def run_prediction((train_data, train_tags, test_data, test_tags, idx)):
logger.info('training sequential model...')
all_values = flatten(train_data)
# binarize
binarizers = fit_binarizers(all_values)
test_data = call_for_each_element(test_data, binarize, [binarizers], data_type='sequential')
train_data = call_for_each_element(train_data, binarize, [binarizers], data_type='sequential')
x_train = np.array([np.array(xi) for xi in train_data])
y_train = np.array([np.array(xi) for xi in train_tags])
x_test = np.array([np.array(xi) for xi in test_data])
y_test = np.array([np.array(xi) for xi in test_tags])
sequence_learner = PystructSequenceLearner()
sequence_learner.fit(x_train, y_train)
structured_hyp = sequence_learner.predict(x_test)
logger.info('scoring sequential model...')
flattened_hyp = flatten(structured_hyp)
flattened_ref = flatten(y_test)
test_tags = flattened_ref
logger.info('Structured prediction f1: ')
cur_res = f1_score(flattened_ref, flattened_hyp, average=None)
logger.info('[ {}, {} ], {}'.format(cur_res[0], cur_res[1], f1_score(flattened_ref, flattened_hyp, pos_label=None)))
return (cur_res, idx)
def run_prediction((train_data, train_tags, test_data, test_tags, idx)):
logger.info('training sequential model...')
all_values = flatten(train_data)
# binarize
binarizers = fit_binarizers(all_values)
test_data = call_for_each_element(test_data,
binarize, [binarizers],
data_type='sequential')
train_data = call_for_each_element(train_data,
binarize, [binarizers],
data_type='sequential')
x_train = np.array([np.array(xi) for xi in train_data])
y_train = np.array([np.array(xi) for xi in train_tags])
x_test = np.array([np.array(xi) for xi in test_data])
y_test = np.array([np.array(xi) for xi in test_tags])
sequence_learner = PystructSequenceLearner()
sequence_learner.fit(x_train, y_train)
structured_hyp = sequence_learner.predict(x_test)
logger.info('scoring sequential model...')
flattened_hyp = flatten(structured_hyp)
flattened_ref = flatten(y_test)
test_tags = flattened_ref
logger.info('Structured prediction f1: ')
cur_res = f1_score(flattened_ref, flattened_hyp, average=None)
logger.info('[ {}, {} ], {}'.format(
cur_res[0], cur_res[1],
f1_score(flattened_ref, flattened_hyp, pos_label=None)))
return (cur_res, idx)
def test_binarizers(self):
contexts = [[3.0, 3.0, 1.0, u'petit', [u'le'], [u'garcon'], 0, 0, 0, 0, 0, 0, u'JJ', [u'Adj']], [3.0, 3.0, 1.0, u'petite', [u'un'], [u'chien'], 0, 0, 0, 0, 2, 0, u'JJ', [u'Adv']], [3.0, 3.0, 1.0, u'petits', [u'un'], [u'chat'], 0, 0, 0, 0, 2, 0, u'JJN', [u'Adj', u'Adv']]]
binarizers = preprocessing_utils.fit_binarizers(contexts)
binarized_features = [preprocessing_utils.binarize(val, binarizers) for val in contexts]
self.assertTrue(np.allclose(binarized_features[0], np.array([3., 3., 1., 1., 0., 0., 1., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 1., 0.])))
self.assertTrue(np.allclose(binarized_features[1], np.array([3., 3., 1., 0., 1., 0., 0., 1., 0., 1., 0., 0., 0., 0., 0., 2., 0., 0., 0., 1.])))
self.assertTrue(np.allclose(binarized_features[2], np.array([3., 3., 1., 0., 0., 1., 0., 1., 1., 0., 0., 0., 0., 0., 0., 2., 0., 1., 1., 1.])))
