def __init__(self, graph, path):
Embedding.__init__(self, graph)
self.graph = graph
self.walks = None
self.embedding = None
self.path = path
self.set_paths(path)
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'use_dan',
dimensions=512,
corpus_size='na',
vocabulary_size='230k',
download_url='https://storage.googleapis.com/tfhub-modules/'
'google/universal-sentence-encoder/2.tar.gz',
format='tar.gz',
architecture='DAN',
trained_data='wikipedia and other sources',
language='en'),
Embedding(name=u'use_transformer_large',
dimensions=512,
corpus_size='na',
vocabulary_size='230k',
download_url='https://storage.googleapis.com/tfhub-modules/'
'google/universal-sentence-encoder-large/3.tar.gz',
format='tar.gz',
architecture='Transformer',
trained_data='wikipedia and other sources',
language='en'),
Embedding(name=u'use_transformer_lite',
dimensions=512,
corpus_size='na',
vocabulary_size='na',
download_url='https://storage.googleapis.com/tfhub-modules/'
'google/universal-sentence-encoder-lite/2.tar.gz',
format='tar.gz',
architecture='Transformer',
trained_data='wikipedia and other sources',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
def __init__(self):
self.sess = tf.Session()
self.sess.run(
[tf.global_variables_initializer(),
tf.tables_initializer()])
self.use_module = None
self.model = None
def load_model(self, model: str, model_path: str):
self.use_module = hub.Module(model_path)
self.sess.run(tf.initializers.global_variables())
self.model = model
def encode(self,
texts: list,
pooling: Optional[str] = None) -> Optional[np.array]:
return self.sess.run(self.use_module(texts))
def __init__(
self, num_of_actions, epsilon=0.0001, num_of_neighbours=10, cluster_distance=0.008,
pseudo_counts=0.001, maximum_similarity=8, episodic_memory_capacity=30000):
self.epsilon = epsilon
self.num_of_neighbours = num_of_neighbours
self.cluster_distance = cluster_distance
self.pseudo_counts = pseudo_counts
self.maximum_similarity = maximum_similarity
self.episodic_memory = deque([], maxlen=episodic_memory_capacity)
self.moving_average = MovingAverage()
self.network = Embedding(num_of_actions)
self.optimizer = tf.keras.optimizers.Adam()
def train(params, files):
binary = str2bool(params['binary'])
data_set, peptide_n_mer = read_data_set(files,
test_size=0.05,
binary=binary)
print('Train data shape is {}'.format(data_set['X_train'].shape))
print('Train data shape is {}'.format(data_set['X_test'].shape))
# variable batch size depending on number of data points
batch_size = int(np.ceil(len(data_set['X_train']) / 100.0))
epochs = int(params['epochs'])
nb_filter = int(params['filter_size'])
filter_length = int(params['filter_length'])
dropout = float(params['dropout'])
lr = float(params['lr'])
# manual drop last
for name in data_set.keys():
if data_set[name].shape[0] % batch_size != 0:
data_set[name] = data_set[name][:-(data_set[name].shape[0] %
batch_size)]
# load in learned distributed representation HLA-Vec
hla_vec_obj = Word2Vec.load(files['vector_embedding'])
hla_vec_embed = hla_vec_obj.wv
embed_shape = hla_vec_embed.syn0.shape
embedding_weights = np.random.rand(embed_shape[0] + 1, embed_shape[1])
for key in AA_IDX.keys():
embedding_weights[AA_IDX[key], :] = hla_vec_embed[key]
embedded_dim = embed_shape[1]
embedding = Embedding(embedded_dim, embedding_weights)
train_embedding = embedding(torch.from_numpy(data_set['X_train'])).numpy()
train_embedding = train_embedding.reshape((train_embedding.shape[0], -1))
test_embedding = embedding(torch.from_numpy(data_set['X_test'])).numpy()
test_embedding = test_embedding.reshape((test_embedding.shape[0], -1))
if str2bool(params['binary']):
data_set['Y_train'] = np.argmax(data_set['Y_train'], -1)[:, np.newaxis]
data_set['Y_test'] = np.argmax(data_set['Y_test'], -1)[:, np.newaxis]
else:
data_set['Y_train'] = data_set['Y_train'][:, np.newaxis]
data_set['Y_test'] = data_set['Y_test'][:, np.newaxis]
# weight_space(train_embedding, test_embedding, data_set)
infinite_fcn(train_embedding, test_embedding, data_set, binary=binary)
#infinite_resnet(train_embedding, test_embedding, data_set)
print("The result of gaussian process of regression is:")
gaussian_process(train_embedding,
test_embedding,
data_set,
is_classifier=False,
binary=binary)
from typing import List, Dict
from models import Embedding
EMBEDDING_MODELS: List[Embedding] = [
Embedding(
name=u'use',
dimensions=512,
corpus_size='na',
vocabulary_size='230k',
download_url='https://tfhub.dev/google/universal-sentence-encoder/2',
format='.tar.gz',
architecture='DAN',
trained_data='wikipedia and other sources',
language='en'),
Embedding(name=u'use_large',
dimensions=512,
corpus_size='na',
vocabulary_size='230k',
download_url=
'https://tfhub.dev/google/universal-sentence-encoder-large/3',
format='.tar.gz',
architecture='Transformer',
trained_data='wikipedia and other sources',
language='en'),
Embedding(name=u'use_lite',
dimensions=512,
corpus_size='na',
vocabulary_size='na',
download_url=
'https://tfhub.dev/google/universal-sentence-encoder-lite/2',
def __init__(self, graph, save_path):
Embedding.__init__(self, graph)
self.set_paths(save_path)
self.walker = RandomWalker(graph)
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(
name=u'google_news_300',
dimensions=300,
corpus_size='100B',
vocabulary_size='3M',
download_url=
'https://s3.amazonaws.com/dl4j-distribution/GoogleNews-vectors-negative300.bin.gz',
format='gz',
architecture='skip-gram',
trained_data='Google News',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
def __init__(self):
self.word_vectors: Dict[Any, Any] = {}
self.model = None
@classmethod
def _tokens(cls, text: str) -> List[str]:
return [x.lower().strip() for x in text.split()]
def load_model(self, model: str, model_path: str):
try:
encoding = 'utf-8'
unicode_errors = 'strict'
model_file = [
f for f in os.listdir(model_path)
if os.path.isfile(os.path.join(model_path, f))
]
f = open(os.path.join(model_path, model_file[0]), 'rb')
header = to_unicode(f.readline(), encoding=encoding)
vocab_size, vector_size = (int(x) for x in header.split()
) # throws for invalid file format
binary_len = dtype(real).itemsize * vector_size
for _ in tqdm(range(vocab_size)):
word = []
while True:
ch = f.read(1)
if ch == b' ':
break
if ch == b'':
raise EOFError(
"unexpected end of input; is count incorrect or file otherwise damaged?"
