def text_prep(text_doc, count):
text_doc = [digit_removal(d) for d in text_doc]
text_doc = [stop_word_removal(d) for d in text_doc]
maxlength_doc = 80000
text_doc = [unicode(clean(d)) for d in text_doc]
print(text_doc)
tokens, vocab = preprocess.tokenize(text_doc,
maxlength_doc,
merge=False,
n_threads=4)
print(tokens, vocab)
corpus = Corpus()
corpus.update_word_count(tokens)
corpus.finalize()
compact = corpus.to_compact(tokens)
pruned = corpus.filter_count(compact, min_count=50)
bow = corpus.compact_to_bow(pruned)
clean_data = corpus.subsample_frequent(pruned)
doc_ids = numpy.arange(pruned.shape[0])
flattened, (doc_ids, ) = corpus.compact_to_flat(pruned, doc_ids)
assert flattened.min() >= 0
pickle.dump(
vocab, open(os.path.join(result_folder,
str(count) + 'vocab.pkl'), 'w'))
pickle.dump(
corpus,
open(os.path.join(result_folder,
str(count) + 'corpus.pkl'), 'w'))
numpy.save("flattened", flattened)
numpy.save("doc_ids", doc_ids)
numpy.save("pruned", pruned)
numpy.save("bow", bow)
def make_corpus(tokens, min_count=50):
""" Creates LDA2vec corpus
:param text:
:return:
"""
corpus = Corpus()
corpus.update_word_count(tokens)
corpus.finalize()
compact = corpus.to_compact(tokens)
pruned = corpus.filter_count(compact, min_count=min_count)
clean = corpus.subsample_frequent(pruned)
doc_ids = np.arange(pruned.shape[0])
corpus, flattened, (doc_ids,) = corpus.compact_to_flat(pruned, doc_ids)
return corpus, flattened, doc_ids, clean
def make_corpus(tokens, min_count=50):
""" Creates LDA2vec corpus
:param text:
:return:
"""
corpus = Corpus()
corpus.update_word_count(tokens)
corpus.finalize()
compact = corpus.to_compact(tokens)
pruned = corpus.filter_count(compact, min_count=min_count)
clean = corpus.subsample_frequent(pruned)
doc_ids = np.arange(pruned.shape[0])
corpus, flattened, (doc_ids, ) = corpus.compact_to_flat(pruned, doc_ids)
return corpus, flattened, doc_ids, clean
def process_data(tokens, vocab, model):
"""
preprocessing of the data by counting word occurrences and filtering according to these.
The most frequent words are subsampled, and cleans the vocabulary words according to the
word2vec models vocabulary
:param tokens: spacy tokens
:param vocab: spacy vocabulary
:param model: word2vec model name
:return:
"""
corpus = Corpus()
# Make a ranked list of rare vs frequent words
corpus.update_word_count(tokens)
corpus.finalize()
# The tokenization uses spaCy indices, and so may have gaps
# between indices for words that aren't present in our dataset.
# This builds a new compact index
compact = corpus.to_compact(tokens)
# Remove extremely rare words
pruned = corpus.filter_count(compact, min_count=15)
# Convert the compactified arrays into bag of words arrays
bow = corpus.compact_to_bow(pruned)
# Words tend to have power law frequency, so selectively
# downsample the most prevalent words
clean = corpus.subsample_frequent(pruned)
# Now flatten a 2D array of document per row and word position
# per column to a 1D array of words. This will also remove skips
# and OoV words
doc_ids = np.arange(pruned.shape[0])
flattened, (doc_ids, ) = corpus.compact_to_flat(pruned, doc_ids)
assert flattened.min() >= 0
# Fill in the pretrained word vectors
#n_dim = 300
fn_wordvc = model
print("starts to compact word vectors")
vectors, s, f = corpus.compact_word_vectors(vocab, filename=fn_wordvc)
print("done with compact word vectors")
# Save all of the preprocessed files
print("now saving files")
pickle.dump(vocab, open('vocab_' + id + '.pkl', 'w'))
pickle.dump(corpus, open('corpus_' + id + '.pkl', 'w'))
np.save('flattened_' + id, flattened)
np.save('doc_ids_' + id, doc_ids)
np.save('pruned_' + id, pruned)
#np.save('bow_'+id, bow) Does not seem to be neccessary for lda2vec_run.py
np.save('vectors_' + id, vectors)
n_threads=4)
corpus = Corpus()
# Make a ranked list of rare vs frequent words
corpus.update_word_count(tokens)
corpus.finalize()