def main(config):
workers = config['workers']
tmp_dir = config['tmp_dir'] if 'tmp_dir' in config else None
tmp_dir = mk_tmp_dir(tmp_dir)
time_stamp = str(time.time())
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
train_data_generators = build_objects(config['datasets']['training'])
train_data = {}
for gen in train_data_generators:
data = gen.generate()
for key in data:
if key not in train_data:
train_data[key] = []
train_data[key].extend(data[key])
# test
test_data_generator = build_object(config['datasets']['test'][0])
test_data = test_data_generator.generate()
logger.info("Train data keys: {}".format(train_data.keys()))
logger.info("Train data sequences: {}".format(len(train_data['target'])))
logger.info("Sample sequence: {}".format([w.encode('utf-8') for w in train_data['target'][0]]))
# logger.info("Sample sequence: {}".format(train_data['similarity'][0]))
# sys.exit()
# additional representations
if 'representations' in config:
representation_generators = build_objects(config['representations'])
else:
representation_generators = []
for r in representation_generators:
train_data = r.generate(train_data)
test_data = r.generate(test_data)
# borders = config['borders'] if 'borders' in config else False
# if 'multiply_data_train' not in config:
# pass
# elif config['multiply_data_train'] == 'ngrams':
# train_data = multiply_data_ngrams(train_data, borders=borders)
# elif config['multiply_data_train'] == '1ton':
# train_data = multiply_data(train_data, borders=borders)
# elif config['multiply_data_train'] == 'duplicate':
# train_data = multiply_data_base(train_data)
# elif config['multiply_data_train'] == 'all':
# train_data = multiply_data_all(train_data, borders=borders)
# else:
# print("Unknown 'multiply data train' value: {}".format(config['multiply_data_train']))
# logger.info("Extended train representations: {}".format(len(train_data['target'])))
# logger.info("Simple test representations: {}".format(len(test_data['target'])))
# if 'multiply_data_test' not in config:
# pass
# elif config['multiply_data_test'] == 'ngrams':
# test_data = multiply_data_ngrams(test_data, borders=borders)
# elif config['multiply_data_test'] == '1ton':
# test_data = multiply_data(test_data, borders=borders)
# else:
# print("Unknown 'multiply data test' value: {}".format(config['multiply_data_test']))
# logger.info("Extended test representations: {}".format(len(test_data['target'])))
logger.info('here are the keys in your representations: {}'.format(train_data.keys()))
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['contexts'] if 'contexts' in config else 'plain'
test_contexts = create_contexts(test_data, data_type=data_type)
test_contexts_seq = create_contexts(test_data, data_type='sequential')
train_contexts = create_contexts(train_data, data_type=data_type)
logger.info('Vocabulary comparison -- coverage for each dataset: ')
logger.info(compare_vocabulary([train_data['target'], test_data['target']]))
# END REPRESENTATION GENERATION
# FEATURE EXTRACTION
train_tags = call_for_each_element(train_contexts, tags_from_contexts, data_type=data_type)
test_tags = call_for_each_element(test_contexts, tags_from_contexts, data_type=data_type)
test_tags_seq = call_for_each_element(test_contexts_seq, tags_from_contexts, data_type='sequential')
logger.info('creating feature extractors...')
feature_extractors = build_objects(config['feature_extractors'])
logger.info('mapping the feature extractors over the contexts for test...')
test_features = call_for_each_element(test_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
logger.info('mapping the feature extractors over the contexts for train...')
train_features = call_for_each_element(train_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
logger.info('number of training instances: {}'.format(len(train_features)))
logger.info('number of testing instances: {}'.format(len(test_features)))
logger.info('All of your features now exist in their raw representation, but they may not be numbers yet')
# END FEATURE EXTRACTION
# BEGIN CONVERTING FEATURES TO NUMBERS
logger.info('binarization flag: {}'.format(config['features']['binarize']))
# flatten so that we can properly binarize the features
if config['features']['binarize'] is True:
logger.info('Binarizing your features...')
all_values = []
if data_type == 'sequential':
all_values = flatten(train_features)
elif data_type == 'plain':
all_values = train_features
elif data_type == 'token':
all_values = flatten(train_features.values())
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
features_num = len(feature_names)
true_features_num = len(all_values[0])
logger.info('fitting binarizers...')
binarizers = fit_binarizers(all_values)
logger.info('binarizing test data...')
test_features = call_for_each_element(test_features, binarize, [binarizers], data_type=data_type)
logger.info('binarizing training data...')