)
if ch != b'\n': # ignore newlines in front of words (some binary files have)
word.append(ch)
word = to_unicode(b''.join(word),
encoding=encoding,
errors=unicode_errors)
weights = fromstring(f.read(binary_len),
dtype=real).astype(real)
self.word_vectors[word] = weights
self.model = model
print("Model loaded Successfully !")
return self
except Exception as e:
print('Error loading Model, ', str(e))
def encode(self, texts: list, pooling: str = 'mean', **kwargs) -> np.array:
text = texts[0]
result = np.zeros(Embeddings.EMBEDDING_MODELS[self.model].dimensions,
dtype="float32")
tokens = Embeddings._tokens(text)
vectors = np.array([
self.word_vectors[token] for token in tokens
if token in self.word_vectors.keys()
])
if pooling == 'mean':
result = np.mean(vectors, axis=0)
elif pooling == 'max':
result = np.max(vectors, axis=0)
elif pooling == 'sum':
result = np.sum(vectors, axis=0)
elif pooling == 'tf-idf-sum':
if not kwargs.get('tfidf_dict'):
print('Must provide tfidf dict')
return result
tfidf_dict = kwargs.get('tfidf_dict')
weighted_vectors = np.array([
tfidf_dict.get(token) * self.word_vectors.get(token)
for token in tokens
if token in self.word_vectors.keys() and token in tfidf_dict
])
result = np.mean(weighted_vectors, axis=0)
else:
print(
f'Given pooling method "{pooling}" not implemented in "{self.model}"'
)
return result
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'wiki_news_300',
dimensions=300,
corpus_size='16B',
vocabulary_size='1M',
download_url=
'https://dl.fbaipublicfiles.com/fasttext/vectors-english/'
'wiki-news-300d-1M.vec.zip',
format='zip',
architecture='CBOW',
trained_data='Wikipedia 2017',
language='en'),
Embedding(name=u'wiki_news_300_sub',
dimensions=300,
corpus_size='16B',
vocabulary_size='1M',
download_url=
'https://dl.fbaipublicfiles.com/fasttext/vectors-english/'
'wiki-news-300d-1M-subword.vec.zip',
format='zip',
architecture='CBOW',
trained_data='Wikipedia 2017',
language='en'),
Embedding(name=u'common_crawl_300',
dimensions=300,
corpus_size='600B',
vocabulary_size='2M',
download_url=
'https://dl.fbaipublicfiles.com/fasttext/vectors-english/'
'crawl-300d-2M.vec.zip',
format='zip',
architecture='CBOW',
trained_data='Common Crawl (600B tokens)',
language='en'),
Embedding(name=u'common_crawl_300_sub',
dimensions=300,
corpus_size='600B',
vocabulary_size='2M',
download_url=
'https://dl.fbaipublicfiles.com/fasttext/vectors-english/'
'crawl-300d-2M-subword.zip',
format='zip',
architecture='CBOW',
trained_data='Common Crawl (600B tokens)',
language='en'),
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
def __init__(self):
self.word_vectors: Dict[Any, Any] = {}
self.model = None
@classmethod
def _tokens(cls, text):
return [x.lower().strip() for x in text.split()]
def load_model(self, model: str, model_path: str):
try:
model_file = [
f for f in os.listdir(model_path)
if os.path.isfile(os.path.join(model_path, f))
]
f = open(os.path.join(model_path, model_file[0]), 'r')
next(f)
for line in tqdm(f):
split_line = line.split()
word = split_line[0]
self.word_vectors[word] = np.array(
[float(val) for val in split_line[1:]])
print("Model loaded Successfully !")
