def elmo_embeddings_flair_lib_tokenization(sentences, output_file=None):
if output_file:
f = open(output_file, 'w')
# init embedding
# For English biomedical data you can use 'pubmed'
embedding = ELMoEmbeddings(
'original') # English 4096-hidden, 2 layers, 93.6M parameters
for i, sent in enumerate(sentences):
print("Encoding the {}th input sentence!".format(i))
# create a sentence
sentence = Sentence(sent[0]) # [sent] --> sent
# embed words in sentence
embedding.embed(sentence)
for token in sentence:
if output_file:
f.write(
token.text + " " +
" ".join([str(num)
for num in token.embedding.tolist()]) + '\n')
else:
print(token.text + " " +
" ".join([str(num)
for num in token.embedding.tolist()]) + '\n')
f.write('\n')
def main(directory, embeddings, strategy):
# 1. find corpora in data directory
corpora = {"train": None, "dev": None, "test": None}
for labelset in corpora:
for file in sorted(os.listdir(directory)):
if infer_split(file) == labelset:
corpora[labelset] = pd.read_csv(
os.path.join(directory, file),
sep="\t",
names=["text", "pos", "lemma", "label"],
engine="python",
error_bad_lines=False,
quoting=csv.QUOTE_NONE).fillna("")
break
if embeddings == "elmo":
embedder = ELMoEmbeddings("original")
elif embeddings == "flair":
embedder = FlairEmbeddings("news-forward")
elif embeddings == "bert":
embedder = TransformerWordEmbeddings('bert-base-cased')
embeddings_dir = os.path.join(directory, embeddings + "_embeddings")
if not os.path.exists(embeddings_dir):
os.makedirs(embeddings_dir, exist_ok=True)
strategy = np.mean if strategy == "mean" else np.max if strategy == "max" else np.sum if strategy == "sum" else None
for labelset, corpus in corpora.items():
if corpus is None:
print(f"empty corpus: {labelset}")
continue
voc = sorted(corpus["text"].unique())
print(f"Unique tokens: {len(voc)}")
with open(os.path.join(embeddings_dir, labelset + ".w2v"), "w") as f:
for word in voc:
sentence = Sentence(word)
if len(sentence) == 0:
continue
embedder.embed(sentence)
token_embedding = strategy(
[token.embedding.cpu().numpy() for token in sentence],
axis=0)
f.write(
word + " " +
" ".join([str(num)
for num in token_embedding.tolist()]) + '\n')
def use_flair_to_extract_context_embeddings(file, dest_folder, embedding_type, embedding_size, pretrained_model=None):
if embedding_type.lower() == 'elmo':
context_embedding = ELMoEmbeddings(model='pubmed')
elif embedding_type.lower() == 'elmo_transformer':
context_embedding = ELMoTransformerEmbeddings()
elif embedding_type.lower() == 'flair':
context_embedding = PooledFlairEmbeddings()
elif embedding_type.lower() == 'bioflair':
flair_1 = PooledFlairEmbeddings('pubmed-forward')
flair_2 = PooledFlairEmbeddings('pubmed-backward')
elmo = ELMoEmbeddings(model='pubmed')
#bert = BertEmbeddings(bert_model_or_path='bert-base-multilingual-cased', layers='-1')
context_embedding = StackedEmbeddings(embeddings=[flair_1, flair_2, elmo])
elif embedding_type.lower() == 'biobert' or embedding_type.lower() == 'bert':
context_embedding = BertEmbeddings(bert_model_or_path=pretrained_model, layers='-1')
data = {}
dest_name = os.path.basename(file).split('.')
print(dest_folder)
with open(file, 'r') as f, open('{}/{}.pickle'.format(dest_folder, dest_name[0]), 'wb') as d:
sentence = ''
instance = []
j = 0
for i in f.readlines():
if i != '\n':
i = i.split()
sentence += ' '+i[0]
elif i == '\n':
sent = Sentence(sentence.strip())
context_embedding.embed(sent)
v = ''
for i in sent:
instance.append((i.text, i.embedding[:embedding_size]))
sentence = ''
if instance:
data[j] = list(zip(*(instance.copy())))
j += 1
instance.clear()
pickle.dump(data, d)
f.close()
d.close()
def elmo_embeddings(sentences, tokenized_contents, output_file=None):
if output_file:
f = open(output_file, 'w')
# init embedding
# For English biomedical data you can use 'pubmed'
embedding = ELMoEmbeddings(
'original') # English 4096-hidden, 2 layers, 93.6M parameters
for i, (sent, sent_tokens) in enumerate(zip(sentences,
tokenized_contents)):
print("Encoding the {}th input sentence for ELMO embedding!".format(i))
