def first_pass_data_and_labels(notes):
'''
first_pass_data_and_labels()
Purpose: Interface with notes object to get text data and labels
@param notes. List of Note objects
@return <tuple> whose elements are:
0) list of tokenized sentences
1) list of labels for tokenized sentences
>>> import os
>>> from notes.note import Note
>>> base_dir = os.path.join(os.getenv('CLINER_DIR'), 'tests', 'data')
>>> txt = os.path.join(base_dir, 'single.txt')
>>> con = os.path.join(base_dir, 'single.con')
>>> note_tmp = Note('i2b2')
>>> note_tmp.read(txt, con)
>>> notes = [note_tmp]
>>> first_pass_data_and_labels(notes)
([['The', 'score', 'stood', 'four', 'to', 'two', ',', 'with', 'but', 'one', 'inning', 'more', 'to', 'play', ',']], [['B', 'I', 'I', 'I', 'I', 'I', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']])
'''
# Get the data and annotations from the Note objects
l_tokenized_sentences = [note.getTokenizedSentences() for note in notes]
l_iob_labels = [note.getIOBLabels() for note in notes]
tokenized_sentences = flatten(l_tokenized_sentences)
iob_labels = flatten(l_iob_labels)
return tokenized_sentences, iob_labels
def __first_train(self, tokenized_sentences, Y, do_grid=False):
"""
Model::__first_train()
Purpose: Train the first pass classifiers (for IOB chunking)
@param tokenized_sentences. <list> of tokenized sentences
@param Y. <list-of-lists> of IOB labels for words
@param do_grid. <boolean> whether to perform a grid search
@return None
"""
if globals_cliner.verbosity > 0:
print('first pass')
if globals_cliner.verbosity > 0:
print('\textracting features (pass one)')
# Seperate into prose v nonprose
nested_prose_data, nested_prose_Y = list(
zip(*[
line_iob_tup for line_iob_tup in zip(tokenized_sentences, Y)
if is_prose_sentence(line_iob_tup[0])
]))
nested_nonprose_data, nested_nonprose_Y = list(
zip(*[
line_iob_tup for line_iob_tup in zip(tokenized_sentences, Y)
if not is_prose_sentence(line_iob_tup[0])
]))
# extract features
nested_prose_feats = feat_obj.IOB_prose_features(nested_prose_data)
nested_nonprose_feats = feat_obj.IOB_nonprose_features(
nested_nonprose_data)
# Flatten lists (because classifier will expect flat)
prose_Y = flatten(nested_prose_Y)
nonprose_Y = flatten(nested_nonprose_Y)
# rename because code uses it
pchunks = prose_Y
nchunks = nonprose_Y
prose = nested_prose_feats
nonprose = nested_nonprose_feats
# Train classifiers for prose and nonprose
pvec, pclf = self.__generic_first_train('prose', prose, pchunks,
do_grid)
nvec, nclf = self.__generic_first_train('nonprose', nonprose, nchunks,
do_grid)
# Save vectorizers
self._first_prose_vec = pvec
self._first_nonprose_vec = nvec
# Save classifiers
self._first_prose_clf = pclf
self._first_nonprose_clf = nclf
def __generic_first_predict(self,
p_or_n,
text_features,
dvect,
clf,
do_grid=False):
'''
Model::__generic_first_predict()
Purpose: Train that works for both prose and nonprose
@param p_or_n. <string> either "prose" or "nonprose"
@param text_features. <list-of-lists> of feature dictionaries
@param dvect. <DictVectorizer>
@param clf. scikit-learn classifier
@param do_grid. <boolean> indicating whether to perform grid search
'''
# If nothing to predict, skip actual prediction
if len(text_features) == 0:
print('\tnothing to predict (pass one) ' + p_or_n)
return []
# Save list structure to reconstruct after vectorization
offsets = save_list_structure(text_features)
if globals_cliner.verbosity > 0:
print('\tvectorizing features (pass one) ' + p_or_n)
# Vectorize features
X_feats = dvect.transform(flatten(text_features))
if globals_cliner.verbosity > 0:
print('\tpredicting labels (pass one) ' + p_or_n)
# CRF requires reconstruct lists
if self._crf_enabled:
X_feats = reconstruct_list(list(X_feats), offsets)
lib = crf
else:
lib = sci
# for X in X_feats:
# for x in X:
# print x
# print
# print '\n'
# Predict IOB labels
out = lib.predict(clf, X_feats)
# Format labels from output
predictions = reconstruct_list(out, offsets)
return predictions
def __second_train(self,
chunked_data,