self.model = model
return self
except Exception as e:
print('Error loading Model, ', str(e))
return self
def encode(self, texts: list, pooling: str = 'mean', **kwargs) -> np.array:
text = texts[0]
result = np.zeros(Embeddings.EMBEDDING_MODELS[self.model].dimensions,
dtype="float32")
tokens = Embeddings._tokens(text)
vectors = np.array([
self.word_vectors[token] for token in tokens
if token in self.word_vectors.keys()
])
if pooling == 'mean':
result = np.mean(vectors, axis=0)
elif pooling == 'max':
result = np.max(vectors, axis=0)
elif pooling == 'sum':
result = np.sum(vectors, axis=0)
elif pooling == 'tf-idf-sum':
if not kwargs.get('tfidf_dict'):
print('Must provide tfidf dict')
return result
tfidf_dict = kwargs.get('tfidf_dict')
weighted_vectors = np.array([
tfidf_dict.get(token) * self.word_vectors.get(token)
for token in tokens
if token in self.word_vectors.keys() and token in tfidf_dict
])
result = np.mean(weighted_vectors, axis=0)
else:
print(f'Given pooling method "{pooling}" not implemented')
return result
def __init__(self,
vocab_size,
nb_negative,
embed_dims=128,
context_dims=128,
negprob_table=None,
optimizer='adam'):
super(NCELangModelV2, self).__init__(weighted_inputs=False)
self.vocab_size = vocab_size
self.embed_dim = embed_dims
self.optimizer = optimizers.get(optimizer)
self.nb_negative = nb_negative
self.loss = categorical_crossentropy
self.loss_fnc = objective_fnc(self.loss)
if negprob_table is None:
negprob_table_ = np.ones(shape=(vocab_size, ),
dtype=theano.config.floatX) / vocab_size
negprob_table = theano.shared(negprob_table_)
self.neg_prob_table = negprob_table_
else:
self.neg_prob_table = negprob_table.astype(theano.config.floatX)
negprob_table = theano.shared(
negprob_table.astype(theano.config.floatX))
self.sampler = TableSampler(self.neg_prob_table)
self.add_input(name='idxes', ndim=3, dtype='int32')
self.add_node(Split(split_at=1, split_axis=0),
name=('pos_sents', ''),
inputs='idxes')
seq = containers.Sequential()
seq.add(self.nodes['pos_sents'])
seq.add(Embedding(vocab_size, embed_dims))
seq.add(LangLSTMLayer(embed_dims, output_dim=context_dims))
# seq.add(Dropout(0.5))
self.add_node(seq, name='seq')
self.add_node(PartialSoftmax(input_dim=context_dims,
output_dim=vocab_size),
name='part_prob',
inputs=('idxes', 'seq'))
self.add_node(Dense(input_dim=context_dims,
output_dim=1,
activation='exponential'),
name='normalizer',
inputs='seq')
self.add_node(LookupProb(negprob_table),
name='lookup_prob',
inputs='idxes')
test_node = Dense(input_dim=context_dims,
output_dim=vocab_size,
activation='exponential')
test_node.params = []
test_node.W = self.nodes['part_prob'].W
test_node.b = self.nodes['part_prob'].b
self.add_node(test_node, name='true_unrm_prob', inputs='seq')
# self.add_node(ActivationLayer(name='normalization'), name='true_prob', inputs='true_unrm_prob')
self.add_output('pos_prob', node='part_prob')
self.add_output('neg_prob', node='lookup_prob')
# self.add_output('pred_prob', node='true_prob')
self.add_output('normalizer', node='normalizer')
self.add_output('unrm_prob', node='true_unrm_prob')
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'elmo_bi_lm',
dimensions=512,
corpus_size='1B',
vocabulary_size='5.5B',
download_url='https://storage.googleapis.com/tfhub-modules/google/elmo/2.tar.gz',
format='tar.gz',
architecture='Embedding layer,cnn_layer_with_maxpool,2 lstm layers',
trained_data='One Billion Word Benchmark',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {embedding.name: embedding for embedding in EMBEDDING_MODELS}
def __init__(self):
self.elmo_module = None
self.model = None
@classmethod
def tokenize(cls, text: str):
return [word.strip() for word in text.lower().strip().split()]
@classmethod
def padded_tokens(cls, tokens: List[str], max_seq_length: int):
padded_token = ""
len_tokens = len(tokens)
if len_tokens >= max_seq_length:
return tokens[:max_seq_length]
else:
padded_len = max_seq_length - len_tokens
return tokens + [padded_token] * padded_len
def load_model(self, model: str, model_path: str):
self.elmo_module = hub.Module(model_path)
self.model = model
def encode(self, texts: list, pooling: str = 'mean', **kwargs) -> Optional[np.array]:
text_tokens = [Embeddings.tokenize(text) for text in texts]
max_seq_length = kwargs.get('max_seq_length')
if max_seq_length:
text_tokens = [Embeddings.padded_tokens(tokens, max_seq_length) for tokens in text_tokens]
seq_length = [max_seq_length] * len(texts)
else:
seq_length = [len(tokens) for tokens in text_tokens]
embeddings = self.elmo_module(inputs={"tokens": text_tokens, "sequence_len": seq_length},
signature="tokens", as_dict=True)["elmo"]
if not pooling:
return embeddings
if pooling == 'mean':
return tf.reduce_mean(embeddings, 0)
elif pooling == 'max':
return tf.reduce_max(embeddings, 0)
elif pooling == 'min':
return tf.reduce_min(embeddings, 0)
elif pooling == 'mean_max':
return tf.concat(values=[tf.reduce_mean(embeddings, 0), tf.reduce_max(embeddings, 0)], axis=0)
else:
print(f"Pooling method \"{pooling}\" not implemented")
