobs != 1 and (options.method != KMEANS or not with_sklearn):
logging.warning('jobs > 1 only supported scikit-learn %s' % KMEANS)
options.jobs = 1
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.k is None:
options.k = int(math.ceil((len(wv.words()) / 2)**0.5))
logging.info('set k=%d (%d words)' % (options.k, len(wv.words())))
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
logging.info('normalize features to unit variance')
vectors = scipy.cluster.vq.whiten(vectors)
return words, vectors, options
def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.threshold is not None and options.threshold < 0.0:
raise ValueError('threshold must be >= 0')
if options.tolerance is not None and options.tolerance < 0.0:
raise ValueError('tolerance must be >= 0')
if options.approximate and not options.threshold:
raise ValueError('approximate only makes sense with a threshold')
if options.approximate and options.metric != 'cosine':
raise NotImplementedError('approximate only supported for cosine')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
# whitening should be implemented in wvlib to support together with
# approximate similarity
if options.approximate:
raise NotImplemenedError
logging.info('normalize features to unit variance')
vectors = whiten(vectors)
return words, vectors, wv, options
def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.threshold is not None and options.threshold < 0.0:
raise ValueError('threshold must be >= 0')
if options.tolerance is not None and options.tolerance < 0.0:
raise ValueError('tolerance must be >= 0')
if options.approximate and not options.threshold:
raise ValueError('approximate only makes sense with a threshold')
if options.approximate and options.metric != 'cosine':
raise NotImplementedError('approximate only supported for cosine')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
# whitening should be implemented in wvlib to support together with
# approximate similarity
if options.approximate:
raise NotImplemenedError
logging.info('normalize features to unit variance')
vectors = whiten(vectors)
return words, vectors, wv, options
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.quiet:
logging.getLogger().setLevel(logging.ERROR)
wordsets = read_wordsets(options.wordset)
if not enough_data(wordsets):
return 1
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank).normalize()
w2v = wv.word_to_vector_mapping()
word_count, oov_count = 0, 0
filtered_wordsets = {}
for k, wordset in wordsets.items():
filtered = []
for w in wordset:
if w in w2v:
filtered.append(w)
else:
logging.warning('ignoring out-of-vocabulary word "%s"' % w)
oov_count += 1
word_count += 1
if filtered:
filtered_wordsets[k] = filtered
else:
logging.warning('wordset %s empty after OOV filtering, removing' %
k)
wordsets = filtered_wordsets
if not enough_data(wordsets):
return 1
results = []
for n1, n2 in combinations(wordsets.keys(), 2):
result = compare_sets(wordsets[n1], n1, wordsets[n2], n2, w2v, options)
if result is not None:
results.append(result)
if not options.quiet:
print('out of vocabulary %d/%d (%.2f%%)' % \
(oov_count, word_count, 100.*oov_count/word_count),
file=sys.stderr)
if results:
print('OVERALL AVERAGE (macro):\t%.2f%%\t(%.2f%% OOV)' % \
(100*sum(results)/len(results), 100.*oov_count/word_count))
else:
print('All comparisons failed!', file=sys.stderr)
def main(argv=None):
if argv is None:
argv = sys.argv
options = process_args(argv[1:])
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
wv = wv.normalize()
except Exception, e:
print >> sys.stderr, 'Error: %s' % str(e)
return 1
def main(argv=None):
if argv is None:
argv = sys.argv
# TODO: remove irrelevant options
options = process_args(argv[1:])
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
except Exception, e:
print >> sys.stderr, 'Error: %s' % str(e)
return 1
def main(argv=None):
if argv is None:
argv = sys.argv
options = process_args(argv[1:])
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
wv = wv.normalize()
except Exception, e:
print >> sys.stderr, 'Error: %s' % str(e)
return 1
def main():
if not (os.path.isfile(model_path)):
# Train a word2vec model
sentences = LineSentence(token_path)
model = Word2Vec(sentences, size=300, window=4, min_count=10)
model.wv.save_word2vec_format('model.txt', binary=False)
del model
else:
# Generate sentences for each unsimplified sentence
wv = wvlib.load(model_path)
f = open('test.txt', 'r')
for line in f:
sent = word_tokenize(line)
sent_len = len(sent)
# Loop through length of sentence
for i in range(0, len(sent)):
# Get nearest neighbors for each word
for j in range(0, NEIGHBOR_NUM):
nearest = wv.nearest(sent[i])[j]
# Absolute cut-off for cosine distance
if (nearest[1] >= DISTANCE_NUM):
