def test_model(sentence: str, model_dir: str) -> None:
"""Performs NER analysis on sentence
(defaults to using base model which can be trained with train_base_model())
Args:
sentence (str): text file to perform analysis on
model_dir (str): path to model to use for analysis
"""
model = anago.Sequence.load(model_dir)
tagger = Tagger(model.model, preprocessor=model.p)
data = sentence.strip().split()
pred = tagger.predict(data)
tags = tagger._get_tags(pred)
probs = tagger._get_prob(pred)
res = tagger._build_response(data, tags, probs)
print()
print(list(zip(data, tags, probs)))
print()
if not res['entities']:
print("No entities found.")
else:
print("Entities Found: ")
for entity in res['entities']:
print(f"\t{entity['text']} = {entity['type']}")
class ElmoBiLSTM_CRFProcessor(CustomProcessor):
def __init__(self, process_proper_nouns=False):
super().__init__(process_proper_nouns)
model = load_model(os.path.join(ELMO_TAGGER_PATH, 'weights.h5'),
os.path.join(ELMO_TAGGER_PATH, 'params.json'))
it = IndexTransformer.load(
os.path.join(ELMO_TAGGER_PATH, 'preprocessor.pkl'))
self.pos_tagger = Tagger(model,
preprocessor=it,
tokenizer=wordpunct_tokenize)
def extract_phrase_by_type(self, token, type):
return self._extract_phrase(
list(
zip(self.pos_tagger.tokenizer(token),
self.pos_tagger.predict(token))), type)
def run_model(text: str, model_dir: str=BASE_MODEL_PATH) -> List:
"""Performs NER analysis on sentence
(defaults to using base model which can be trained with train_base_model())
Args:
text (str): text to perform analysis on
model (str): path to model to use for analysis
"""
model = anago.Sequence.load(model_dir)
tagger = Tagger(model.model, preprocessor=model.p)
data = text.strip().split()
pred = tagger.predict(data)
tags = tagger._get_tags(pred)
probs = tagger._get_prob(pred)
res = tagger._build_response(data, tags, probs)
return res['entities']
class BiLstmCrfNER(NERModel):
def __init__(self,
word_embedding_dim=100,
char_embedding_dim=25,
word_lstm_size=100,
char_lstm_size=25,
fc_dim=100,
dropout=0.5,
embeddings=None,
use_char=True,
use_crf=True,
batch_size=16,
learning_rate=0.001,
max_iter=10):
""" Construct a BiLSTM-CRF NER model. Model is augmented with character
level embeddings as well as word embeddings by default. Implementation
is provided by the Anago project.
Parameters
----------
word_embedding_dim : int, optional, default 100
word embedding dimensions.
char_embedding_dim : int, optional, default 25
character embedding dimensions.
word_lstm_size : int, optional, default 100
character LSTM feature extractor output dimensions.
char_lstm_size : int, optional, default 25
word tagger LSTM output dimensions.
fc_dim : int, optional, default 100
output fully-connected layer size.
dropout : float, optional, default 0.5
dropout rate.
embeddings : numpy array
word embedding matrix.
use_char : bool, optional, default True
add char feature.
use_crf : bool, optional, default True
use crf as last layer.
batch_size : int, optional, default 16
training batch size.
learning_rate : float, optional, default 0.001
learning rate for Adam optimizer
max_iter : int
number of epochs of training
Attributes
----------
preprocessor_ : reference to preprocessor
model_ : reference to generated model
trainer_ : internal reference to Anago Trainer (model)
tagger_ : internal reference to Anago Tagger (predictor)
"""
super().__init__()
self.word_embedding_dim = word_embedding_dim
self.char_embedding_dim = char_embedding_dim
self.word_lstm_size = word_lstm_size
self.char_lstm_size = char_lstm_size
self.fc_dim = fc_dim
self.dropout = dropout
self.embedding = None
self.use_char = True
self.use_crf = True
self.batch_size = batch_size
self.learning_rate = learning_rate
self.max_iter = max_iter
# populated by fit() and load(), expected by save() and transform()
self.preprocessor_ = None
self.model_ = None
self.trainer_ = None
self.tagger_ = None
def fit(self, X, y):
""" Trains the NER model. Input is list of list of tokens and tags.
Parameters
----------
X : list(list(str))
list of list of tokens
y : list(list(str))
list of list of BIO tags
Returns
-------
self
"""
log.info("Preprocessing dataset...")
self.preprocessor_ = IndexTransformer(use_char=self.use_char)
self.preprocessor_.fit(X, y)
log.info("Building model...")
self.model_ = BiLSTMCRF(
char_embedding_dim=self.char_embedding_dim,
word_embedding_dim=self.word_embedding_dim,
char_lstm_size=self.char_lstm_size,
word_lstm_size=self.word_lstm_size,
char_vocab_size=self.preprocessor_.char_vocab_size,
word_vocab_size=self.preprocessor_.word_vocab_size,
num_labels=self.preprocessor_.label_size,
dropout=self.dropout,
use_char=self.use_char,
use_crf=self.use_crf)
self.model_, loss = self.model_.build()
optimizer = Adam(lr=self.learning_rate)
self.model_.compile(loss=loss, optimizer=optimizer)
self.model_.summary()
log.info('Training the model...')
self.trainer_ = Trainer(self.model_, preprocessor=self.preprocessor_)
x_train, x_valid, y_train, y_valid = train_test_split(X, y,
test_size=0.1, random_state=42)
self.trainer_.train(x_train, y_train, x_valid=x_valid, y_valid=y_valid,
batch_size=self.batch_size, epochs=self.max_iter)
self.tagger_ = Tagger(self.model_, preprocessor=self.preprocessor_)
return self
def predict(self, X):
""" Predicts using the NER model.