return None
from typing import List, Dict
from models import Embedding
EMBEDDING_MODELS: List[Embedding] = [
Embedding(
name=u'infersent_glove',
dimensions=300,
corpus_size='570k human-generated English sentence pairs',
vocabulary_size='na',
download_url='https://dl.fbaipublicfiles.com/infersent/infersent1.pkl',
format='tar.gz',
architecture='cbow',
trained_data='SNLI dataset',
language='en'),
Embedding(
name=u'infersent_fasttext',
dimensions=300,
corpus_size='570k human-generated English sentence pairs',
vocabulary_size='na',
download_url='https://dl.fbaipublicfiles.com/infersent/infersent2.pkl',
format='tar.gz',
architecture='cbow',
trained_data='SNLI dataset',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
#
vocab.append_sents(valid_sents, fixed_vocab_set=fixed_vocab_set)
vocab.append_sents(test_sents, fixed_vocab_set=fixed_vocab_set)
#
print('vocab size {} before shrink'.format(vocab.vocab_len))
vocab.shrink_vocab(2)
print('vocab size {} after shrink'.format(vocab.vocab_len))
print('read vec')
word_list = [vocab.idx2word[i] for i in range(len(vocab.idx2word))]
vec = read_vec(pubmed_w2v_path, word_list)
assert vec.shape[0] == vocab.vocab_len
print('build emb layer')
emb = Embedding(vocab.vocab_len,
vec.shape[1],
padding_idx=0,
trainable=False)
emb.initialize_embedding(vec)
emb.cuda()
torch.save(emb.state_dict(), emb_path)
print('dump data')
train_sents = convert_sents_to_idx(train_sents, vocab)
test_sents = convert_sents_to_idx(test_sents, vocab)
valid_sents = convert_sents_to_idx(valid_sents, vocab)
dump_preprocessed_data(opt.train_path, train_sents, train_labels)
dump_preprocessed_data(opt.test_path, test_sents, test_labels)
dump_preprocessed_data(opt.valid_path, valid_sents, valid_labels)
dump_vocab(opt.vocab_path, vocab)
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'twitter_100',
dimensions=100,
corpus_size='27B',
vocabulary_size='1.2M',
download_url='https://www.dropbox.com/s/q2wof83a0yq7q74/glove.twitter.27B.100d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Twitter 2B Tweets',
language='en'),
Embedding(name=u'twitter_200',
dimensions=200,
corpus_size='27B',
vocabulary_size='1.2M',
download_url='https://www.dropbox.com/s/hfw00m77ibz24y5/glove.twitter.27B.200d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Twitter 2B Tweets',
language='en'),
Embedding(name=u'twitter_25',
dimensions=25,
corpus_size='27B',
vocabulary_size='1.2M',
download_url='https://www.dropbox.com/s/jx97sz8skdp276k/glove.twitter.27B.25d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Twitter 2B Tweets',
language='en'),
Embedding(name=u'twitter_50',
dimensions=50,
corpus_size='27B',
vocabulary_size='1.2M',
download_url='https://www.dropbox.com/s/9mutj8syz3q20e3/glove.twitter.27B.50d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Twitter 2B Tweets',
language='en'),
Embedding(name=u'wiki_100',
dimensions=100,
corpus_size='6B',
vocabulary_size='0.4M',
download_url='https://www.dropbox.com/s/g0inzrsy1ds3u63/glove.6B.100d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Wikipedia+Gigaword',
language='en'),
Embedding(name=u'wiki_200',
dimensions=200,
corpus_size='6B',
vocabulary_size='0.4M',
download_url='https://www.dropbox.com/s/pmj2ycd882qkae5/glove.6B.200d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Wikipedia+Gigaword',
language='en'),
Embedding(name=u'wiki_300',
dimensions=300,
corpus_size='6B',
vocabulary_size='0.4M',
download_url='https://www.dropbox.com/s/9jbbk99p0d0n1bw/glove.6B.300d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Wikipedia+Gigaword',
language='en'),
Embedding(name=u'wiki_50',
dimensions=50,
corpus_size='6B',
vocabulary_size='0.4M',
download_url='https://www.dropbox.com/s/o3axsz1j47043si/glove.6B.50d.txt.zip?dl=1',
format='zip',
architecture='glove',
trained_data='Wikipedia+Gigaword',
language='en'),
Embedding(name=u'crawl_42B_300',
dimensions=300,
corpus_size='42B',
vocabulary_size='1.9M',
download_url='http://nlp.stanford.edu/data/glove.42B.300d.zip',
format='zip',
architecture='glove',
trained_data='Common Crawl (42B tokens)',
language='en'),
Embedding(name=u'crawl_840B_300',
dimensions=300,
corpus_size='840B',
vocabulary_size='2.2M',
download_url='http://nlp.stanford.edu/data/glove.840B.300d.zip',
format='zip',
architecture='glove',
trained_data='Common Crawl (840B tokens)',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {embedding.name: embedding for embedding in EMBEDDING_MODELS}
def __init__(self):
self.word_vectors: Dict[Any, Any] = {}
self.model = None
@classmethod
def _tokens(cls, text: str) -> List[str]:
return [x.lower().strip() for x in text.split()]
def load_model(self, model: str, model_path: str):
try:
model_file = [f for f in os.listdir(model_path) if os.path.isfile(os.path.join(model_path, f))]
f = open(os.path.join(model_path, model_file[0]), 'r')
for line in tqdm(f):
split_line = line.split()
word = split_line[0]
self.word_vectors[word] = np.array([float(val) for val in split_line[1:]])
print("Model loaded Successfully !")