# TODO: this line hangs with alignment+w2v
train_features = call_for_each_element(train_features, binarize, [binarizers], data_type=data_type)
logger.info('All of your features are now scalars in numpy arrays')
logger.info('training and test sets successfully generated')
# the way that we persist depends upon the structure of the data (plain/sequence/token_dict)
# TODO: remove this once we have a list containing all datasets
if config['features']['persist']:
if 'persist_format' in config['features']:
persist_format = config['features']['persist_format']
else:
persist_format = 'crf++'
experiment_datasets = [{'name': 'test', 'features': test_features, 'tags': test_tags}, {'name': 'train', 'features': train_features, 'tags': train_tags}]
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
if config['features']['persist_dir']:
persist_dir = config['features']['persist_dir']
else:
persist_dir = os.path.getcwd()
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
for dataset_obj in experiment_datasets:
persist_features(dataset_obj['name'], dataset_obj['features'], persist_dir, feature_names=feature_names, tags=dataset_obj['tags'], file_format=persist_format)
# BEGIN LEARNING
# TODO: different sequence learning modules need different representation, we should wrap them in a class
# TODO: create a consistent interface to sequence learners, will need to use *args and **kwargs because APIs are very different
from sklearn.metrics import f1_score, precision_score, recall_score
import numpy as np
experiment_datasets = [{'name': 'test', 'features': test_features, 'tags': test_tags}, {'name': 'train', 'features': train_features, 'tags': train_tags}]
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
print("FEATURE NAMES: ", feature_names)
persist_dir = tmp_dir
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
if 'persist_format' not in config:
config['persist_format'] = 'crf_suite'
for dataset_obj in experiment_datasets:
persist_features(dataset_obj['name']+time_stamp, dataset_obj['features'], persist_dir, feature_names=feature_names, tags=dataset_obj['tags'], file_format=config['persist_format'])
feature_num = len(train_features[0][0])
train_file = os.path.join(tmp_dir, 'train'+time_stamp+'.crf')
test_file = os.path.join(tmp_dir, 'test'+time_stamp+'.crf')
tag_map = {u'OK': 1, u'BAD': 0, 0: 0, 1: 1}
if config['persist_format'] == 'crf++':
# generate a template for CRF++ feature extractor
generate_crf_template(feature_num, 'template', tmp_dir)
# train a CRF++ model
call(['crf_learn', '-a', 'MIRA', os.path.join(tmp_dir, 'template'), train_file, os.path.join(tmp_dir, 'crfpp_model_file'+time_stamp)])
# tag a test set
call(['crf_test', '-m', os.path.join(tmp_dir, 'crfpp_model_file'+time_stamp), '-o', test_file+'.tagged', test_file])
elif config['persist_format'] == 'crf_suite':
crfsuite_algorithm = config['crfsuite_algorithm']
call(['crfsuite', 'learn', '-a', crfsuite_algorithm, '-m', os.path.join(tmp_dir, 'crfsuite_model_file'+time_stamp), train_file])
test_out = open(test_file+'.tagged', 'w')
call(['crfsuite', 'tag', '-tr', '-m', os.path.join(tmp_dir, 'crfsuite_model_file'+time_stamp), test_file], stdout=test_out)
test_out.close()
else:
print("Unknown persist format: {}".format(config['persist_format']))
# parse CRFSuite output
flattened_ref, flattened_hyp = [], []
tag_map = {'OK': 1, 'BAD': 0}
for line in open(test_file+'.tagged'):
if line == "\n":
continue
chunks = line.strip('\n').split('\t')
if len(chunks) != 2:
continue
try:
flattened_ref.append(tag_map[chunks[-2]])
flattened_hyp.append(tag_map[chunks[-1]])
except KeyError:
continue
print("Ref, hyp: ", len(flattened_ref), len(flattened_hyp))
logger.info('Structured prediction f1: ')
print(f1_score(flattened_ref, flattened_hyp, average=None))
print(f1_score(flattened_ref, flattened_hyp, average='weighted', pos_label=None))
logger.info("Sequence correlation: ")
def main(config):
workers = config['workers']
tmp_dir = config['tmp_dir']
tmp_dir = mk_tmp_dir(tmp_dir)
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
# train_data_generators = build_objects(config['datasets']['training'])
# train_data = {}
# for gen in train_data_generators:
# data = gen.generate()
# for key in data:
# if key not in train_data:
# train_data[key] = []
# train_data[key].extend(data[key])
train_data_generator = build_object(config['datasets']['training'][0])
