def create_model(self, fname, max_news=99, n_proc=1, window=5, splits=100):
name = clean_name(fname)
model = word2vec.Word2Vec(window=window, workers=n_proc)
if name == 'text8':
sentences = word2vec.Text8Corpus(os.path.join('res', 'model', 'text8'))
model.train(sentences)
elif name == 'brown':
# sentences = word2vec.BrownCorpus(fpath)
sentences = brown.sents()
model.train(sentences)
elif name.startswith('news'):
target_fpath = os.path.join('res', 'model', name+'.txt')
if not os.path.exists(target_fpath):
build_news_corpus(name, max_news, n_proc, target_fpath)
sentences = word2vec.LineSentence(target_fpath)
model.build_vocab(sentences)
model.train(sentences)
# elif name.startswith('wikipedia.deps'):
# target_fpath = os.path.join('res', 'model', name+'.txt')
# if not os.path.exists(target_fpath):
# build_wikipedia_corpus(name, max_news, n_proc, target_fpath)
elif name.startswith('spanishEtiquetado'):
target_fpath = os.path.join('res', 'model', name+'.txt')
if not os.path.exists(target_fpath):
path = os.path.join('res', 'model', 'spanishEtiquetado')
max_pos_len = re.search('\d+', name)
if max_pos_len:
max_pos_len = int(max_pos_len.group(0))
build_corpus(path, name.endswith('pos'), target_fpath, max_pos_len)
sentences = word2vec.LineSentence(target_fpath)
# with open(target_fpath) as fp:
# sentences = fp.readlines()
model.build_vocab(sentences)
model.train(sentences)
else:
target_fpath = os.path.join('res', 'model', name+'.txt')
file_to_lower(target_fpath)
sentences = word2vec.LineSentence(target_fpath)
model.build_vocab(sentences)
model.train(sentences)
# n_sents = len(sentences)
# print(n_sents)
# if splits == 0:
# splits = 1
# split_size = int(n_sents/splits)
# for i in range(splits):
# print(str(i) + '\r')
# split_sentences = sentences[i*split_size:(i+1)*split_size-1]
# model.save_word2vec_format(os.path.join('res', 'model', fname), binary=fname.endswith('.bin'))
# model.save()
# model.save(os.path.join('res',name+'.model'))
model.save_word2vec_format(os.path.join('res', 'model', fname), binary=fname.endswith('.bin'))
def main():
parser = options.get_parser('Trainer')
options.add_dataset_args(parser)
options.add_preprocessing_args(parser)
options.add_model_args(parser)
options.add_optimization_args(parser)
options.add_checkpoint_args(parser)
args = parser.parse_args()
print(args)
args.cuda = not args.disable_cuda and torch.cuda.is_available()
# checkpoint
checkpoint_dir = os.path.dirname(args.checkpoint)
if not os.path.isdir(checkpoint_dir):
os.mkdir(checkpoint_dir)
# load dataset
train_raw_corpus, val_raw_corpus, test_raw_corpus = utils.load_corpus(args.processed_dir)
assert train_raw_corpus and val_raw_corpus and test_raw_corpus, 'Corpus not found, please run preprocess.py to obtain corpus!'
train_corpus = [(line.sent, line.type, line.p1, line.p2) for line in train_raw_corpus]
val_corpus = [(line.sent, line.type, line.p1, line.p2) for line in val_raw_corpus]
test_corpus = [(line.sent, line.type, line.p1, line.p2) for line in test_raw_corpus]
start_epoch = 0
caseless = args.caseless
batch_size = args.batch_size
num_epoch = args.num_epoch
# preprocessing
sents = [tup[0] for tup in train_corpus + val_corpus]
feature_map = utils.build_vocab(sents, min_count=args.min_count, caseless=caseless)
##
# target_map = {c:i for i, c in enumerate(['null', 'true'])}
target_map = ddi2013.target_map
train_features, train_targets = utils.build_corpus(train_corpus, feature_map, target_map, caseless)
val_features, val_targets = utils.build_corpus(val_corpus, feature_map, target_map, caseless)
test_features, test_targets = utils.build_corpus(test_corpus, feature_map, target_map, caseless)
class_weights = torch.Tensor(utils.get_class_weights(train_targets)) if args.class_weight else None
train_loader = utils.construct_bucket_dataloader(train_features, train_targets, feature_map['PAD'], batch_size, args.position_bound, is_train=True)