inds_list,
con_labels,
do_grid=False):
"""
Model::__second_train()
Purpose: Train the first pass classifiers (for IOB chunking)
@param data <list> of tokenized sentences after collapsing chunks
@param inds_list <list-of-lists> of indices
- assertion: len(data) == len(inds_list)
- one line of 'inds_list' contains a list of indices
into the corresponding line for 'data'
@param con_labels <list> of concept label strings
- assertion: there are sum(len(inds_list)) labels
AKA each index from inds_list maps to a label
@param do_grid <boolean> indicating whether to perform a grid search
@return None
"""
if globals_cliner.verbosity > 0:
print('second pass')
# Extract features
if globals_cliner.verbosity > 0:
print('\textracting features (pass two)')
text_features = [
feat_obj.concept_features(s, inds)
for s, inds in zip(chunked_data, inds_list)
]
flattened_text_features = flatten(text_features)
if globals_cliner.verbosity > 0:
print('\tvectorizing features (pass two)')
# Vectorize labels
numeric_labels = [concept_labels[y] for y in con_labels]
# Vectorize features
self._second_vec = DictVectorizer()
vectorized_features = self._second_vec.fit_transform(
flattened_text_features)
if globals_cliner.verbosity > 0:
print('\ttraining classifier (pass two)')
# Train the model
self._second_clf = sci.train(vectorized_features, numeric_labels,
do_grid)
def second_pass_data_and_labels(notes):
'''
second_pass_data_and_labels()
Purpose: Interface with notes object to get text data and labels
@param notes. List of Note objects
@return <tuple> whose elements are:
0) list of chunked sentences
0) list of list-of-indices designating chunks
1) list of labels for chunks
>>> import os
>>> from notes.note import Note
>>> base_dir = os.path.join(os.getenv('CLINER_DIR'), 'tests', 'data')
>>> txt = os.path.join(base_dir, 'single.txt')
>>> con = os.path.join(base_dir, 'single.con')
>>> note_tmp = Note('i2b2')
>>> note_tmp.read(txt, con)
>>> notes = [note_tmp]
>>> second_pass_data_and_labels(notes)
([['The score stood four to two', ',', 'with', 'but', 'one', 'inning', 'more', 'to', 'play', ',']], [[0]], ['problem'])
'''
# Get the data and annotations from the Note objects
l_chunked_sentences = [note.getChunkedText() for note in notes]
l_inds_list = [note.getConceptIndices() for note in notes]
l_con_labels = [note.getConceptLabels() for note in notes]
chunked_sentences = flatten(l_chunked_sentences)
inds_list = flatten(l_inds_list)
con_labels = flatten(l_con_labels)
# print 'labels: ', len(con_labels)
# print 'inds: ', sum(map(len,inds_list))
# exit()
return chunked_sentences, inds_list, con_labels
def train(self, train_notes, val=[], test=[]):
"""
ClinerModel::train()
Purpose: Train a Machine Learning model on annotated data
@param notes. A list of Note objects (containing text and annotations)
@return None
"""
# Extract formatted data
train_sents = flatten([n.getTokenizedSentences() for n in train_notes])
train_labels = flatten([n.getTokenLabels() for n in train_notes])
if test:
test_sents = flatten([n.getTokenizedSentences() for n in test])
test_labels = flatten([n.getTokenLabels() for n in test])
else:
test_sents = []
test_labels = []
if val:
print("VAL")
val_sents = flatten([n.getTokenizedSentences() for n in val])
val_labels = flatten([n.getTokenLabels() for n in val])
self.train_fit(train_sents,
train_labels,
val_sents=val_sents,
val_labels=val_labels,
test_sents=test_sents,
test_labels=test_labels)
else:
print("NO DEV")
self.train_fit(train_sents,
train_labels,
dev_split=0.1,
test_sents=test_sents,
test_labels=test_labels)
self._train_files = [n.getName() for n in train_notes + val]
def generic_predict(p_or_n, tokenized_sents, vocab, clf, use_lstm,
hyperparams):
'''
generic_predict()
Train a model that works for both prose and nonprose
@param p_or_n. A string that indicates "prose", "nonprose", or "all"
@param tokenized_sents. A list of sentences, where each sentence is tokenized
into words
@param vocab. A dictionary mapping word tokens to numeric indices.