train_data = train_data_generator.generate()
dev, test = False, False
# test
if 'test' in config['datasets']:
test = True
test_data_generator = build_object(config['datasets']['test'][0])
test_data = test_data_generator.generate()
# dev
if 'dev' in config['datasets']:
dev = True
dev_data_generator = build_object(config['datasets']['dev'][0])
dev_data = dev_data_generator.generate()
# additional representations
# print("IN MAIN")
# print(train_data['alignments_file'])
# print(dev_data['alignments_file'])
# print(test_data['alignments_file'])
if 'representations' in config:
representation_generators = build_objects(config['representations'])
else:
representation_generators = []
for r in representation_generators:
train_data = r.generate(train_data)
if test:
test_data = r.generate(test_data)
if dev:
dev_data = r.generate(dev_data)
print("TEST DATA", test_data['alignments'][0])
logger.info("Simple representations: {}".format(len(train_data['target'])))
logger.info('here are the keys in your representations: {}'.format(train_data.keys()))
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['data_type']
print("DATA TYPE:", data_type)
# sys.exit()
print("Train data: ", len(train_data['target']))
if dev:
print("Dev data: ", len(dev_data['target']))
if test:
print("Test data: ", len(test_data['target']))
print("In different representations: ")
for rep in train_data:
print(rep, len(train_data[rep]))
# print('Source dependencies: {}'.format(train_data['source_dependencies'][0]))
# print('Target dependencies: {}'.format(train_data['target_dependencies'][0]))
# print('Source root: {}'.format(train_data['source_root'][0]))
# print('Target root: {}'.format(train_data['target_root'][0]))
train_contexts = create_contexts(train_data, data_type=data_type)
if test:
test_contexts = create_contexts(test_data, data_type=data_type)
logger.info('Vocabulary comparison -- coverage for test dataset: ')
logger.info(compare_vocabulary([train_data['target'], test_data['target']]))
if dev:
dev_contexts = create_contexts(dev_data, data_type=data_type)
# print("TEST CONTEXT", test_contexts[0])
print("Train contexts: ", len(train_contexts))
if dev:
print("Dev contexts: ", len(dev_contexts))
if test:
print("Test contexts: ", len(test_contexts))
print('Train context example: {}'.format(train_contexts[0]))
# END REPRESENTATION GENERATION
# FEATURE EXTRACTION
train_tags = call_for_each_element(train_contexts, tags_from_contexts, data_type=data_type)
if test:
test_tags = call_for_each_element(test_contexts, tags_from_contexts, data_type=data_type)
if dev:
dev_tags = call_for_each_element(dev_contexts, tags_from_contexts, data_type=data_type)
print("Train tags: ", len(train_tags))
if dev:
print("Dev tags: ", len(dev_tags))
if test:
print("Test tags: ", len(test_tags))
logger.info('creating feature extractors...')
feature_extractors = build_objects(config['feature_extractors'])
if test:
logger.info('mapping the feature extractors over the contexts for test...')
test_features = call_for_each_element(test_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
print("Test features sample: ", test_features[0])
if dev:
logger.info('mapping the feature extractors over the contexts for dev...')
dev_features = call_for_each_element(dev_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
logger.info('mapping the feature extractors over the contexts for train...')
train_features = call_for_each_element(train_contexts, contexts_to_features, [feature_extractors, 1], data_type=data_type)
print("Train features sample: ", train_features[0])
logger.info('number of training instances: {}'.format(len(train_features)))
if dev:
logger.info('number of development instances: {}'.format(len(dev_features)))
if test:
logger.info('number of testing instances: {}'.format(len(test_features)))
logger.info('All of your features now exist in their raw representation, but they may not be numbers yet')
# END FEATURE EXTRACTION
# binarizing features
logger.info('binarization flag: {}'.format(config['features']['binarize']))
# flatten so that we can properly binarize the features
if config['features']['binarize'] is True:
logger.info('Binarizing your features...')