val_loader = utils.construct_bucket_dataloader(val_features, val_targets, feature_map['PAD'], batch_size, args.position_bound, is_train=False)
test_loader = utils.construct_bucket_dataloader(test_features, test_targets, feature_map['PAD'], batch_size, args.position_bound, is_train=False)
print('Preprocessing done! Vocab size: {}'.format(len(feature_map)))
# build model
vocab_size = len(feature_map)
tagset_size = len(target_map)
model = utils.build_model(args, vocab_size, tagset_size)
# loss
criterion = utils.build_loss(args, class_weights=class_weights)
# load states
if os.path.isfile(args.load_checkpoint):
print('Loading checkpoint file from {}...'.format(args.load_checkpoint))
checkpoint_file = torch.load(args.load_checkpoint)
start_epoch = checkpoint_file['epoch'] + 1
model.load_state_dict(checkpoint_file['state_dict'])
# optimizer.load_state_dict(checkpoint_file['optimizer'])
else:
print('no checkpoint file found: {}, train from scratch...'.format(args.load_checkpoint))
if not args.rand_embedding:
pretrained_word_embedding, in_doc_word_indices = utils.load_word_embedding(args.emb_file, feature_map, args.embedding_dim)
print(pretrained_word_embedding.size())
print(vocab_size)
model.load_pretrained_embedding(pretrained_word_embedding)
if args.disable_fine_tune:
model.update_part_embedding(in_doc_word_indices) # update only non-pretrained words
model.rand_init(init_embedding=args.rand_embedding)
# trainer
trainer = SeqTrainer(args, model, criterion)
if os.path.isfile(args.load_checkpoint):
dev_prec, dev_rec, dev_f1, _ = evaluate(trainer, val_loader, target_map, cuda=args.cuda)
test_prec, test_rec, test_f1, _ = evaluate(trainer, test_loader, target_map, cuda=args.cuda)
print('checkpoint dev_prec: {:.4f}, dev_rec: {:.4f}, dev_f1: {:.4f}, test_prec: {:.4f}, test_rec: {:.4f}, test_f1: {:.4f}'.format(
dev_prec, dev_rec, dev_f1, test_prec, test_rec, test_f1))
track_list = []
best_f1 = float('-inf')
patience_count = 0
start_time = time.time()
for epoch in range(start_epoch, num_epoch):
epoch_loss = train(train_loader, trainer, epoch)
# update lr
trainer.lr_step()
dev_prec, dev_rec, dev_f1, dev_loss = evaluate(trainer, val_loader, target_map, cuda=args.cuda)
if dev_f1 >= best_f1:
patience_count = 0
best_f1 = dev_f1
test_prec, test_rec, test_f1, _ = evaluate(trainer, test_loader, target_map, cuda=args.cuda)
track_list.append({'epoch': epoch, 'loss': epoch_loss,
'dev_prec': dev_prec, 'dev_rec': dev_rec, 'dev_f1': dev_f1, 'dev_loss': dev_loss,
'test_prec': test_prec, 'test_rec': test_rec, 'test_f1': test_f1})
print('epoch: {}, loss: {:.4f}, dev_f1: {:.4f}, dev_loss: {:.4f}, test_f1: {:.4f}\tsaving...'.format(epoch, epoch_loss, dev_f1, dev_loss, test_f1))
try:
utils.save_checkpoint({
'epoch': epoch,
'state_dict': model.state_dict(),
'optimizer': trainer.optimizer.state_dict(),
'f_map': feature_map,
't_map': target_map,
}, {'track_list': track_list,
'args': vars(args)
}, args.checkpoint + '_lstm')
except Exception as inst:
print(inst)
else:
patience_count += 1
track_list.append({'epoch': epoch,'loss': epoch_loss, 'dev_prec': dev_prec, 'dev_rec': dev_rec, 'dev_f1': dev_f1, 'dev_loss': dev_loss})
print('epoch: {}, loss: {:.4f}, dev_f1: {:.4f}, dev_loss: {:.4f}'.format(epoch, epoch_loss, dev_f1, dev_loss))
print('epoch: {} in {} take: {} s'.format(epoch, args.num_epoch, time.time() - start_time))
if patience_count >= args.patience:
break
def train_model_gensim_cross_validation(authors,
label_type,
pipeline,
config="",
token_level="word",
verbose=1):
'''
Takes a doc2vec model and trains it on the specified corpus.
Takes a classifier and trains it on the doc2vec model vectors.
Processes a cross-validation algorithm (K-fold) in order to evaluate the
quality of the overall model.
Returns the best trained pipeline (in terms of macro f-score).
'''
labels = get_labels(lang=authors[0]["lang"], label_type=label_type)
if not (labels):
abort_clean("Could not extract labels")
if verbose:
print("Labels extraction succeded.")