@param clf. An encoding of the trained keras model.
@param use_lstm. Bool indicating whether clf is a CRF or LSTM.
'''
# use_lstm=self._use_lstm
if use_lstm:
#parameters=hd.load_parameters_from_file("LSTM_parameters.txt")
parameters['use_pretrained_model'] = True
#model_folder="./models/NN_models"
predictions = []
sys.stdout.write('\n use_lstm \n')
dataset = Exp.Dataset()
fictional_labels = copy.deepcopy(tokenized_sents)
for idx, x in enumerate(fictional_labels):
for val_id, value in enumerate(x):
fictional_labels[idx][val_id] = 'O'
Datasets_tokens = {}
Datasets_labels = {}
Datasets_tokens['deploy'] = tokenized_sents
Datasets_labels['deploy'] = fictional_labels
token_to_vector = dataset.load_dataset(
Datasets_tokens,
Datasets_labels,
"",
parameters,
token_to_vector=tokens_to_vec,
pretrained_dataset=pretrained_dataset)
print(dataset.token_indices.keys())
parameters['Feature_vector_length'] = dataset.feature_vector_size
parameters['use_features_before_final_lstm'] = False
dataset.update_dataset("", ['deploy'], Datasets_tokens,
Datasets_labels)
del Datasets_tokens
del Datasets_labels
#model=current_model
model = entity_model.EntityLSTM(dataset, parameters)
os.mkdir(parameters['conll_like_result_folder'])
test_temp = os.path.join(parameters['conll_like_result_folder'],
'test/')
train_temp = os.path.join(parameters['conll_like_result_folder'],
'train/')
valid_temp = os.path.join(parameters['conll_like_result_folder'],
'valid/')
os.mkdir(test_temp)
os.mkdir(train_temp)
os.mkdir(valid_temp)
sess = tf.Session()
with sess.as_default():
#model=entity_model.EntityLSTM(dataset,parameters)
transition_params_trained = model.restore_from_pretrained_model(
parameters,
dataset,
sess,
token_to_vector=token_to_vector,
pretrained_dataset=pretrained_dataset)
del token_to_vector
predictions = training_predict_LSTM.prediction_step(
sess, dataset, "deploy", model, 0,
parameters['conll_like_result_folder'],
transition_params_trained)
sess.close()
tf.reset_default_graph()
shutil.rmtree(parameters['conll_like_result_folder'])
return predictions, model
# If nothing to predict, skip actual prediction
if len(tokenized_sents) == 0:
sys.stdout.write('\tnothing to predict %s\n' % p_or_n)
return []
sys.stdout.write('\tvectorizing words %s\n' % p_or_n)
if use_lstm:
print('todo: incorporate lstm')
# vectorize tokenized sentences
#X = []
#for sent in tokenized_sents:
# id_seq = []
# for w in sent:
# if w in vocab:
# id_seq.append(vocab[w])
# else:
# id_seq.append(vocab['oov'])
# X.append(id_seq)
else:
from cliner.feature_extraction.features import extract_features
# vectorize validation X
text_features = extract_features(tokenized_sents)
flat_X_feats = vocab.transform(flatten(text_features))
X = reconstruct_list(flat_X_feats, save_list_structure(text_features))
sys.stdout.write('\tpredicting labels %s\n' % p_or_n)
# Predict labels
if use_lstm:
print("TEST_PREDICT")
exit()
else:
from cliner.machine_learning import crf
predictions = crf.predict(clf, X)
# Format labels from output
return predictions
def generic_train(p_or_n,
train_sents,
train_labels,
use_lstm,
val_sents=None,
val_labels=None,
test_sents=None,
test_labels=None,
dev_split=None):
'''
generic_train()
Train a model that works for both prose and nonprose
@param p_or_n. A string that indicates "prose", "nonprose", or "all"
@param train_sents. A list of sentences; each sentence is tokenized into words
@param train_labels. Parallel to `train_sents`, 7-way labels for concept spans
@param use_lstm Bool indicating whether to train CRF or LSTM.