all_values = []
if data_type == 'sequential':
all_values = flatten(train_features)
elif data_type == 'plain':
all_values = train_features
elif data_type == 'token':
all_values = flatten(train_features.values())
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
features_num = len(feature_names)
true_features_num = len(all_values[0])
logger.info('fitting binarizers...')
binarizers = fit_binarizers(all_values)
logger.info('binarizing test data...')
test_features = call_for_each_element(test_features, binarize, [binarizers], data_type=data_type)
logger.info('binarizing training data...')
# TODO: this line hangs with alignment+w2v
train_features = call_for_each_element(train_features, binarize, [binarizers], data_type=data_type)
logger.info('All of your features are now scalars in numpy arrays')
logger.info('training and test sets successfully generated')
# persisting features
logger.info('training and test sets successfully generated')
experiment_datasets = [{'name': 'train', 'features': train_features, 'tags': train_tags}]
if test:
experiment_datasets.append({'name': 'test', 'features': test_features, 'tags': test_tags})
if dev:
experiment_datasets.append({'name': 'dev', 'features': dev_features, 'tags': dev_tags})
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
persist_dir = config['persist_dir'] if 'persist_dir' in config else config['features']['persist_dir']
persist_dir = mk_tmp_dir(persist_dir)
persist_format = config['persist_format'] if 'persist_format' in config else config['features']['persist_format']
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
for dataset_obj in experiment_datasets:
# persist_features(dataset_obj['name'], dataset_obj['features'], persist_dir, feature_names=feature_names, tags=dataset_obj['tags'], file_format=persist_format)
persist_features(dataset_obj['name'], dataset_obj['features'], persist_dir, feature_names=feature_names, tags=dataset_obj['tags'], file_format=persist_format)
# generate a template for CRF++ feature extractor
feature_num = len(feature_names)
if persist_format == 'crf++':
generate_crf_template(feature_num, 'template', persist_dir)
logger.info('Features persisted to: {}'.format(', '.join([os.path.join(persist_dir, nn) for nn in [obj['name'] for obj in experiment_datasets]])))
def main(config):
workers = config['workers']
tmp_dir = config['tmp_dir']
tmp_dir = mk_tmp_dir(tmp_dir)
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
train_data_generators = build_objects(config['datasets']['training'])
train_data = {}
for gen in train_data_generators:
data = gen.generate()
for key in data:
if key not in train_data:
train_data[key] = []
train_data[key].extend(data[key])
dev, test = False, False
# test
if 'test' in config['datasets']:
test = True
test_data_generator = build_object(config['datasets']['test'][0])
test_data = test_data_generator.generate()
# dev
if 'dev' in config['datasets']:
dev = True
dev_data_generator = build_object(config['datasets']['dev'][0])
dev_data = dev_data_generator.generate()
# additional representations
if 'representations' in config:
representation_generators = build_objects(config['representations'])
else:
representation_generators = []
for r in representation_generators:
train_data = r.generate(train_data)
if test:
test_data = r.generate(test_data)
if dev:
dev_data = r.generate(dev_data)
logger.info("Simple representations: {}".format(len(train_data['target'])))
logger.info('here are the keys in your representations: {}'.format(train_data.keys()))
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['contexts']
print("DATA TYPE:", data_type)
# sys.exit()
train_contexts = create_contexts(train_data, data_type=data_type)
if test:
test_contexts = create_contexts(test_data, data_type=data_type)
if dev:
dev_contexts = create_contexts(dev_data, data_type=data_type)
logger.info('Vocabulary comparison -- coverage for each dataset: ')
logger.info(compare_vocabulary([train_data['target'], test_data['target']]))
# END REPRESENTATION GENERATION
# FEATURE EXTRACTION
train_tags = call_for_each_element(train_contexts, tags_from_contexts, data_type=data_type)
if test:
test_tags = call_for_each_element(test_contexts, tags_from_contexts, data_type=data_type)
if dev:
dev_tags = call_for_each_element(dev_contexts, tags_from_contexts, data_type=data_type)
logger.info('creating feature extractors...')