self.model = model
return self
except Exception as e:
print('Error loading Model, ', str(e))
return self
def encode(self, text: str, pooling: str = 'mean', **kwargs) -> np.array:
result = np.zeros(Embeddings.EMBEDDING_MODELS[self.model].dimensions, dtype="float32")
tokens = Embeddings._tokens(text)
vectors = np.array([self.word_vectors[token] for token in tokens if token in self.word_vectors.keys()])
if pooling == 'mean':
result = np.mean(vectors, axis=0)
elif pooling == 'max':
result = np.max(vectors, axis=0)
elif pooling == 'sum':
result = np.sum(vectors, axis=0)
elif pooling == 'tf-idf-sum':
if not kwargs.get('tfidf_dict'):
print('Must provide tfidf dict')
return result
tfidf_dict = kwargs.get('tfidf_dict')
weighted_vectors = np.array([tfidf_dict.get(token) * self.word_vectors.get(token)
for token in tokens if token in self.word_vectors.keys()
and token in tfidf_dict])
result = np.mean(weighted_vectors, axis=0)
else:
print(f'Given pooling method "{pooling}" not implemented in "{self.model}"')
return result
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'bert_base_uncased',
dimensions=768,
corpus_size='3300M',
vocabulary_size='30522(sub-word)',
download_url='https://storage.googleapis.com/tfhub-modules/'
'google/bert_uncased_L-12_H-768_A-12/1.tar.gz',
format='tar.gz',
architecture='Transformer, Layers=12, Hidden = 768, heads = 12',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en'),
Embedding(name=u'bert_base_cased',
dimensions=768,
corpus_size='3300M',
vocabulary_size='30522(sub-word)',
download_url='https://storage.googleapis.com/tfhub-modules/google/'
'bert_cased_L-12_H-768_A-12/1.tar.gz',
format='tar.gz',
architecture='Transformer Layers=12, Hidden = 768, heads = 12',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en'),
Embedding(name=u'bert_multi_cased',
dimensions=768,
corpus_size='3300M',
vocabulary_size='30522 (sub-word)',
download_url='https://storage.googleapis.com/tfhub-modules/google/'
'bert_multi_cased_L-12_H-768_A-12/1.tar.gz',
format='tar.gz',
architecture='Transformer Layers=12, Hidden = 768, heads = 12',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en'),
Embedding(name=u'bert_large_uncased',
dimensions=1024,
corpus_size='3300M',
vocabulary_size='30522 (sub-word)',
download_url='https://storage.googleapis.com/tfhub-modules/google/'
'bert_uncased_L-24_H-1024_A-16/1.tar.gz',
format='tar.gz',
architecture='Transformer Layers=24, Hidden = 1024, heads = 16',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en'),
Embedding(name=u'bert_large_uncased',
dimensions=1024,
corpus_size='3300M',
vocabulary_size='30522 (sub-word)',
download_url='https://storage.googleapis.com/tfhub-modules/google/'
'bert_uncased_L-24_H-1024_A-16/1.tar.gz',
format='tar.gz',
architecture='Transformer Layers=24, Hidden = 1024, heads = 16',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {embedding.name: embedding for embedding in EMBEDDING_MODELS}
tokenizer: FullTokenizer = None
def __init__(self):
self.sess = tf.Session()
self.bert_module = None
self.model = None
def create_tokenizer_from_hub_module(self, model_path: str):
"""Get the vocab file and casing info from the Hub module."""
tokenization_info = self.bert_module(signature="tokenization_info", as_dict=True)
vocab_file, do_lower_case = self.sess.run(
[
tokenization_info["vocab_file"],
tokenization_info["do_lower_case"],
]
)
Embeddings.tokenizer = FullTokenizer(vocab_file=vocab_file, do_lower_case=do_lower_case)
@staticmethod
def _model_single_input(text: str, max_seq_length: int) -> Tuple[List[int], List[int], List[int]]:
tokens_a = Embeddings.tokenizer.tokenize(text)
if len(tokens_a) > max_seq_length - 2:
tokens_a = tokens_a[0: (max_seq_length - 2)]
tokens = []
segment_ids = []
tokens.append("[CLS]")
segment_ids.append(0)
for token in tokens_a:
tokens.append(token)
segment_ids.append(0)
tokens.append("[SEP]")
segment_ids.append(0)
input_ids = Embeddings.tokenizer.convert_tokens_to_ids(tokens)
# The mask has 1 for real tokens and 0 for padding tokens. Only real
# tokens are attended to.
input_mask = [1] * len(input_ids)
# Zero-pad up to the sequence length.
while len(input_ids) < max_seq_length:
input_ids.append(0)
input_mask.append(0)
segment_ids.append(0)
assert len(input_ids) == max_seq_length
assert len(input_mask) == max_seq_length
assert len(segment_ids) == max_seq_length
return input_ids, input_mask, segment_ids
def load_model(self, model: str, model_path: str):
self.bert_module = hub.Module(model_path)
self.sess.run(tf.initializers.global_variables())
self.create_tokenizer_from_hub_module(model_path)
self.model = model
print("Model loaded Successfully !")