Parameters
----------
X : list(list(str))
list of list of tokens.
Returns
-------
y : list(list(str))
list of list of predicted BIO tags.
"""
if self.tagger_ is None:
raise ValueError("No tagger found, either run fit() to train or load() a trained model")
log.info("Predicting from model...")
ypreds = [self.tagger_.predict(" ".join(x)) for x in X]
return ypreds
def save(self, dirpath):
""" Saves model to local disk, given a dirpath
Parameters
----------
dirpath : str
a directory where model artifacts will be saved.
Model saves a weights.h5 weights file, a params.json parameter
file, and a preprocessor.pkl preprocessor file.
Returns
-------
None
"""
if self.model_ is None or self.preprocessor_ is None:
raise ValueError("No model artifacts to save, either run fit() to train or load() a trained model")
if not os.path.exists(dirpath):
os.makedirs(dirpath)
weights_file = os.path.join(dirpath, "weights.h5")
params_file = os.path.join(dirpath, "params.json")
preprocessor_file = os.path.join(dirpath, "preprocessor.pkl")
save_model(self.model_, weights_file, params_file)
self.preprocessor_.save(preprocessor_file)
write_param_file(self.get_params(), os.path.join(dirpath, "params.yaml"))
def load(self, dirpath):
""" Loads a trained model from local disk, given the dirpath
Parameters
----------
dirpath : str
a directory where model artifacts are saved.
Returns
-------
self
"""
if not os.path.exists(dirpath):
raise ValueError("Model directory not found: {:s}".format(dirpath))
weights_file = os.path.join(dirpath, "weights.h5")
params_file = os.path.join(dirpath, "params.json")
preprocessor_file = os.path.join(dirpath, "preprocessor.pkl")
if not (os.path.exists(weights_file) or
os.path.exists(params_file) or
os.path.exists(preprocessor_file)):
raise ValueError("Model files may be corrupted, exiting")
self.model_ = load_model(weights_file, params_file)
self.preprocessor_ = IndexTransformer.load(preprocessor_file)
self.tagger_ = Tagger(self.model_, preprocessor=self.preprocessor_)
return self
from CRF.anago.data import prepare_preprocessor
DATA_ROOT = 'data/phenebank/'
train_path = os.path.join(DATA_ROOT, 'train.txt')
x_train, y_train = load_data_and_labels(train_path)
p = prepare_preprocessor(x_train, y_train)
model_config = ModelConfig()
SAVE_ROOT = './models' # trained model
weights = 'model_weights.h5'
tagger = anago.Tagger(model_config,
weights,
save_path=SAVE_ROOT,
preprocessor=p)
test_path = "data/phenebank/test.txt"
with open(test_path) as ifile:
this_sentence = []
all_sentences = []
this_output = []
all_outputs = []
for line in ifile:
line = line.strip()
if len(line) == 0:
this_output = tag.predict(tag, this_sentence)
print this_sentence, this_output
else:
this_sentence.append(line.split("\t")[0])
class ElmoNER(NERModel):
def __init__(self,
word_embedding_dim=100,
char_embedding_dim=25,
word_lstm_size=100,
char_lstm_size=25,
fc_dim=100,
dropout=0.5,
embeddings=None,
embeddings_file="glove.6B.100d.txt",
batch_size=16,
learning_rate=0.001,
max_iter=2):
""" Construct a ELMo based NER model. Model is similar to the BiLSTM-CRF
model except that the word embeddings are contextual, since they are
returned by a trained ELMo model. ELMo model requires an additional
embedding, which is Glove-100 by default. ELMo model is provided by
the (dev) Anago project.
Parameters
----------
word_embedding_dim : int, optional, default 100
word embedding dimensions.
char_embedding_dim : int, optional, default 25
character embedding dimensions.
word_lstm_size: int, optional, default 100
character LSTM feature extractor output dimensions.
char_lstm_size : int, optional, default 25
word tagger LSTM output dimensions.
fc_dim : int, optional, default 100
output fully-connected layer size.
dropout : float, optional, default 0.5
dropout rate.
embeddings : numpy array
word embedding matrix.
embeddings_file : str
path to embedding file.
batch_size : int, optional, default 16
training batch size.
learning_rate : float, optional, default 0.001
learning rate for Adam optimizer.
max_iter : int, optional, default 2
number of epochs of training.