@param val_sents. Validation data. Same format as train_sents
@param val_labels. Validation data. Same format as train_labels
@param dev_split. A real number from 0 to 1
'''
# Must have data to train on:
if len(train_sents) == 0:
raise Exception('Training must have %s training examples' % p_or_n)
# if you should split the data into train/dev yourself
if (not val_sents) and (dev_split > 0.0) and (len(train_sents) > 10):
p = int(dev_split * 100)
sys.stdout.write('\tCreating %d/%d train/dev split\n' % (100 - p, p))
perm = list(range(len(train_sents)))
random.shuffle(perm)
train_sents = [train_sents[i] for i in perm]
train_labels = [train_labels[i] for i in perm]
ind = int(dev_split * len(train_sents))
val_sents = train_sents[:ind]
train_sents = train_sents[ind:]
val_labels = train_labels[:ind]
train_labels = train_labels[ind:]
else:
sys.stdout.write('\tUsing existing validation data\n')
sys.stdout.write('\tvectorizing words %s\n' % p_or_n)
if use_lstm:
print("TESTING NEW DATSET OBJECT")
dataset = Exp.Dataset()
parameters = hd.load_parameters_from_file("LSTM_parameters.txt")
parameters['use_pretrained_model'] = False
Datasets_tokens = {}
Datasets_labels = {}
Datasets_tokens['train'] = train_sents
Datasets_labels['train'] = train_labels
if val_sents != None:
Datasets_tokens['valid'] = val_sents
Datasets_labels['valid'] = val_labels
if test_sents != None:
Datasets_tokens['test'] = test_sents
Datasets_labels['test'] = test_labels
dataset.load_dataset(Datasets_tokens, Datasets_labels, "", parameters)
pickle.dump(
dataset,
open(os.path.join(parameters['model_folder'], 'dataset.pickle'),
'wb'))
print(Datasets_tokens['valid'][0])
print(Datasets_tokens['test'][0])
parameters['Feature_vector_length'] = dataset.feature_vector_size
parameters['use_features_before_final_lstm'] = False
parameters['learning_rate'] = 0.005
sess = tf.Session()
number_of_sent = list(range(len(dataset.token_indices['train'])))
with sess.as_default():
model = entity_model.EntityLSTM(dataset, parameters)
sess.run(tf.global_variables_initializer())
model.load_pretrained_token_embeddings(sess, dataset, parameters)
epoch_number = -1
transition_params_trained = np.random.rand(5 + 2, 5 + 2)
values = {}
values["best"] = 0
f1_dictionary = {}
f1_dictionary['best'] = 0
model_saver = tf.train.Saver(max_to_keep=100)
print("START TRAINING")
eval_dir = os.path.join(
tmo_dir, 'cliner_eval_%d' % random.randint(0, 256) + os.sep)
parameters['conll_like_result_folder'] = eval_dir
test_temp = os.path.join(parameters['conll_like_result_folder'],
'test/')
train_temp = os.path.join(parameters['conll_like_result_folder'],
'train/')
valid_temp = os.path.join(parameters['conll_like_result_folder'],
'valid/')
os.mkdir(parameters['conll_like_result_folder'])
os.mkdir(test_temp)
os.mkdir(train_temp)
os.mkdir(valid_temp)
while epoch_number < 90:
average_loss_per_phrase = 0
accuracy_per_phase = 0
step = 0
epoch_number += 1
if epoch_number != 0:
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
loss, accuracy, transition_params_trained = training_predict_LSTM.train_step(
sess, dataset, sequence_number, model)
average_loss_per_phrase += loss
accuracy_per_phase += accuracy
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done\n'.format(
step / len(sequence_numbers) * 100))
model_saver.save(
sess,
os.path.join(parameters['model_folder'],
'model_{0:05d}.ckpt'.format(epoch_number)))
total_loss = average_loss_per_phrase
total_accuracy = accuracy_per_phase