def encode(self, texts: list, pooling: Optional[str] = None, **kwargs) -> Optional[np.array]:
max_seq_length = kwargs.get('max_seq_length', 128)
input_ids, input_masks, segment_ids = [], [], []
for text in tqdm(texts, desc="Converting texts to features"):
input_id, input_mask, segment_id = self._model_single_input(text, max_seq_length)
input_ids.append(input_id)
input_masks.append(input_mask)
segment_ids.append(segment_id)
bert_inputs = dict(
input_ids=np.array(input_ids),
input_mask=np.array(input_masks),
segment_ids=np.array(segment_ids))
bert_outputs = self.bert_module(bert_inputs, signature="tokens", as_dict=True)
sequence_output = bert_outputs["sequence_output"]
token_embeddings = self.sess.run(sequence_output)
if not pooling:
return token_embeddings
else:
if pooling not in ["mean", "max", "mean_max", "min"]:
print(f"Pooling method \"{pooling}\" not implemented")
return None
pooling_func = POOL_FUNC_MAP[pooling]
pooled = pooling_func(token_embeddings, axis=1)
return pooled
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(
name=u'elmo_bi_lm',
dimensions=512,
corpus_size='1B',
vocabulary_size='5.5B',
download_url=
'https://storage.googleapis.com/tfhub-modules/google/elmo/2.tar.gz',
format='tar.gz',
architecture='Embedding layer,cnn_layer_with_maxpool,2 lstm layers',
trained_data='One Billion Word Benchmark',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
def __init__(self):
self.elmo_module = None
self.model = None
self.sess = tf.Session()
@classmethod
def tokenize(cls, text: str):
return [word.strip() for word in text.lower().strip().split()]
@classmethod
def padded_tokens(cls, tokens: List[str], max_seq_length: int):
padded_token = ""
len_tokens = len(tokens)
if len_tokens >= max_seq_length:
return tokens[:max_seq_length]
else:
padded_len = max_seq_length - len_tokens
return tokens + [padded_token] * padded_len
def load_model(self, model: str, model_path: str):
self.elmo_module = hub.Module(model_path)
self.sess.run(tf.initializers.global_variables())
self.model = model
def encode(self,
texts: list,
pooling: Optional[str] = None,
**kwargs) -> Optional[np.array]:
text_tokens = [Embeddings.tokenize(text) for text in texts]
max_seq_length = kwargs.get('max_seq_length')
if max_seq_length:
text_tokens = [
Embeddings.padded_tokens(tokens, max_seq_length)
for tokens in text_tokens
]
seq_length = [max_seq_length] * len(texts)
else:
seq_length = [len(tokens) for tokens in text_tokens]
sequence_output = self.elmo_module(inputs={
"tokens": text_tokens,
"sequence_len": seq_length
},
signature="tokens",
as_dict=True)["elmo"]
token_embeddings = self.sess.run(sequence_output)
if not pooling:
return token_embeddings
else:
if pooling not in ["mean", "max", "mean_max", "min"]:
print(f"Pooling method \"{pooling}\" not implemented")
return None
pooling_func = POOL_FUNC_MAP[pooling]
pooled = pooling_func(token_embeddings, axis=1)
return pooled
class Embeddings(object):
EMBEDDING_MODELS: List[Embedding] = [
Embedding(
name=u'xlnet_large_cased',
dimensions=1024,
corpus_size='32.89B',
vocabulary_size='32000',
download_url='https://storage.googleapis.com/xlnet/released_models/'
'cased_L-24_H-1024_A-16.zip',
format='zip',
architecture='Transformer, 24-layer, 1024-hidden, 16-heads',
trained_data=
'BooksCorpus(800M) English Wikipedia (2500M) words, Giga5 (16gb), '
'ClueWeb 2012-B(19gb), Common Crawl(78gb)',
language='en'),
Embedding(
name=u'xlnet_base_cased',
dimensions=768,
corpus_size='3.86B',
vocabulary_size='32000',
download_url='https://storage.googleapis.com/xlnet/released_models/'
'cased_L-12_H-768_A-12.zip',
format='zip',
architecture='Transformer 12-layer, 768-hidden, 12-heads.',
trained_data='BooksCorpus(800M) English Wikipedia (2500M) words',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
tokenizer: spm.SentencePieceProcessor = None
mode_config_path: str = 'xlnet_config.json'
sentence_piece_model_path: str = 'spiece.model'
def __init__(self):
self.xlnet_config = None
self.run_config = None
self.model = None
self.sess = tf.Session()
@staticmethod
def load_tokenizer(model_path: str):
"""Get the vocab file and casing info from the Hub module."""
sp_model = spm.SentencePieceProcessor()
sp_model.Load(
os.path.join(model_path, Embeddings.sentence_piece_model_path))
Embeddings.tokenizer = sp_model
@classmethod
def tokenize_fn(cls, text):
text = preprocess_text(text, lower=False)
return encode_ids(cls.tokenizer, text)
@staticmethod
def _model_single_input(
text: str,
max_seq_length: int) -> Tuple[List[int], List[int], List[int]]:
tokens_a = Embeddings.tokenize_fn(text)
if len(tokens_a) > max_seq_length - 2:
tokens_a = tokens_a[0:(max_seq_length - 2)]
tokens = []
segment_ids = []
for token in tokens_a:
tokens.append(token)
segment_ids.append(SEG_ID_A)
tokens.append(SEP_ID)
segment_ids.append(SEG_ID_A)
tokens.append(CLS_ID)
segment_ids.append(SEG_ID_CLS)
input_ids = tokens
# The mask has 0 for real tokens and 1 for padding tokens. Only real
# tokens are attended to.
input_mask = [0] * len(input_ids)
# Zero-pad up to the sequence length.
if len(input_ids) < max_seq_length:
delta_len = max_seq_length - len(input_ids)
input_ids = [0] * delta_len + input_ids
input_mask = [1] * delta_len + input_mask
segment_ids = [SEG_ID_PAD] * delta_len + segment_ids
assert len(input_ids) == max_seq_length
assert len(input_mask) == max_seq_length
assert len(segment_ids) == max_seq_length
return input_ids, input_mask, segment_ids
def load_model(self, model: str, model_path: str):
model_path = os.path.join(model_path, next(os.walk(model_path))[1][0])
self.xlnet_config = xlnet.XLNetConfig(
json_path=os.path.join(model_path, Embeddings.mode_config_path))
self.run_config = xlnet.create_run_config(is_training=True,
is_finetune=True,
FLAGS=Flags)
self.load_tokenizer(model_path)
self.model = model
print("Model loaded Successfully !")