print("Available labels : " + " / ".join(labels) + "\n")
if verbose:
t0 = time()
print("Starting model Cross Validation ... (this may take some time)")
# load doc2vec conf
conf = []
if config:
conf = load_config(config)["extractors"][0] # legacy conf files
if verbose:
print("loading doc2vec config file from disk :")
print(" - vector_size = " +
str(conf["configuration"]["vector_size"]))
print(" - window = " + str(conf["configuration"]["window"]))
print(" - min_count = " +
str(conf["configuration"]["min_count"]))
# load the tokenizer
tknzr = Tokenizer(token_level)
if verbose:
print("Selected token level : " + token_level + "\n")
# Kfold parameters.
confusion = array([[0 for x in range(len(labels))]
for y in range(len(labels))])
scores = []
best_f_score = 0
best_pipeline = None
best_model = None
scores_micro = []
scores_macro = []
n_run = 1
k_fold = KFold(n_splits=10, shuffle=True)
authors = array(authors)
# start Kfold cross validation.
for train_indices, test_indices in k_fold.split(authors):
# import gensim lib (heavy load)
from gensim import models as gensim_models
# get doc2vec model
model_dm = get_doc2vec(conf, 1, verbose)
model_pv = get_doc2vec(conf, 0, verbose)
# build train corpus
train_authors = authors[train_indices]
train_corpus = build_corpus(authors=train_authors,
label_type=label_type,
verbosity=verbose)
# build test corpus
test_authors = authors[test_indices]
# learn the vocabulary (tokenisation of each tweet)
tweets = list(zip(train_corpus["labels"], train_corpus["tweets"]))
processed_tweets = []
idxs = [0 for l in labels]
for t in tweets:
prefix = t[0] + "_" + str(idxs[labels.index(t[0])])
idxs[labels.index(t[0])] += 1
processed_tweets.append(
gensim_models.doc2vec.LabeledSentence(words=tknzr.tokenize(
t[1]),
tags=[prefix]))
tweets = processed_tweets
model_dm.build_vocab(tweets)
model_pv.build_vocab(tweets)
# train doc2vec model
shuffle(tweets)
model_dm.train(sentences=tweets,
total_examples=model_dm.corpus_count,
epochs=100,
start_alpha=0.025,
end_alpha=0.0025)
model_dm.delete_temporary_training_data()
model_pv.train(sentences=tweets,
total_examples=model_pv.corpus_count,
epochs=100,
start_alpha=0.025,
end_alpha=0.0025)
model_pv.delete_temporary_training_data()
# train dataset conversion (doc->vectors)
train_vectors = zeros((sum(idxs), model_dm.vector_size * 2))
train_labels = []
for i, tag in enumerate(model_dm.docvecs.doctags):
train_vectors[i] = concatenate(
(model_dm.docvecs[tag], model_pv.docvecs[tag]), axis=0)
train_labels.append(tag.split('_')[0])
train_labels = array(train_labels)
# train classifier
pipeline.fit(train_vectors, train_labels)
# test models
truthes = []
predictions = []
for author in test_authors:
# test dataset conversion (doc->vectors)
tweet_vectors = [
concatenate((model_dm.infer_vector(tknzr.tokenize(tweet)),
model_pv.infer_vector(tknzr.tokenize(tweet))),
axis=0) for tweet in author["tweets"]
]
author_tmp = {"tweets": tweet_vectors}
var_classes, var_predictions = predict_author_proba(
author=author_tmp, model=pipeline)
var_max_idx = var_predictions.index(max(var_predictions))
label_predicted = var_classes[var_max_idx]
predictions.append(label_predicted)
truthes.append(author[label_type])
# compute metrics
confusion += confusion_matrix(truthes, predictions, labels=labels)
score_micro = f1_score(truthes,
predictions,
labels=labels,
average="micro")
score_macro = f1_score(truthes,
predictions,
labels=labels,
average="macro")
if verbose:
print("Fold " + str(n_run) + " : micro_f1=" + str(score_micro) +
" macrof1=" + str(score_macro))
# store for avg
scores_micro.append(score_micro)
scores_macro.append(score_macro)
n_run += 1
# save the pipeline if better than the current one
if score_macro > best_f_score:
best_model = [model_dm, model_pv]
best_pipeline = clone(pipeline, True)
best_f_score = score_macro
if verbose:
print("Model Cross Validation complete in %.3f seconds.\n" %
(time() - t0))
scores = {
"mean_score_micro": sum(scores_micro) / len(scores_micro),
"mean_score_macro": sum(scores_macro) / len(scores_macro),
"confusion_matrix": confusion,
"best_macro_score": best_f_score,
"labels": labels
}
return best_model, best_pipeline, scores
def optimize(options):
'''
Optimize the given classifier or/and features extractor on a specified list
of parameters
Will proceed as follows :
- loads the dataset
- builds the corpus
- load the parameters for tuning
- loads the classifiers
- loads the features extractors
- builds the execution pipelines
- trains and compares the different classifiers on the corpus
- outputs the best set of parameters found
'''
#--------------------------------------------------------------------------
# Check basic requirements
if not (options["label-type"]):
abort_clean("Label type not specified", "expected 'v' or 'g'")
if not (options["hyper-parameters"]):
abort_clean("hyper parameters not specified")
if not (options["aggregation"]):
abort_clean("Aggregation strategy not specified")
#--------------------------------------------------------------------------
# Load the tweets in one language for variety or gender classification
Authors = parse_tweets_from_dir(input_dir=options["input-dir"],
output_dir=options["processed-tweets-dir"],
label=True,
aggregation=options["aggregation"],
verbosity_level=options["verbosity"])
if not (Authors):
abort_clean("Tweets loading failed")
#--------------------------------------------------------------------------
# Load the optimize parameters
try:
params = load_config(options["hyper-parameters"])
except:
abort_clean("Configuration couldn't be loaded",
"given path: " + options["hyper-parameters"])
#--------------------------------------------------------------------------
# Load the classifier
t0 = time()
classifier = get_classifier(classifier_str=params["classifier-call"],
config=None,
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Load the features extractors
features_extr = get_features_extr(
features_str_list=params["features-extractr-call"],
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Build the execution pipeline
pipeline = get_pipeline(features_extr=features_extr,
classifier=classifier,
verbose=options["verbosity"])
# Set the classifier and the parameters to be tuned
tuning_parameters = get_opt_parameters(params)
scores = params["scores"]
if options["verbosity"]:
print("Starting the optimization process ...")