average_loss_per_phrase = average_loss_per_phrase / len(
number_of_sent)
accuracy_per_phase = accuracy_per_phase / len(number_of_sent)
if epoch_number > 0:
""
f1, predictions = training_predict_LSTM.prediction_step(
sess, dataset, "test", model, epoch_number,
parameters['conll_like_result_folder'],
transition_params_trained)
f1_train, _ = training_predict_LSTM.prediction_step(
sess, dataset, "train", model, epoch_number,
parameters['conll_like_result_folder'],
transition_params_trained)
f1_valid, _ = training_predict_LSTM.prediction_step(
sess, dataset, "valid", model, epoch_number,
parameters['conll_like_result_folder'],
transition_params_trained)
correctly_predicted_tokens = training_predict_LSTM.compute_train_accuracy(
parameters['conll_like_result_folder'] + "valid" + os.sep +
"epoche_" + str(epoch_number) + ".txt")
if f1_dictionary['best'] < float(f1_valid):
f1_dictionary['epoche'] = epoch_number
f1_dictionary['best'] = float(f1_valid)
if values["best"] < correctly_predicted_tokens:
values["epoche"] = epoch_number
values["best"] = correctly_predicted_tokens
#print ("Number of correctly predicted tokens -test "+str(correctly_predicted_tokens))
print("NEW EPOCHE" + " " + str(epoch_number))
print("Current F1 on train" + " " + str(f1_train))
print("Current F1 on valid" + " " + str(f1_valid))
print("Current F1 on test" + " " + str(f1))
print("Current F1 best (validation): ")
print(f1_dictionary)
shutil.rmtree(parameters['conll_like_result_folder'])
return parameters, dataset, f1_dictionary['best']
else:
########
# CRF
########
from cliner.feature_extraction.features import extract_features
# vectorize tokenized sentences
text_features = extract_features(train_sents)
# type(text_features): <type 'list'>
# Collect list of feature types
enabled_features = set()
for sf in text_features:
for wf in sf:
for (feature_type, instance), value in wf.items():
if feature_type.startswith('prev'):
feature_type = 'PREV*'
if feature_type.startswith('next'):
feature_type = 'NEXT*'
enabled_features.add(feature_type)
enabled_features = sorted(enabled_features)
# Vectorize features
vocab = DictVectorizer()
flat_X_feats = vocab.fit_transform(flatten(text_features))
X_feats = reconstruct_list(flat_X_feats,
save_list_structure(text_features))
# vectorize IOB labels
Y_labels = [[tag2id[y] for y in y_seq] for y_seq in train_labels]
assert len(X_feats) == len(Y_labels)
for i in range(len(X_feats)):
assert X_feats[i].shape[0] == len(Y_labels[i])
# if there is specified validation data, then vectorize it
if val_sents:
# vectorize validation X
val_text_features = extract_features(val_sents)
flat_val_X_feats = vocab.transform(flatten(val_text_features))
val_X = reconstruct_list(flat_val_X_feats,
save_list_structure(val_text_features))
# vectorize validation Y
val_Y = [[tag2id[y] for y in y_seq] for y_seq in val_labels]
# if there is specified test data, then vectorize it
if test_sents:
# vectorize test X
test_text_features = extract_features(test_sents)
flat_test_X_feats = vocab.transform(flatten(test_text_features))
test_X = reconstruct_list(flat_test_X_feats,
save_list_structure(test_text_features))
# vectorize test Y
test_Y = [[tag2id[y] for y in y_seq] for y_seq in test_labels]
else:
test_X = None
test_Y = None
sys.stdout.write('\ttraining classifiers %s\n' % p_or_n)
if use_lstm:
# train using lstm
clf, dev_score = keras_ml.train(X_seq_ids,
Y_labels,
tag2id,
len(vocab),
val_X_ids=val_X,