# The tokenization uses spaCy indices, and so may have gaps
# between indices for words that aren't present in our dataset.
# This builds a new compact index
compact = corpus.to_compact(tokens)
# Remove extremely rare words
pruned = corpus.filter_count(compact, min_count=30)
# Convert the compactified arrays into bag of words arrays
bow = corpus.compact_to_bow(pruned)
# Words tend to have power law frequency, so selectively
# downsample the most prevalent words
clean = corpus.subsample_frequent(pruned)
# Now flatten a 2D array of document per row and word position
# per column to a 1D array of words. This will also remove skips
# and OoV words
doc_ids = np.arange(pruned.shape[0])
flattened, (doc_ids, ) = corpus.compact_to_flat(pruned, doc_ids)
assert flattened.min() >= 0
# Fill in the pretrained word vectors
# n_dim = 300
# fn_wordvc = 'GoogleNews-vectors-negative300.bin'
# vectors, s, f = corpus.compact_word_vectors(vocab, filename=fn_wordvc)
# Save all of the preprocessed files
pickle.dump(vocab, open('vocab.pkl', 'w'))
pickle.dump(corpus, open('corpus.pkl', 'w'))
np.save("flattened", flattened)
np.save("doc_ids", doc_ids)
# Preprocess data max_length = 1000 # Limit of 1k words per document tokens, vocab = preprocess.tokenize(texts, max_length, tag=False, parse=False, entity=False) corpus = Corpus() # Make a ranked list of rare vs frequent words corpus.update_word_count(tokens) corpus.finalize() # The tokenization uses spaCy indices, and so may have gaps # between indices for words that aren't present in our dataset. # This builds a new compact index compact = corpus.to_compact(tokens) # Remove extremely rare words pruned = corpus.filter_count(compact, min_count=5) # Words tend to have power law frequency, so selectively # downsample the most prevalent words clean = corpus.subsample_frequent(pruned) # Now flatten a 2D array of document per row and word position # per column to a 1D array of words. This will also remove skips # and OoV words doc_ids = np.arange(clean.shape[0]) flattened, (doc_ids,) = corpus.compact_to_flat(clean, doc_ids) # Model Parameters # Number of documents n_docs = len(texts) # Number of unique words in the vocabulary n_words = flattened.max() + 1 # Number of dimensions in a single word vector n_hidden = 128 # Number of topics to fit n_topics = 5
class Lda2VecFeaturizer:
def __init__(self,\
clambda=200,\
n_topics=10,\
batchsize=4096,\
power=0.75,\
words_pretrained=True,\
temperature=1,\
max_length=1000,\
min_count=0,\
word2vec_path=None):
# 'Strength' of the dircihlet prior; 200.0 seems to work well
self.clambda = clambda
# Number of topics to fit
self.n_topics = n_topics #int(os.getenv('n_topics', 10))
self.batchsize = batchsize
# Power for neg sampling
self.power = power #float(os.getenv('power', 0.75))
# Intialize with pretrained word vectors
self.words_pretrained = words_pretrained #bool(int(os.getenv('pretrained', True)))
self.temp = temperature
self.max_length = max_length
self.min_count = min_count
self.word2vec_model = KeyedVectors.load_word2vec_format(word2vec_path, binary=True)
def preprocess(self, docs=None):
""" Uses spaCy to quickly tokenize text and return an array
of indices.