# Launch the tuning of hyper parameters
for score in scores:
print("Tuning hyper-parameters for %s" % score)
optimize_corpus = build_corpus(authors=Authors,
label_type=options["label-type"],
verbosity=options["verbosity"])
clf_optimizer = GridSearchCV(estimator=pipeline,
param_grid=tuning_parameters,
scoring='%s_macro' % score,
fit_params=None,
n_jobs=-1,
pre_dispatch='2*n_jobs',
iid=True,
cv=None,
refit=True,
verbose=options["verbosity"],
error_score='raise',
return_train_score=True)
# Start optimisation
clf_optimizer.fit(optimize_corpus["tweets"], optimize_corpus["labels"])
if options["verbosity"]:
print("Best parameters set found on development set:")
best_parameters = clf_optimizer.best_params_
for param_name in sorted(best_parameters.keys()):
print("\t%s: %r" % (param_name, best_parameters[param_name]))
print()
if options["verbosity"] > 1:
print("Grid scores on development set:")
means = clf_optimizer.cv_results_['mean_test_score']
stds = clf_optimizer.cv_results_['std_test_score']
for mean, std, params in zip(means, stds,
clf_optimizer.cv_results_['params']):
print("%0.3f (+/-%0.03f) for %r" % (mean, std * 2, params))
# saving results
save_optimisation_results(grid=clf_optimizer,
output_dir=options["output-dir"],
score=score,
verbose=options["verbosity"])
def train_model_cross_validation(authors, label_type, pipeline, verbose=1):
'''
Takes a pipeline and train it on the specified corpus.
Processes a cross-validation algorithm (K-fold) in order to evaluate the
quality of the model.
Returns the best trained pipeline (in terms of macro f-score).
'''
labels = get_labels(lang=authors[0]["lang"], label_type=label_type)
if not (labels):
abort_clean("Could not extract labels")
if verbose:
print("Labels extraction succeded.")
print("Available labels : " + " / ".join(labels) + "\n")
if verbose:
t0 = time()
print("Starting model Cross Validation ... (this may take some time)")
confusion = array([[0 for x in range(len(labels))]
for y in range(len(labels))])
scores = []
best_f_score = 0
best_pipeline = None
scores_micro = []
scores_macro = []
# start Kfold cross validation.
n_run = 1
k_fold = KFold(n_splits=10, shuffle=True)
authors = array(authors)
for train_indices, test_indices in k_fold.split(authors):
# build train corpus
train_authors = authors[train_indices]
train_corpus = build_corpus(authors=train_authors,
label_type=label_type,
verbosity=verbose)
# build test corpus
test_authors = authors[test_indices]
# train model
pipeline = train_model(corpus=train_corpus,
pipeline=pipeline,
verbose=0)
# test model
truthes = []
predictions = []
for author in test_authors:
var_classes, var_predictions = predict_author_proba(author=author,
model=pipeline)
var_max_idx = var_predictions.index(max(var_predictions))
label_predicted = var_classes[var_max_idx]
predictions.append(label_predicted)
truthes.append(author[label_type])
# compute metrics
confusion += confusion_matrix(truthes, predictions, labels=labels)
score_micro = f1_score(truthes,
predictions,
labels=labels,
average="micro")
score_macro = f1_score(truthes,
predictions,
labels=labels,
average="macro")
if verbose:
print("Fold " + str(n_run) + " : micro_f1=" + str(score_micro) +
" macrof1=" + str(score_macro))
# store for avg
scores_micro.append(score_micro)
scores_macro.append(score_macro)
n_run += 1
# save the pipeline if better than the current one
if score_macro > best_f_score:
best_pipeline = clone(pipeline, True)
best_f_score = score_macro
if verbose:
print("Model Cross Validation complete in %.3f seconds.\n" %
(time() - t0))
scores = {
"mean_score_micro": sum(scores_micro) / len(scores_micro),
"mean_score_macro": sum(scores_macro) / len(scores_macro),
"confusion_matrix": confusion,
"best_macro_score": best_f_score,
"labels": labels
}
return best_pipeline, scores
def train(options):
'''
Trains a specified classifier on a specified dataset using specified
feature extractors.