Attributes
----------
preprocessor_ : reference to Anago preprocessor.
model_ : reference to the internal Anago ELModel
trainer_ : reference to the internal Anago Trainer object.
tagger_ : reference to the internal Anago Tagger object.
"""
super().__init__()
self.word_embedding_dim = word_embedding_dim
self.char_embedding_dim = char_embedding_dim
self.word_lstm_size = word_lstm_size
self.char_lstm_size = char_lstm_size
self.fc_dim = fc_dim
self.dropout = dropout
self.embeddings = embeddings
self.embeddings_file = embeddings_file
self.batch_size = batch_size
self.learning_rate = learning_rate
self.max_iter = max_iter
# populated by fit() and load(), expected by save() and transform()
self.preprocessor_ = None
self.model_ = None
self.trainer_ = None
self.tagger_ = None
def fit(self, X, y):
""" Trains the NER model. Input is list of AnnotatedDocuments.
Parameters
----------
X : list(list(str))
list of list of tokens
y : list(list(str))
list of list of BIO tags
Returns
-------
self
"""
if self.embeddings is None and self.embeddings_file is None:
raise ValueError(
"Either embeddings or embeddings_file should be provided, exiting."
)
log.info("Preprocessing dataset...")
self.preprocessor_ = ELMoTransformer()
self.preprocessor_.fit(X, y)
if self.embeddings is None:
self.embeddings = load_glove(self.embeddings_file)
embeddings_dim != self.embeddings[list(
self.embeddings.keys())[0]].shape[0]
self.embeddings = filter_embeddings(
self.embeddings, self.preprocessor_._word_vocab.vocab,
embeddings_dim)
log.info("Building model...")
self.model_ = ELModel(
char_embedding_dim=self.char_embedding_dim,
word_embedding_dim=self.word_embedding_dim,
char_lstm_size=self.char_lstm_size,
word_lstm_size=self.word_lstm_size,
char_vocab_size=self.preprocessor_.char_vocab_size,
word_vocab_size=self.preprocessor_.word_vocab_size,
num_labels=self.preprocessor_.label_size,
embeddings=self.embeddings,
dropout=self.dropout)
self.model_, loss = self.model_.build()
optimizer = Adam(lr=self.learning_rate)
self.model_.compile(loss=loss, optimizer=optimizer)
self.model_.summary()
log.info('Training the model...')
self.trainer_ = Trainer(self.model_, preprocessor=self.preprocessor_)
x_train, x_valid, y_train, y_valid = train_test_split(X,
y,
test_size=0.1,
random_state=42)
self.trainer_.train(x_train,
y_train,
x_valid=x_valid,
y_valid=y_valid,
batch_size=self.batch_size,
epochs=self.max_iter)
self.tagger_ = Tagger(self.model_, preprocessor=self.preprocessor_)
return self
def predict(self, X):
""" Predicts using the NER model.
Parameters
----------
X : list(list(str))
list of list of tokens.
Returns
-------
y : list(list(str))
list of list of predicted BIO tags.
"""
if self.tagger_ is None:
raise ValueError(
"No tagger found, either run fit() to train or load() a trained model"
)
log.info("Predicting from model...")
ypreds = [self.tagger_.predict(" ".join(x)) for x in X]
return ypreds
def save(self, dirpath):
""" Saves model to local disk, given a dirpath
Parameters
-----------
dirpath : str
a directory where model artifacts will be saved. Model saves a
weights.h5 weights file, a params.json parameter file, and a
preprocessor.pkl preprocessor file.
Returns
-------
None
"""
if self.model_ is None or self.preprocessor_ is None:
raise ValueError(
"No model artifacts to save, either run fit() to train or load() a trained model"
)
if not os.path.exists(dirpath):
os.makedirs(dirpath)
weights_file = os.path.join(dirpath, "weights.h5")
params_file = os.path.join(dirpath, "params.json")
preprocessor_file = os.path.join(dirpath, "preprocessor.pkl")
save_model(self.model_, weights_file, params_file)
self.preprocessor_.save(preprocessor_file)
write_param_file(self.get_params(),
os.path.join(dirpath, "params.yaml"))
def load(self, dirpath):
""" Loads a trained model from local disk, given the dirpath
Parameters
----------
dirpath : str
a directory where model artifacts are saved.
Returns
-------
self
"""
if not os.path.exists(dirpath):
raise ValueError("Model directory not found: {:s}".format(dirpath))
weights_file = os.path.join(dirpath, "weights.h5")
params_file = os.path.join(dirpath, "params.json")
preprocessor_file = os.path.join(dirpath, "preprocessor.pkl")
if not (os.path.exists(weights_file) or os.path.exists(params_file)
or os.path.exists(preprocessor_file)):
raise ValueError("Model files may be corrupted, exiting")
self.model_ = load_model(weights_file, params_file)
self.preprocessor_ = ELMoTransformer.load(preprocessor_file)
self.tagger_ = Tagger(self.model_, preprocessor=self.preprocessor_)
return self