# Filter open-class words
word_tag = nltk.pos_tag(nltk.word_tokenize(sent[i]))
neighbor_tag = nltk.pos_tag(
nltk.word_tokenize(nearest[0]))
if word_tag[0][1] and neighbor_tag[0][1] in {
'NN', 'NNS', 'RB', 'RBR', 'RBS', 'VB', 'VBD',
'VBG', 'VBN', 'VBP', 'VBZ', 'JJ', 'JJR', 'JJS'
}:
word = []
word.append(nearest[0]) # word
word.append(nearest[1]) # distance score
sent.append(word)
heap = []
# Generate all possible sentence candidates by combining and averaging word vectors
# Each sentence is the average of its words
for sent_gen in itertools.permutations(sent, sent_len):
temp = []
score = 0
for word in sent_gen:
if isinstance(word, list):
score += word[1]
temp.append(word[0])
else:
score += 1
temp.append(word)
average = score / sent_len
# Ignore reordering of original words
if (average != 1):
heapq.heappush(heap, (average, temp))
# Output top CANDIDATE_NUM sentences
for k in heapq.nlargest(CANDIDATE_NUM, heap):
candidate = ' '.join(k[1])
print candidate, k[0]
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.quiet:
logging.getLogger().setLevel(logging.ERROR)
wordsets = read_wordsets(options.wordset)
if not enough_data(wordsets):
return 1
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank).normalize()
w2v = wv.word_to_vector_mapping()
word_count, oov_count = 0, 0
filtered_wordsets = {}
for k, wordset in wordsets.items():
filtered = []
for w in wordset:
if w in w2v:
filtered.append(w)
else:
logging.warn('ignoring out-of-vocabulary word "%s"' % w)
oov_count += 1
word_count += 1
if filtered:
filtered_wordsets[k] = filtered
else:
logging.warn('wordset %s empty after OOV filtering, removing' % k)
wordsets = filtered_wordsets
if not enough_data(wordsets):
return 1
results = []
for n1, n2 in combinations(wordsets.keys(), 2):
result = compare_sets(wordsets[n1], n1, wordsets[n2], n2, w2v, options)
if result is not None:
results.append(result)
if not options.quiet:
print >> sys.stderr, 'out of vocabulary %d/%d (%.2f%%)' % \
(oov_count, word_count, 100.*oov_count/word_count)
if results:
print 'OVERALL AVERAGE (macro):\t%.2f%%\t(%.2f%% OOV)' % \
(100*sum(results)/len(results), 100.*oov_count/word_count)
else:
print >> sys.stderr, 'All comparisons failed!'
def main(argv=None):
if argv is None:
argv = sys.argv
options = process_args(argv[1:])
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
wv = wv.normalize()
except Exception as e:
print('Error: %s' % str(e), file=sys.stderr)
return 1
return query_loop(wv, options, process_query, query_count=3)
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.quiet:
logging.getLogger().setLevel(logging.ERROR)
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
wv = wv.normalize()
except Exception, e:
print >> sys.stderr, 'Error: %s' % str(e)
return 1
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.quiet:
logging.getLogger().setLevel(logging.ERROR)
try:
wv = wvlib.load(options.vectors, max_rank=options.max_rank)
wv = wv.normalize()
except Exception, e:
print >> sys.stderr, 'Error: %s' % str(e)
return 1
def get_nearest(vectors, queries, nncount=100, options=None):
nearest = {}
wv = wvlib.load(vectors).normalize()
for query in queries:
words = query.split()
v = query_vector(wv, words)
if v is not None:
if options is None or not options.approximate:
word_sim = wv.nearest(v, n=nncount, exclude=words)
else:
word_sim = wv.approximate_nearest(v, n=nncount, exclude=words,
evalnum=10*nncount)
nearest[query] = [ws[0] for ws in word_sim]
else:
nearest[query] = [] # out of vocabulary
return nearest
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
wv = wvlib.load(options.input, options.input_format,
max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
wv.save(options.output, vector_format=options.vector_format)
return 0
def main(argv=None):
if argv is None:
argv = sys.argv
options = argparser().parse_args(argv[1:])
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
wv = wvlib.load(options.input, options.input_format,
max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
wv.save(options.output, vector_format=options.vector_format)
return 0
def main():
wv = wvlib.load(model_path).normalize()
fp = open('test.txt', 'r')
for line in fp:
sent = word_tokenize(line)
sent.insert(0,'<s>')
sent.append('</s>')
prev = '<s>'
# The FST
f = fst.new()
for i in range(1, len(sent) - 1):
if (sent[i] in wv.vocab):
f.add_arc(prev, sent[i], prev, sent[i], -1)
for j in range(0, NEIGHBOR_NUM):
nearest = wv.nearest(sent[i])[j]
# Absolute cut-off for cosine distance
if (nearest[1] >= DISTANCE_NUM):
# Filter open-class words
word_tag = nltk.pos_tag(nltk.word_tokenize(sent[i]))
neighbor_tag = nltk.pos_tag(nltk.word_tokenize(nearest[0]))
if word_tag[0][1] and neighbor_tag[0][1] in open_class:
f.add_arc(prev, sent[i], prev, nearest[0], -nearest[1])
else:
f.add_arc(prev, sent[i], prev, prev, -1)
# Update prev
prev = sent[i]
# Final state
f.add_arc(prev, '</s>', '<epsilon>', '<epsilon>', 0)
f.set_start('<s>')
f.set_final('</s>')
f.printf()
sp = fst.shortest_path_list(f, CANDIDATE_NUM)
for path in sp:
print("%.2f\t%s" % (path[0], path[2]))
def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.eps <= 0.0:
raise ValueError('eps must be > 0')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
logging.info('normalize features to unit variance')
vectors = scipy.cluster.vq.whiten(vectors)
return words, vectors, options
def process_options(args):
options = argparser().parse_args(args)
if options.max_rank is not None and options.max_rank < 1:
raise ValueError('max-rank must be >= 1')
if options.eps <= 0.0:
raise ValueError('eps must be > 0')
wv = wvlib.load(options.vectors[0], max_rank=options.max_rank)
if options.normalize:
logging.info('normalize vectors to unit length')
wv.normalize()
words, vectors = wv.words(), wv.vectors()
if options.whiten:
logging.info('normalize features to unit variance')
vectors = scipy.cluster.vq.whiten(vectors)
return words, vectors, options
import sys
sys.path.insert(0, "wvlib-master/")
import wvlib
vec = wvlib.load('PubMed-and-PMC-ri.tar.gz')
vec.save_bin('PubMed-and-PMC-ri.bin')
def main():
if not (os.path.isfile(model_path)):
# Train a word2vec model
sentences = LineSentence(token_path)
model = Word2Vec(sentences, size=300, window=4, min_count=10)
model.wv.save_word2vec_format('model.txt', binary=False)
del model
else:
# Generate sentences for each unsimplified sentence
wv = wvlib.load(model_path).normalize()
f = open('test.txt', 'r')
line_num = sum(1 for _ in f)
f.seek(0)
count = 0
# Build lattice graph for every sentence
for line in f:
count += 1
print "Sentence", count, "of", line_num
sent = word_tokenize(line)
G = nx.DiGraph()
G.add_node("START")
temp = []
words = []
# Loop through length of sentence
for i in range(0, len(sent)):
node = sent[i] + '*' + str(
i) + '*' # Unique identifier for nodes
G.add_node(node)
# Connect edges
if (i == 0):
G.add_edge("START", node, weight=-1)
else:
prev_node = sent[i - 1] + '*' + str(i - 1) + '*'
G.add_edge(prev_node, node, weight=-1)
for w in range(0, len(words)):
G.add_edge(words[w], node, weight=-1)
# "Save" nodes to connect back to the edges
temp = words
words = []
# Get nearest neighbors for each word
if (sent[i] in wv.vocab):
for j in range(0, NEIGHBOR_NUM):
nearest = wv.nearest(sent[i])[j]
# Absolute cut-off for cosine distance
if (nearest[1] >= DISTANCE_NUM):
# Filter open-class words
word_tag = nltk.pos_tag(nltk.word_tokenize(
sent[i]))
neighbor_tag = nltk.pos_tag(
nltk.word_tokenize(nearest[0]))
if word_tag[0][1] and neighbor_tag[0][1] in {
'NN', 'NNS', 'RB', 'RBR', 'RBS', 'VB',
'VBD', 'VBG', 'VBN', 'VBP', 'VBZ', 'JJ',
'JJR', 'JJS'
}:
neighbor_node = nearest[0] + '*' + str(
j) + '*' # Unique identifier for nodes
words.append(neighbor_node)
G.add_node(neighbor_node)
# Connect edges
if (i == 0):
G.add_edge("START",
neighbor_node,
weight=-round(nearest[1], 5))
else:
G.add_edge(prev_node,
neighbor_node,
weight=-round(nearest[1], 5))
for t in range(0, len(temp)):
G.add_edge(
temp[t],
neighbor_node,
weight=-round(nearest[1], 5))
# Add END node
G.add_node("END")
G.add_edge(node, "END", weight=-1)
for w in range(0, len(words)):
G.add_edge(words[w], "END", weight=-1)
f = open('output.txt', 'a+')
candidate_list = []
# Write sentence candidates from the lattice to file
# We find the shortest path because we use negative weights
for path in k_shortest_paths(G, "START", "END", CANDIDATE_NUM):
H = G.subgraph(path)
# Candidate sentences only
candidate = []
if (len(k_shortest_paths(
G, "START", "END",
CANDIDATE_NUM)) == 1): # sentences with no candidates
for c in range(0, CANDIDATE_NUM):
candidate_list.append('-------')
continue
if (-(len(sent) + 1) != nx.shortest_path_length(
H, "START", "END", weight='weight')):
for word in path: # remove unique identifiers
candidate.append(re.sub(r'\*.*\*', '', word))
candidate = [c.decode('utf-8') for c in candidate]
candidate = ' '.join(candidate[1:-1])
candidate_list.append(candidate)
else:
candidate_list.append('-------')
# # Draw sub-lattice
# pos = nx.spring_layout(H)
# new_labels = dict(map(lambda x:((x[0],x[1]), str(x[2]['weight'])), H.edges(data=True)))
# nx.draw_networkx(H, pos=pos, font_weight='bold', font_size=15, edge_color='g')
# nx.draw_networkx_edge_labels(H, pos=pos, font_weight='bold', width=4, edge_labels=new_labels)
# nx.draw_networkx_edges(H, pos, with_labels=True, width=2, arrows=False)
# plt.show()
for sent in range(0, len(candidate_list)):
f.write(candidate_list[sent].encode('utf-8') + '\n')
f.close()