def encode(self,
texts: list,
pooling: Optional[str] = None,
**kwargs) -> Optional[np.array]:
max_seq_length = kwargs.get('max_seq_length', 128)
input_ids, input_masks, segment_ids = [], [], []
for text in tqdm(texts, desc="Converting texts to features"):
input_id, input_mask, segment_id = self._model_single_input(
text, max_seq_length)
input_ids.append(input_id)
input_masks.append(input_mask)
segment_ids.append(segment_id)
# Construct an XLNet model
xlnet_model = xlnet.XLNetModel(xlnet_config=self.xlnet_config,
run_config=self.run_config,
input_ids=np.array(input_ids,
dtype=np.int32),
seg_ids=np.array(segment_ids,
dtype=np.int32),
input_mask=np.array(input_masks,
dtype=np.float32))
self.sess.run(tf.initializers.global_variables())
# Get a sequence output
sequence_output = xlnet_model.get_sequence_output()
token_embeddings = self.sess.run(sequence_output)
if not pooling:
return token_embeddings
else:
if pooling not in ["mean", "max", "mean_max", "min"]:
print(f"Pooling method \"{pooling}\" not implemented")
return None
pooling_func = POOL_FUNC_MAP[pooling]
pooled = pooling_func(token_embeddings, axis=1)
return pooled
def main():
opt = Options()
print('Use {}'.format(opt.pooling_type_str_dict[opt.pooling_type]))
train_sents, train_labels = pickle.load(open(opt.train_path, 'rb'))
valid_sents, valid_labels = pickle.load(open(opt.valid_path, 'rb'))
test_sents, test_labels = pickle.load(open(opt.test_path, 'rb'))
#
np.set_printoptions(precision=3)
np.set_printoptions(threshold=np.inf)
#
emb = Embedding(opt.vocab_size, 200, padding_idx=0, trainable=False)
cnn = ML_CNN.CNN_Module(n_classes=opt.classifier_output_size)
if opt.use_cuda:
emb.cuda()
cnn.cuda()
param = []
param.extend(emb.parameters())
param.extend(cnn.parameters())
# optimizer = torch.optim.Adam(param, lr=opt.lr, weight_decay=0.01)
# optimizer = torch.optim.Adam(param, lr=opt.lr, weight_decay=0.00001)
optimizer = torch.optim.Adam(param, lr=opt.lr)
criteron = torch.nn.CrossEntropyLoss()
if opt.restore:
if os.path.exists(opt.feature_net_path):
print("Load pretrained embedding")
emb.load_state_dict(torch.load(opt.feature_net_path))
else:
print("No pretrained embedding")
if os.path.exists(opt.classifier_net_path):
print("Load pretrained cnn classifier")
cnn.load_state_dict(torch.load(opt.classifier_net_path))
else:
print("No pretrained cnn classifier")
best_acc = -1
for epoch in range(opt.max_epochs):
print("Starting epoch %d" % epoch)
kf = get_minibatches_idx(len(train_sents), opt.batch_size, shuffle=True)
epoch_losses = []
cnn.train()
emb.train()
for iteridx, train_index in kf:
if len(train_index) <= 1:
continue
sents = [train_sents[t] for t in train_index]
labels = [train_labels[t] for t in train_index]
# X_batch, X_lengths, X_labels = prepare_data_for_rnn(sents, labels)
X_batch, X_labels = prepare_data_for_cnn(sents, labels)
X_batch = Variable(X_batch)
X_labels = Variable(X_labels)
if opt.use_cuda:
X_batch = X_batch.cuda()
X_labels = X_labels.cuda()
optimizer.zero_grad()
features = emb(X_batch)
output = cnn(features)
loss = criteron(output, X_labels)
local_loss = loss.data[0]
epoch_losses.append(local_loss)
loss.backward()
optimizer.step()
if iteridx % opt.print_freq == 0:
count = output.size(0)
topK_correct = test_result(output.cpu().data, X_labels.cpu().data, topK=topK)
topK_acc = [float(tmp) / count for tmp in topK_correct]
topK_str = " , ".join(["acc@{}: {}".format(k, tmp_acc) for k, tmp_acc in zip(topK, topK_acc)])
print("Epoch {} Iteration {} loss: {} , {}".format(epoch + 1, iteridx + 1, local_loss, topK_str))
ave_loss = sum(epoch_losses) / len(epoch_losses)
kf = get_minibatches_idx(len(valid_sents), opt.batch_size, shuffle=True)
count = 0
all_topK_correct = np.zeros(len(topK), dtype=int)
for _, valid_index in kf:
emb.eval()
cnn.eval()
sents = [valid_sents[t] for t in valid_index]
labels = [valid_labels[t] for t in valid_index]
X_batch, X_labels = prepare_data_for_cnn(sents, labels)
X_batch = Variable(X_batch)
X_labels = Variable(X_labels)
if opt.use_cuda:
X_batch = X_batch.cuda()
X_labels = X_labels.cuda()
features = emb(X_batch)
output = cnn(features)
topK_correct = test_result(output.cpu().data, X_labels.cpu().data, topK=topK)
topK_correct = np.array(topK_correct)
all_topK_correct += topK_correct
bsize = output.size(0)