Will proceed as follows :
- loads the dataset
- builds the corpus
- loads the classifier
- loads the features extractor
- builds the execution pipeline
- trains the classifier on the corpus
- cross-validates the resulting model [optional]
- saves the resulting model [optional]
'''
#--------------------------------------------------------------------------
# Check basic requirements
if not (options["label-type"]):
abort_clean("Labels not specified", "expected 'l', 'g' or 'v'")
if not (options["features"]) and not (options["gensim"]):
abort_clean("Features not specified")
if not (options["classifier"]):
abort_clean("Classifier not specified")
if not (options["aggregation"]):
abort_clean("Aggregation strategy not specified")
#--------------------------------------------------------------------------
# Load the tweets in one language for variety or gender classification
Authors = parse_tweets_from_dir(input_dir=options["input-dir"],
output_dir=options["processed-tweets-dir"],
label=True,
aggregation=options["aggregation"],
verbosity_level=options["verbosity"])
if not (Authors):
abort_clean("Tweets loading failed")
#--------------------------------------------------------------------------
# Load the classifier
t0 = time()
classifier = get_classifier(classifier_str=options["classifier"][0],
config=None,
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Load the features extractors
features_extr = None
if not (options["gensim"]):
features_extr = get_features_extr(
features_str_list=options["features"][0],
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Build the execution pipeline
pipeline = get_pipeline(features_extr=features_extr,
classifier=classifier,
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Train the execution pipeline
# train and cross validate results
if (options["cross-validation"]):
if (options["verbosity"]):
print("Model Training with cross validation\n")
if options["gensim"]:
model, pipeline, scores = train_model_gensim_cross_validation(
authors=Authors,
label_type=options["label-type"],
pipeline=pipeline,
config=options["hyper-parameters"],
token_level=options["token-level"],
verbose=options["verbosity"])
else:
pipeline, scores = train_model_cross_validation(
authors=Authors,
label_type=options["label-type"],
pipeline=pipeline,
verbose=options["verbosity"])
if options["verbosity"]:
print_scores(scores)
if options["output-dir"]:
if options["gensim"]:
filename = str("doc2vec" + "-siz_" +
str(model[0].vector_size) + "-win_" +
str(model[0].window) + "-cnt_" +
str(model[0].min_count) +
get_classifier_name(classifier))
else:
filename = str(
get_features_extr_name(features_extr) + "+" +
get_classifier_name(classifier))
save_scores(scores=scores,
output_dir=options["output-dir"],
filename=filename,
verbose=options["verbosity"])
# train without validation --> output-dir required
else:
if options["verbosity"]:
print("Model Training without cross validation\n")
if not (options["output-dir"]):
abort_clean("No output directory specified.",
"Training without persisting is not allowed")
train_corpus = build_corpus(authors=Authors,
label_type=options["label-type"],
verbosity=options["verbosity"])
pipeline = train_model(corpus=train_corpus,
pipeline=pipeline,
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# Save the resulting model
if options["gensim"]:
filename = "doc2vec+" + get_classifier_name(classifier)
else:
filename = str(
get_features_extr_name(features_extr) + "+" +
get_classifier_name(classifier))
save_model(pipeline=pipeline,
output_dir=options["output-dir"],
filename=filename,
verbose=options["verbosity"])
#--------------------------------------------------------------------------
# End Execution
if options["verbosity"]:
print("Training task complete in " + str(round(time() - t0)) + " s")
def main():
parser = options.get_parser('Generator')
options.add_dataset_args(parser)
options.add_preprocessing_args(parser)
options.add_model_args(parser)
options.add_optimization_args(parser)
options.add_checkpoint_args(parser)
options.add_generation_args(parser)
args = parser.parse_args()
print(args)
args.cuda = not args.disable_cuda and torch.cuda.is_available()
caseless = args.caseless
batch_size = args.batch_size
if os.path.isfile(args.load_checkpoint):
print('Loading checkpoint file from {}...'.format(args.load_checkpoint))
checkpoint_file = torch.load(args.load_checkpoint)
else:
print('No checkpoint file found: {}'.format(args.load_checkpoint))
raise OSError
train_raw_corpus, val_raw_corpus, test_raw_corpus = utils.load_corpus(args.processed_dir, ddi=True)
test_corpus = [(line.sent, line.type, line.p1, line.p2) for line in test_raw_corpus]
# preprocessing
feature_map = checkpoint_file['f_map']
target_map = checkpoint_file['t_map']
test_features, test_targets = utils.build_corpus(test_corpus, feature_map, target_map, caseless)
# train/val split
test_loader = utils.construct_bucket_dataloader(test_features, test_targets, feature_map['PAD'], batch_size, args.position_bound, is_train=False)
# build model
vocab_size = len(feature_map)
tagset_size = len(target_map)
model = utils.build_model(args, vocab_size, tagset_size)
# loss
criterion = utils.build_loss(args)
# load states
model.load_state_dict(checkpoint_file['state_dict'])
# trainer
trainer = SeqTrainer(args, model, criterion)
if args.cuda:
model.cuda()
y_true, y_pred, att_weights = predict(trainer, test_loader, target_map, cuda=args.cuda)
assert len(y_pred) == len(test_corpus), 'length of prediction is inconsistent with that of data set'
# prediction
print('Predicting...')