feature_extractors = build_objects(config['feature_extractors'])
if test:
logger.info('mapping the feature extractors over the contexts for test...')
test_features = call_for_each_element(test_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
print("Test features sample: ", test_features[0])
if dev:
logger.info('mapping the feature extractors over the contexts for dev...')
dev_features = call_for_each_element(dev_contexts, contexts_to_features, [feature_extractors, workers], data_type=data_type)
logger.info('mapping the feature extractors over the contexts for train...')
train_features = call_for_each_element(train_contexts, contexts_to_features, [feature_extractors, 1], data_type=data_type)
print("Train features sample: ", train_features[0])
logger.info('number of training instances: {}'.format(len(train_features)))
logger.info('number of testing instances: {}'.format(len(test_features)))
logger.info('All of your features now exist in their raw representation, but they may not be numbers yet')
# END FEATURE EXTRACTION
# binarizing features
logger.info('binarization flag: {}'.format(config['features']['binarize']))
# flatten so that we can properly binarize the features
if config['features']['binarize'] is True:
logger.info('Binarizing your features...')
all_values = []
if data_type == 'sequential':
all_values = flatten(train_features)
elif data_type == 'plain':
all_values = train_features
elif data_type == 'token':
all_values = flatten(train_features.values())
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
features_num = len(feature_names)
true_features_num = len(all_values[0])
logger.info('fitting binarizers...')
binarizers = fit_binarizers(all_values)
logger.info('binarizing test data...')
test_features = call_for_each_element(test_features, binarize, [binarizers], data_type=data_type)
logger.info('binarizing training data...')
# TODO: this line hangs with alignment+w2v
train_features = call_for_each_element(train_features, binarize, [binarizers], data_type=data_type)
logger.info('All of your features are now scalars in numpy arrays')
logger.info('training and test sets successfully generated')
# persisting features
logger.info('training and test sets successfully generated')
# experiment_datasets = [{'name': 'train', 'features': train_features, 'tags': train_tags}]
# if test:
# experiment_datasets.append({'name': 'test', 'features': test_features, 'tags': test_tags})
# if dev:
# experiment_datasets.append({'name': 'dev', 'features': dev_features, 'tags': dev_tags})
# feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
feature_names = [f for extractor in feature_extractors for f in extractor.get_feature_names()]
persist_dir = config['persist_dir'] if 'persist_dir' in config else config['features']['persist_dir']
persist_dir = mk_tmp_dir(persist_dir)
# train_file_name, test_file_name, inv_test_file_name = persist_to_svm_dbl(train_features, test_features, feature_names, train_tags, test_tags, persist_dir)
train_file_name, test_file_name = persist_to_svm_blind(train_features, test_features, train_tags, test_tags, feature_names, persist_dir)
model_name = os.path.join(persist_dir, 'model')
logger.info("Start training")
kernel = 0 # linear kernel (default)
if 'svm_params' in config:
kernel = int(config['svm_params']['kernel']) if kernel <= 4 else 0
call(['/export/tools/varvara/svm_multiclass/svm_light/svm_learn', '-t', str(kernel), train_file_name, model_name])
logger.info("Training completed, start testing")
test_file = os.path.join(persist_dir, 'out')
# inverse_test_file = os.path.join(persist_dir, 'out_inv')
call(['/export/tools/varvara/svm_multiclass/svm_light/svm_classify', '-f', '0', test_file_name, model_name, test_file])
# call(['/export/tools/varvara/svm_multiclass/svm_light/svm_classify', '-f', '0', inv_test_file_name, model_name, inverse_test_file])
logger.info("Testing completed")
# predicted = get_test_score(test_file, inverse_test_file)
predicted = get_test_score_blind(test_file)
tag_map = {'OK': 1, 'BAD': 0}
test_tags_num = [tag_map[t] for t in test_tags]
logger.info(f1_score(predicted, test_tags_num, average=None))
logger.info(f1_score(predicted, test_tags_num, average='weighted', pos_label=None))
def main(config):
workers = config['workers']
tmp_dir = config['tmp_dir']
tmp_dir = mk_tmp_dir(tmp_dir)
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