val_Y_ids=val_Y,
test_X_ids=test_X,
test_Y_ids=test_Y)
else:
# train using crf
from machine_learning import crf
clf, dev_score = crf.train(X_feats,
Y_labels,
val_X=val_X,
val_Y=val_Y,
test_X=test_X,
test_Y=test_Y)
return vocab, clf, dev_score, enabled_features
def __generic_first_train(self,
p_or_n,
text_features,
iob_labels,
do_grid=False):
'''
Model::__generic_first_train()
Purpose: Train that works for both prose and nonprose
@param p_or_n. <string> either "prose" or "nonprose"
@param text_features. <list-of-lists> of feature dictionaries
@param iob_labels. <list> of "I", "O", and "B" labels
@param do_grid. <boolean> indicating whether to perform grid search
'''
# Must have data to train on
if len(text_features) == 0:
raise Exception('Training must have %s training examples' % p_or_n)
# Vectorize IOB labels
Y_labels = [IOB_labels[y] for y in iob_labels]
# Save list structure to reconstruct after vectorization
offsets = save_list_structure(text_features)
if globals_cliner.verbosity > 0:
print('\tvectorizing features (pass one) ' + p_or_n)
#X = reconstruct_list(flatten(text_features), offsets)
#Y = reconstruct_list( Y_labels , offsets)
# for a,b in zip(X,Y):
# for x,y in zip(a,b):
# print y
# #print filter(lambda t:t[0]=='word', x.keys())
# print x.keys()
# print
# print '\n\n\n'
# Vectorize features
dvect = DictVectorizer()
X_feats = dvect.fit_transform(flatten(text_features))
# CRF needs reconstructed lists
if self._crf_enabled:
X_feats = reconstruct_list(list(X_feats), offsets)
Y_labels = reconstruct_list(Y_labels, offsets)
lib = crf
else:
lib = sci
if globals_cliner.verbosity > 0:
print('\ttraining classifiers (pass one) ' + p_or_n)
# for i,X in enumerate(X_feats):
# for j,x in enumerate(X):
# print x, '\t', Y_labels[i][j]
# print
# exit()
# Train classifier
clf = lib.train(X_feats, Y_labels, do_grid)
return dvect, clf
def __second_predict(self, chunked_sentences, inds_list):
# If first pass predicted no concepts, then skip
# NOTE: Special case because SVM cannot have empty input
if sum([len(inds) for inds in inds_list]) == 0:
print("first pass predicted no concepts, skipping second pass")
return []
# Create object that is a wrapper for the features
if globals_cliner.verbosity > 0:
print('\textracting features (pass two)')
print('\textracting features (pass two)')
# Extract features
text_features = [
feat_obj.concept_features(s, inds)
for s, inds in zip(chunked_sentences, inds_list)
]
flattened_text_features = flatten(text_features)
print('\tvectorizing features (pass two)')
if globals_cliner.verbosity > 0:
print('\tvectorizing features (pass two)')
# Vectorize features
vectorized_features = self._second_vec.transform(
flattened_text_features)
if globals_cliner.verbosity > 0:
print('\tpredicting labels (pass two)')
# Predict concept labels
out = sci.predict(self._second_clf, vectorized_features)
# Line-by-line processing
o = list(out)
classifications = []
for lineno, inds in enumerate(inds_list):
# Skip empty line
if not inds:
continue
# For each concept
for ind in inds:
# Get next concept
concept = reverse_concept_labels[o.pop(0)]
# Get start position (ex. 7th word of line)
start = 0
for i in range(ind):
start += len(chunked_sentences[lineno][i].split())
# Length of chunk
length = len(chunked_sentences[lineno][ind].split())
# Classification token
classifications.append(
(concept, lineno + 1, start, start + length - 1))
# Return classifications
return classifications