assert len(y_pred) == len(test_corpus), 'length of prediction is inconsistent with that of data set'
# write result: sent_id|e1|e2|ddi|type
with open(args.predict_file, 'w') as f:
for tup, pred in zip(test_raw_corpus, y_pred):
ddi = 0 if pred == 'null' else 1
f.write('|'.join([tup.sent_id, tup.e1, tup.e2, str(ddi), pred]))
f.write('\n')
# error analysis
print('Analyzing...')
with open(args.error_file, 'w') as f:
f.write(' | '.join(['sent_id', 'e1', 'e2', 'target', 'pred']))
f.write('\n')
for tup, target, pred, att_weight in zip(test_raw_corpus, y_true, y_pred, att_weights):
if target != pred:
size = len(tup.sent)
f.write('{}\n'.format(' '.join(tup.sent)))
if args.model != 'InterAttentionLSTM':
att_weight = [att_weight]
for i in range(len(att_weight)):
f.write('{}\n'.format(' '.join(map(lambda x: str(round(x, 4)), att_weight[i][:size]))))
f.write('{}\n\n'.format(' | '.join([tup.sent_id, tup.e1, tup.e2, target, pred])))
# attention
print('Writing attention scores...')
with open(args.att_file, 'w') as f:
f.write(' | '.join(['target', 'sent', 'att_weight']))
f.write('\n')
for tup, target, pred, att_weight in zip(test_raw_corpus, y_true, y_pred, att_weights):
if target == pred and target != 'null':
size = len(tup.sent)
f.write('{}\n'.format(target))
f.write('{}\n'.format(' '.join(tup.sent)))
if args.model != 'InterAttentionLSTM':
att_weight = [att_weight]
for i in range(len(att_weight)):
f.write('{}\n'.format(' '.join(map(lambda x: str(round(x, 4)), att_weight[i][:size]))))
DATABASE = utils.get_file_path(cfg.DATABASE_FILE)
content = help_content.HelpContent(DATABASE)
# print( help( corpora.dictionary ) )
should_rebuild = False
# ### Dictionary ###
dict_file = utils.get_file_path(cfg.DICT_BACKUP)
# dictionary = corpora.dictionary.Dictionary.load(dict_file)
dictionary = utils.build_dictionary(content, should_rebuild, cfg.DICT_BACKUP)
# ### Corpus ###
corpus_file = utils.get_file_path(cfg.CORPUS_BACKUP)
# utils.pickle_save(corpus_file, corpus)
# corpus = corpora.MmCorpus(corpus_file)
corpus = utils.build_corpus(dictionary, content, should_rebuild,
cfg.CORPUS_BACKUP)
# corpus = pickle.load( open( corpus_file, "rb" ) )
# print( cfg.MODEL_NAME )
# ### LDA Model ###
bow = dictionary.doc2bow(utils.get_cleaned_text(query.lower()).split())
# bag_of_words = [word for word in bow]
model = utils.build_model(dictionary, corpus, should_rebuild)
q_vec = model[bow] # "query vector"
# topic_details = list()
topic_details = model.print_topic(max(q_vec, key=lambda item: item[1])[0])
print('Dictionary Size = {}'.format(len(dictionary)))
print('Corpus Size = {}'.format(len(corpus)))
print('Topic Details: ')
features_array.append(features)
inflated_feats = []
for dense in features_array:
sparse = np.zeros(len(features_all))
for i in dense:
sparse[i] = 1
inflated_feats.append(sparse)
A = np.array(inflated_feats)
return scipy.sparse.csr_matrix(A), np.array(labels), features_all
def save_model(clf, features):
joblib.dump(clf, 'model.pkl')
pickle.dump(features, open('feature.pkl', 'wb'))
if __name__ == '__main__':
corpus_file = sys.argv[1]
annot_file = sys.argv[2]
annotations = read_annotation_files(annot_file)
print "Read annotation files " + str(passed_time(start_time))
sentences = ut.build_corpus(open(corpus_file, "r").read().split("\n"))
print "Read the corpus " + str(passed_time(start_time))
features, tags, all_features = build_datas(annotations, sentences)
print "Build the features " + str(passed_time(start_time))
clf = svm.LinearSVC()
clf.fit(features, tags)
save_model(clf, all_features)
print "Saved model " + str(passed_time(start_time))
def main():
parser = options.get_parser('Generator')
options.add_dataset_args(parser)
options.add_preprocessing_args(parser)
options.add_model_args(parser)
options.add_optimization_args(parser)
options.add_checkpoint_args(parser)
options.add_generation_args(parser)
args = parser.parse_args()
model_path = args.load_checkpoint + '.model'
args_path = args.load_checkpoint + '.json'
with open(args_path, 'r') as f:
_args = json.load(f)['args']
[setattr(args, k, v) for k, v in _args.items()]
args.cuda = not args.disable_cuda and torch.cuda.is_available()
print(args)
if args.cuda:
torch.backends.cudnn.benchmark = True
# increase recursion depth
sys.setrecursionlimit(10000)
# load dataset
train_raw_corpus, val_raw_corpus, test_raw_corpus = utils.load_corpus(
args.processed_dir, ddi=False)
assert train_raw_corpus and val_raw_corpus and test_raw_corpus, 'Corpus not found, please run preprocess.py to obtain corpus!'