count += bsize
all_topK_acc = all_topK_correct / float(count)
all_topK_acc = all_topK_acc.tolist()
all_topK_str = " , ".join(["val_acc@{}: {}".format(k, tmp_acc) for k, tmp_acc in zip(topK, all_topK_acc)])
print("Epoch {} Avg_loss: {}, {}".format(epoch+1, ave_loss, all_topK_str))
acc = all_topK_acc[important_K]
if acc > best_acc:
print('Dump current model due to current acc {} > past best acc {}'.format(acc, best_acc))
torch.save(cnn.state_dict(), opt.classifier_net_path)
best_acc = acc
fscore_records = [{k:FScore() for k in topK} for i in range(opt.classifier_output_size)]
kf = get_minibatches_idx(len(test_sents), opt.batch_size, shuffle=True)
emb.eval()
cnn.eval()
for _, test_index in kf:
sents = [test_sents[t] for t in test_index]
labels = [test_labels[t] for t in test_index]
X_batch, X_labels = prepare_data_for_cnn(sents, labels)
X_batch = Variable(X_batch)
X_labels = Variable(X_labels)
if opt.use_cuda:
X_batch = X_batch.cuda()
X_labels = X_labels.cuda()
features = emb(X_batch)
output = cnn(features)
update_F1(output.cpu().data, X_labels.cpu().data, opt.classifier_output_size, topK, fscore_records)
with open('F_score_dir/{}.pkl'.format(epoch+1),'w') as f:
print('dumping fscore in epoch {}'.format(epoch+1))
pickle.dump(fscore_records, f)
print('Loading best model')
cnn.load_state_dict(torch.load(opt.classifier_net_path))
print('Testing Data')
kf = get_minibatches_idx(len(test_sents), opt.batch_size, shuffle=True)
count = 0
all_topK_correct = np.zeros(len(topK), dtype=int)
fscore_records = [{k:FScore() for k in topK} for i in range(opt.classifier_output_size)]
for _, test_index in kf:
emb.eval()
cnn.eval()
sents = [test_sents[t] for t in test_index]
labels = [test_labels[t] for t in test_index]
X_batch, X_labels = prepare_data_for_cnn(sents, labels)
X_batch = Variable(X_batch)
X_labels = Variable(X_labels)
if opt.use_cuda:
X_batch = X_batch.cuda()
X_labels = X_labels.cuda()
features = emb(X_batch)
output = cnn(features)
update_F1(output.cpu().data, X_labels.cpu().data, opt.classifier_output_size, topK, fscore_records)
topK_correct = test_result(output.cpu().data, X_labels.cpu().data, topK=topK)
topK_correct = np.array(topK_correct)
all_topK_correct += topK_correct
bsize = output.size(0)
count += bsize
all_topK_acc = all_topK_correct / float(count)
all_topK_acc = all_topK_acc.tolist()
all_topK_str = " , ".join(["test_acc@{}: {}".format(k, tmp_acc) for k, tmp_acc in zip(topK, all_topK_acc)])
print("Training end {}".format(all_topK_str))
with open('F_score_dir/best.pkl','w') as f:
print('dumping fscore in')
pickle.dump(fscore_records, f)
def __init__(self, graph, path):
Embedding.__init__(self, graph)
self.nodes = np.asarray(list(graph.nodes()))
self.context_embedding = None
self.center_embedding = None
self.set_paths(path)
from typing import List, Dict
from models import Embedding
EMBEDDING_MODELS: List[Embedding] = [
Embedding(name=u'umlfit',
dimensions=300,
corpus_size='570k human-generated English sentence pairs',
vocabulary_size='230k',
download_url='http://files.fast.ai/models/wt103/',
format='.h5',
architecture='cbow',
trained_data='Stephen Merity’s Wikitext 103 dataset',
language='en')
]
EMBEDDING_MODELS: Dict[str, Embedding] = {
embedding.name: embedding
for embedding in EMBEDDING_MODELS
}
def embed_network(self, seed, save_path, algorithm_name, precomputed, training, walks):
'''
methods that embed the network with a given algorithm, the network is replaced by its embedding to save memory
'''
save_path = os.path.join(save_path, 'seed_{}'.format(seed))
if DEBUG:
save_path += '_debug'
try :
os.makedirs(save_path)
except:
pass
if precomputed:
model = Embedding(self.residual_network)
model.set_paths(save_path)
model.load_embedding()
self.residual_network = model.word_vectors
self.embedded = True
elif algorithm_name == 'node2vec':
model = Node2vec(self.residual_network, save_path)
elif algorithm_name == 'deep_walk':
model = DeepWalk(self.residual_network, save_path)
elif algorithm_name == 'efge':
model = Efge(self.residual_network, save_path)
else:
raise NotImplementedError('embedding is not implemented')
model.get_walks(**walks)
model.train(**training)
model.save_embedding()
# we replace the network by its embedding to save memory
self.residual_network = model.word_vectors
self.embedded = True