This method stores a global NLP directory in memory, and takes
up to a minute to run for the time. Later calls will have the
tokenizer in memory."""
assert (isinstance(docs, list)), ("input list of documents")
assert (all(isinstance(doc, unicode) for doc in docs)),("expected unicode, got string")
self.corpus = Corpus()
tokens, self.vocab = preprocess.tokenize(docs, self.max_length, merge=False,n_threads=4)
# Make a ranked list of rare vs frequent words
self.corpus.update_word_count(tokens)
self.corpus.finalize()
# The tokenization uses spaCy indices, and so may have gaps
# between indices for words that aren't present in our dataset.
# This builds a new compact index
compact = self.corpus.to_compact(tokens)
# Remove extremely rare words
pruned = self.corpus.filter_count(compact, min_count=0)
# Convert the compactified arrays into bag of words arrays
bow = self.corpus.compact_to_bow(pruned)
# Words tend to have power law frequency, so selectively
# downsample the most prevalent words
clean = self.corpus.subsample_frequent(pruned)
# Now flatten a 2D array of document per row and word position
# per column to a 1D array of words. This will also remove skips
# and OoV words
self.doc_ids = np.arange(pruned.shape[0])
self.flattened, (self.doc_ids,) = self.corpus.compact_to_flat(pruned, self.doc_ids)
self.vectors, s, f = self.corpus.compact_word_vectors(self.vocab, model = self.word2vec_model)
# vectors = np.delete(vectors,77743,0)
# Model Parameters
# Number of documents
self.n_docs = len(docs) #doc_ids.max() + 1
# Number of unique words in the vocabulary
self.n_vocab=self.flattened.max() + 1
doc_idx, lengths = np.unique(self.doc_ids, return_counts=True)
self.doc_lengths = np.zeros(self.doc_ids.max() + 1, dtype='int32')
self.doc_lengths[doc_idx] = lengths
# Count all token frequencies
tok_idx, freq = np.unique(self.flattened, return_counts=True)
self.term_frequency = np.zeros(self.n_vocab, dtype='int32')
self.term_frequency[tok_idx] = freq
self.fraction = self.batchsize * 1.0 / self.flattened.shape[0]
# Get the string representation for every compact key
self.words = self.corpus.word_list(self.vocab)[:self.n_vocab]
def train(self,docs=None, epochs=200, update_words=False, update_topics=True):
""" Takes the training documents as a list of documents
preprocesses the documents and reurns a dictionary data containing the
Topic distribution
Vocab
document length
and topic word distribution"""
texts = docs
docs = []
for text in texts:
docs.append(unicode(" ".join(word for word in text.split() if word in self.word2vec_model.vocab)))
logging.info("preprocessing...")
self.preprocess(docs)
logging.info('preprocessed!')
self.train_model = LDA2Vec(n_documents=self.n_docs,\
n_document_topics=self.n_topics,\
n_units=300,\
n_vocab=self.n_vocab,\
counts=self.term_frequency,\
n_samples=15,\
power=self.power,\
temperature=self.temp)
if self.words_pretrained:
self.train_model.sampler.W.data = self.vectors[:self.n_vocab, :]
optimizer = O.Adam()
optimizer.setup(self.train_model)
clip = chainer.optimizer.GradientClipping(5.0)
optimizer.add_hook(clip)
j = 0
msgs = defaultdict(list)
for epoch in range(epochs):
print "epoch : ",epoch
data = prepare_topics(cuda.to_cpu(self.train_model.mixture.weights.W.data).copy(),
cuda.to_cpu(self.train_model.mixture.factors.W.data).copy(),
cuda.to_cpu(self.train_model.sampler.W.data).copy(),
self.words)
top_words = print_top_words_per_topic(data)
if j % 100 == 0 and j > 100:
coherence = topic_coherence(top_words)
for j in range(self.n_topics):
print j, coherence[(j, 'cv')]
kw = dict(top_words=top_words, coherence=coherence, epoch=epoch)
#progress[str(epoch)] = pickle.dumps(kw)
data['doc_lengths'] = self.doc_lengths
data['term_frequency'] = self.term_frequency
#np.savez('topics.pyldavis', **data)
for d, f in utils.chunks(self.batchsize, self.doc_ids, self.flattened):
t0 = time.time()
optimizer.zero_grads()
l = self.train_model.fit_partial(d.copy(), f.copy(), update_words=update_words, update_topics=update_topics)
prior = self.train_model.prior()
loss = prior * self.fraction
loss.backward()
optimizer.update()
msg = ("J:{j:05d} E:{epoch:05d} L:{loss:1.3e} "
"P:{prior:1.3e} R:{rate:1.3e}")
prior.to_cpu()
loss.to_cpu()
t1 = time.time()
dt = t1 - t0
rate = self.batchsize / dt
msgs["E"].append(epoch)
msgs["L"].append(float(l))
j += 1
logs = dict(loss=float(l), epoch=epoch, j=j, prior=float(prior.data), rate=rate)
print msg.format(**logs)
print "\n ================================= \n"
#serializers.save_hdf5("lda2vec.hdf5", self.model)
msgs["loss_per_epoch"].append(float(l))
return data, msgs
def initialize_infer(self,\
clambda=200,\
batchsize=4096,\
power=0.75,\
words_pretrained=True,\
temperature=1,\
max_length=1000,\
min_count=0):
""" Initializes parameters for testing, if needed
Usually not called. """
# 'Strength' of the dircihlet prior; 200.0 seems to work well
self.clambda = clambda
# Number of topics to fit
self.batchsize = batchsize
# Power for neg sampling
self.power = power #float(os.getenv('power', 0.75))
# Intialize with pretrained word vectors
self.words_pretrained = words_pretrained #bool(int(os.getenv('pretrained', True)))
self.temp = temperature
self.max_length = max_length
self.min_count = min_count
logging.info('Test parameters initialized!')