train_corpus = [(line.sent, line.type, line.p1, line.p2)
for line in train_raw_corpus]
val_corpus = [(line.sent, line.type, line.p1, line.p2)
for line in val_raw_corpus]
caseless = args.caseless
batch_size = args.batch_size
# build vocab
sents = [tup[0] for tup in train_corpus + val_corpus]
feature_map = utils.build_vocab(sents,
min_count=args.min_count,
caseless=caseless)
target_map = ddi2013.target_map
# get class weights
_, train_targets = utils.build_corpus(train_corpus, feature_map,
target_map, caseless)
class_weights = torch.Tensor(
utils.get_class_weights(train_targets)) if args.class_weight else None
# load dataets
_, _, test_loader = utils.load_datasets(args.processed_dir,
args.train_size,
args,
feature_map,
dataloader=True)
# build model
vocab_size = len(feature_map)
tagset_size = len(target_map)
model = RelationTreeModel(vocab_size, tagset_size, args)
# loss
criterion = utils.build_loss(args, class_weights=class_weights)
# load states
assert os.path.isfile(model_path), "Checkpoint not found!"
print('Loading checkpoint file from {}...'.format(model_path))
checkpoint_file = torch.load(model_path)
model.load_state_dict(checkpoint_file['state_dict'])
# trainer
trainer = TreeTrainer(args, model, criterion)
# predict
y_true, y_pred, treelists, f1_by_len = predict(trainer,
test_loader,
target_map,
cuda=args.cuda)
# assign words to roots
for tup, treelist in zip(test_raw_corpus, treelists):
for t in treelist:
t.idx = tup.sent[t.idx] if t.idx < len(tup.sent) else None
# prediction
print('Predicting...')
# write result: sent_id|e1|e2|ddi|type
with open(args.predict_file, 'w') as f:
for tup, pred in zip(test_raw_corpus, y_pred):
ddi = 0 if pred == 'null' else 1
f.write('|'.join([tup.sent_id, tup.e1, tup.e2, str(ddi), pred]))
f.write('\n')
def print_info(f, tup, target, pred, root):
f.write('{}\n'.format(' '.join(tup.sent)))
f.write('{}\n'.format(' | '.join(
[tup.sent_id, tup.e1, tup.e2, target, pred])))
f.write('{}\n\n'.format(root))
# error analysis
print('Analyzing...')
with open(args.error_file, 'w') as f:
f.write(' | '.join(['sent_id', 'e1', 'e2', 'target', 'pred']))
f.write('\n')
for tup, target, pred, treelist in zip(test_raw_corpus, y_true, y_pred,
treelists):
if target != pred:
print_info(f, tup, target, pred, treelist[-1])
# attention
print('Writing attention scores...')
with open(args.correct_file, 'w') as f:
f.write(' | '.join(['target', 'sent', 'att_weight']))
f.write('\n')
for tup, target, pred, treelist in zip(test_raw_corpus, y_true, y_pred,
treelists):
if target == pred and target != 'null':
print_info(f, tup, target, pred, treelist[-1])
def main():
parser = options.get_parser('Trainer')
options.add_dataset_args(parser)
options.add_preprocessing_args(parser)
options.add_model_args(parser)
options.add_optimization_args(parser)
options.add_checkpoint_args(parser)
args = parser.parse_args()
print(args)
args.cuda = not args.disable_cuda and torch.cuda.is_available()
torch.manual_seed(5)
if args.cuda:
torch.backends.cudnn.benchmark = True
# increase recursion depth
sys.setrecursionlimit(10000)
# checkpoint
checkpoint_dir = os.path.dirname(args.checkpoint)
if not os.path.isdir(checkpoint_dir):
os.mkdir(checkpoint_dir)
# load dataset
train_raw_corpus, val_raw_corpus, test_raw_corpus = utils.load_corpus(args.processed_dir, ddi=False)
assert train_raw_corpus and val_raw_corpus and test_raw_corpus, 'Corpus not found, please run preprocess.py to obtain corpus!'