# Getting the tokens from our own tokenized sentence!
tokens: List[Token] = [Token(token) for token in sent_tokens]
if len(tokens) != len(sent_tokens):
raise ValueError("token length does not match sent_tokens length")
# Create new empty sentence
sentence = Sentence()
# add our own tokens
sentence.tokens = tokens
embedding.embed(sentence)
for token in sentence:
if output_file:
f.write(
token.text + " " +
" ".join([str(num)
for num in token.embedding.tolist()]) + '\n')
else:
print(token.text + " " +
" ".join([str(num)
for num in token.embedding.tolist()]) + '\n')
f.write('\n')
class Database(object):
def __init__(self, docs):
#self.documents_orig = np.loadtxt(docs, delimiter='\n', dtype = str) # only 9999 documents
self.documents_orig = []
with open(docs, 'r') as f: # getting 10k docs using this
self.documents_orig = f.readlines()
self.documents = []
self.elmo = ELMoEmbeddings()
#self.embedding = DocumentPoolEmbeddings([self.elmo])
self.debug = True
def knn(self, query, query_txt, k):
#cos_sim = torch.mm(self.documents, query) / (torch.norm(query) * torch.norm(self.documents))
cos_sim = torch.nn.functional.cosine_similarity(self.documents, query)
topk, topk_indices = torch.topk(cos_sim, k, 0, True)
topk_indices = topk_indices.numpy().astype('int')
topk = topk.numpy().astype('float')
top_combined = np.vstack((topk, topk_indices)).T
if self.debug:
print("\n")
print("Query: ", query_txt, " | index: ", topk_indices.T)
[
print(self.documents_orig[int(i[1])], " --- ", i[0])
for i in top_combined
]
return list(zip(topk, topk_indices)) #used to return tuples
def load_documents_into_embedding(self):
print("Embedding ", len(self.documents_orig), " Documents")
#self.documents_orig = self.documents_orig[0:50]
self.documents = [
self.elmo.embed(Sentence(elem)) for elem in self.documents_orig
]
self.documents = torch.stack([
torch.cat([token.embedding.unsqueeze(0) for token in elem[0]],
dim=0)[0] for elem in self.documents
])
np.save("./documents_embedded.npy", self.documents)
def run_query(self, query, k=None):
"""Run a query on the given documents based on word embeddings
Arguments:
query {str} -- Query string.
Keyword Arguments:
k {int} -- The top documents to return (default: 10)
Returns:
list[tuple[float, int]] -- Sorted list of tuples, which contain the score and the document id.
Made up example to show the formatting with k=5:
[(0.89316645860672, 1567),
(0.6174346804618835, 125),
(0.5975501537321234, 1181),
(0.5779426293373108, 3979),
(0.5110726475715637, 7155)]
"""
if k is None:
k = 10
sentence = Sentence(query)
#self.embedding.embed(sentence)
self.elmo.embed(sentence)
sentence = [token.embedding.unsqueeze(0) for token in sentence][0]
#print(sentence)
# A returned list should look like this for k=5. Btw. the numbers are made up!
#[
# (0.89316645860672, 1567),
# (0.6174346804618835, 125),
# (0.5975501537321234, 1181),
# (0.5779426293373108, 3979),
# (0.5110726475715637, 7155),
# ]
return self.knn(sentence, query, k=k)
def run_query_txt(self, text):
self.queries = np.loadtxt(text, delimiter='\n', dtype=str)
results = []
for query in self.queries:
out = self.run_query(query)
results.append(out)
#saving results
file = open("results.txt", 'w')
for elem in results:
out = ""
for res in elem:
out += str(res[0]) + "," + str(res[1]) + ";"
out = out[:-1]
out += '\n'
file.write(out)
file.close()
)
parser.add_argument(
'--lm_emb_save_path',
default='./wv/elmo.emb.pkl',
action='store',
)
args = parser.parse_args()
embedding = ELMoEmbeddings(args.model_name)
flag = args.dataset
dataset = []
with open(f'./datasets/unified/train.{flag}.json') as f:
dataset += json.load(f)
with open(f'./datasets/unified/valid.{flag}.json') as f:
dataset += json.load(f)
with open(f'./datasets/unified/test.{flag}.json') as f:
dataset += json.load(f)
bert_emb_dict = {}
for item in tqdm(dataset):
tokens = tuple(item['tokens'])
s = form_sentence(tokens)
embedding.embed(s)
emb = get_embs(s)
bert_emb_dict[tokens] = emb.astype('float16')
with open(args.lm_emb_save_path, 'wb') as f:
pickle.dump(bert_emb_dict, f)
import numpy as np
import pickle
import tqdm as tqdm
def get_elmo(word2idx):
"""Returns an ELMo embedding of the word tokens.
Args:
word2idx (dict): word to index pairs {'word': index}
Returns:
embedding_matrix (np.array): embedding matrix of shape (vocabulary_size + 1, embedding_dim=3072)
"""
embedding_matrix = np.zeros((vocabulary_size + 1, 3072))
elmo = ELMoEmbeddings()
for word, index in tqdm(word2idx.items()):
try:
word_ = Sentence(word)
elmo.embed(word_)
embedding_vector = word_[0].embedding.cpu().detach().numpy()
embedding_matrix[index] = embedding_vector
except KeyError:
embedding_matrix[index] = np.random.normal(0, np.sqrt(0.25), 3072)
return embedding_matrix
# save embeddings
pickle_out = open("elmo_3072.pickle","wb")
pickle.dump(embedding_matrix, pickle_out)
pickle_out.close()