def infer(self,docs=None,epochs=200, update_words=False, update_topics=False, topic_vectors=None):
""" Infers the featurs of a new document that is passed in.
By running the Lda2vec algorithm again.
But by updating only the topic distributions"""
texts = docs
docs = []
for text in texts:
docs.append(unicode(" ".join(word for word in text.split() if word in self.word2vec_model.vocab)))
logging.info("preprocessing")
self.preprocess(docs)
logging.info('preprocessed!')
self.infer_model = LDA2Vec(n_documents=self.n_docs,\
n_document_topics=self.n_topics,\
n_units=300,\
n_vocab=self.n_vocab,\
counts=self.term_frequency,\
n_samples=15,\
power=self.power,\
temperature=self.temp)
if self.words_pretrained:
self.infer_model.sampler.W.data = self.vectors[:self.n_vocab, :]
self.infer_model.mixture.factors.W.data = self.train_model.mixture.factors.W.data
if topic_vectors is not None:
assert(topic_vectors.shape==self.infer_model.mixture.factors.W.data.shape), ("topic vectors shape doesn't match")
self.infer_model.mixture.factors.W.data = topic_vectors
optimizer = O.Adam()
optimizer.setup(self.infer_model)
clip = chainer.optimizer.GradientClipping(5.0)
optimizer.add_hook(clip)
j = 0
msgs = defaultdict(list)
for epoch in range(epochs):
print "epoch : ",epoch
data = prepare_topics(cuda.to_cpu(self.infer_model.mixture.weights.W.data).copy(),
cuda.to_cpu(self.infer_model.mixture.factors.W.data).copy(),
cuda.to_cpu(self.infer_model.sampler.W.data).copy(),
self.words)
top_words = print_top_words_per_topic(data)
if j % 100 == 0 and j > 100:
coherence = topic_coherence(top_words)
for j in range(self.n_topics):
print j, coherence[(j, 'cv')]
kw = dict(top_words=top_words, coherence=coherence, epoch=epoch)
#progress[str(epoch)] = pickle.dumps(kw)
data['doc_lengths'] = self.doc_lengths
data['term_frequency'] = self.term_frequency
#np.savez('topics.pyldavis', **data)
for d, f in utils.chunks(self.batchsize, self.doc_ids, self.flattened):
t0 = time.time()
optimizer.zero_grads()
l = self.infer_model.fit_partial(d.copy(), f.copy(), update_words=update_words, update_topics=update_topics)
prior = self.infer_model.prior()
loss = prior * self.fraction
loss.backward()
optimizer.update()
msg = ("J:{j:05d} E:{epoch:05d} L:{loss:1.3e} "
"P:{prior:1.3e} R:{rate:1.3e}")
prior.to_cpu()
loss.to_cpu()
t1 = time.time()
dt = t1 - t0
rate = self.batchsize / dt
msgs["E"].append(epoch)
msgs["L"].append(float(l))
j += 1
logs = dict(loss=float(l), epoch=epoch, j=j, prior=float(prior.data), rate=rate)
print msg.format(**logs)
print "\n ================================= \n"
#serializers.save_hdf5("lda2vec.hdf5", self.model)
msgs["loss_per_epoch"].append(float(l))
return data, msgs