train_corpus = [(line.sent, line.type, line.p1, line.p2) for line in train_raw_corpus]
val_corpus = [(line.sent, line.type, line.p1, line.p2) for line in val_raw_corpus]
start_epoch = 0
caseless = args.caseless
batch_size = args.batch_size
num_epoch = args.num_epoch
# build vocab
sents = [tup[0] for tup in train_corpus + val_corpus]
feature_map = utils.build_vocab(sents, min_count=args.min_count, caseless=caseless)
target_map = ddi2013.target_map
# get class weights
_, train_targets = utils.build_corpus(train_corpus, feature_map, target_map, caseless)
class_weights = torch.Tensor(utils.get_class_weights(train_targets)) if args.class_weight else None
train_loader, val_loader, test_loader = utils.load_datasets(args.processed_dir, args.train_size, args, feature_map, dataloader=True)
# build model
vocab_size = len(feature_map)
tagset_size = len(target_map)
model = RelationTreeModel(vocab_size, tagset_size, args)
# loss
criterion = utils.build_loss(args, class_weights=class_weights)
# load states
if os.path.isfile(args.load_checkpoint):
print('Loading checkpoint file from {}...'.format(args.load_checkpoint))
checkpoint_file = torch.load(args.load_checkpoint)
start_epoch = checkpoint_file['epoch'] + 1
model.load_state_dict(checkpoint_file['state_dict'])
# optimizer.load_state_dict(checkpoint_file['optimizer'])
else:
print('no checkpoint file found: {}, train from scratch...'.format(args.load_checkpoint))
if not args.rand_embedding:
pretrained_word_embedding, in_doc_word_indices = utils.load_word_embedding(args.emb_file, feature_map, args.embedding_dim)
print(pretrained_word_embedding.size())
print(vocab_size)
model.load_pretrained_embedding(pretrained_word_embedding)
if args.disable_fine_tune:
model.update_part_embedding(in_doc_word_indices) # update only non-pretrained words
model.rand_init(init_embedding=args.rand_embedding)
# trainer
trainer = TreeTrainer(args, model, criterion)
best_f1 = float('-inf')
if os.path.isfile(args.load_checkpoint):
dev_prec, dev_rec, dev_f1, _ = evaluate(trainer, val_loader, target_map, cuda=args.cuda)
test_prec, test_rec, test_f1, _ = evaluate(trainer, test_loader, target_map, cuda=args.cuda)
best_f1 = dev_f1
print('checkpoint dev_prec: {:.4f}, dev_rec: {:.4f}, dev_f1: {:.4f}, test_prec: {:.4f}, test_rec: {:.4f}, test_f1: {:.4f}'.format(
dev_prec, dev_rec, dev_f1, test_prec, test_rec, test_f1))
track_list = []
patience_count = 0
start_time = time.time()
q = mp.Queue()
# set start methods
try:
mp.set_start_method('spawn')
except RuntimeError:
pass
for epoch in range(start_epoch, num_epoch):
epoch_loss = train(train_loader, trainer, epoch)
# processes = []
# for rank in range(args.num_processes):
# p = mp.Process(target=train, args=(train_loader, trainer, epoch, q))
# p.start()
# processes.append(p)
# for p in processes:
# p.join()
#
# epoch_loss = q.get()
# update lr
trainer.lr_step(epoch_loss)
dev_prec, dev_rec, dev_f1, dev_loss = evaluate(trainer, val_loader, target_map, cuda=args.cuda)
test_prec, test_rec, test_f1, _ = evaluate(trainer, test_loader, target_map, cuda=args.cuda)
if dev_f1 >= best_f1:
patience_count = 0
best_f1 = dev_f1
track_list.append({'epoch': epoch, 'loss': epoch_loss,
'dev_prec': dev_prec, 'dev_rec': dev_rec, 'dev_f1': dev_f1, 'dev_loss': dev_loss,
'test_prec': test_prec, 'test_rec': test_rec, 'test_f1': test_f1})
print('epoch: {}, loss: {:.4f}, dev_f1: {:.4f}, dev_loss: {:.4f}, test_f1: {:.4f}\tsaving...'.format(epoch, epoch_loss, dev_f1, dev_loss, test_f1))
try:
utils.save_checkpoint({
'epoch': epoch,
'state_dict': model.state_dict(),
'optimizer': trainer.optimizer.state_dict(),
'f_map': feature_map,
't_map': target_map,
}, {'track_list': track_list,
'args': vars(args)
}, args.checkpoint)
except Exception as inst:
print(inst)
else:
patience_count += 1
track_list.append({'epoch': epoch,'loss': epoch_loss, 'dev_prec': dev_prec, 'dev_rec': dev_rec, 'dev_f1': dev_f1, 'dev_loss': dev_loss})
print('epoch: {}, loss: {:.4f}, dev_f1: {:.4f}, dev_loss: {:.4f}, test_f1: {:.4f}'.format(epoch, epoch_loss, dev_f1, dev_loss, test_f1))
print('epoch: {} in {} take: {} s'.format(epoch, args.num_epoch, time.time() - start_time))
if patience_count >= args.patience:
break