# train_data_generators = build_objects(config['datasets']['training'])
# train_data = {}
# for gen in train_data_generators:
# data = gen.generate()
# for key in data:
# if key not in train_data:
# train_data[key] = []
# train_data[key].extend(data[key])
train_data_generator = build_object(config['datasets']['training'][0])
train_data = train_data_generator.generate()
dev, test = False, False
# test
if 'test' in config['datasets']:
test = True
test_data_generator = build_object(config['datasets']['test'][0])
test_data = test_data_generator.generate()
# dev
if 'dev' in config['datasets']:
dev = True
dev_data_generator = build_object(config['datasets']['dev'][0])
dev_data = dev_data_generator.generate()
# additional representations
# print("IN MAIN")
# print(train_data['alignments_file'])
# print(dev_data['alignments_file'])
# print(test_data['alignments_file'])
if 'representations' in config:
representation_generators = build_objects(config['representations'])
else:
representation_generators = []
for r in representation_generators:
train_data = r.generate(train_data)
if test:
test_data = r.generate(test_data)
if dev:
dev_data = r.generate(dev_data)
print("TEST DATA", test_data['alignments'][0])
logger.info("Simple representations: {}".format(len(train_data['target'])))
logger.info('here are the keys in your representations: {}'.format(
train_data.keys()))
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['contexts']
print("DATA TYPE:", data_type)
# sys.exit()
train_contexts = create_contexts(train_data, data_type=data_type)
if test:
test_contexts = create_contexts(test_data, data_type=data_type)
logger.info('Vocabulary comparison -- coverage for test dataset: ')
logger.info(
compare_vocabulary([train_data['target'], test_data['target']]))
if dev:
dev_contexts = create_contexts(dev_data, data_type=data_type)
# END REPRESENTATION GENERATION
# FEATURE EXTRACTION
train_tags = call_for_each_element(train_contexts,
tags_from_contexts,
data_type=data_type)
if test:
test_tags = call_for_each_element(test_contexts,
tags_from_contexts,
data_type=data_type)
if dev:
dev_tags = call_for_each_element(dev_contexts,
tags_from_contexts,
data_type=data_type)
logger.info('creating feature extractors...')
feature_extractors = build_objects(config['feature_extractors'])
if test:
logger.info(
'mapping the feature extractors over the contexts for test...')
test_features = call_for_each_element(test_contexts,
contexts_to_features,
[feature_extractors, workers],
data_type=data_type)
print("Test features sample: ", test_features[0])
if dev:
logger.info(
'mapping the feature extractors over the contexts for dev...')
dev_features = call_for_each_element(dev_contexts,
contexts_to_features,
[feature_extractors, workers],
data_type=data_type)
logger.info(
'mapping the feature extractors over the contexts for train...')
train_features = call_for_each_element(train_contexts,
contexts_to_features,
[feature_extractors, 1],
data_type=data_type)
print("Train features sample: ", train_features[0])
logger.info('number of training instances: {}'.format(len(train_features)))
logger.info('number of testing instances: {}'.format(len(test_features)))
logger.info(
'All of your features now exist in their raw representation, but they may not be numbers yet'
)
# END FEATURE EXTRACTION
# binarizing features
logger.info('binarization flag: {}'.format(config['features']['binarize']))
# flatten so that we can properly binarize the features
if config['features']['binarize'] is True:
logger.info('Binarizing your features...')
all_values = []
if data_type == 'sequential':
all_values = flatten(train_features)
elif data_type == 'plain':
all_values = train_features
elif data_type == 'token':
all_values = flatten(train_features.values())
feature_names = [
f for extractor in feature_extractors
for f in extractor.get_feature_names()
]
features_num = len(feature_names)
true_features_num = len(all_values[0])
logger.info('fitting binarizers...')
binarizers = fit_binarizers(all_values)
logger.info('binarizing test data...')
test_features = call_for_each_element(test_features,
binarize, [binarizers],
data_type=data_type)
logger.info('binarizing training data...')
# TODO: this line hangs with alignment+w2v
train_features = call_for_each_element(train_features,
binarize, [binarizers],
data_type=data_type)
logger.info('All of your features are now scalars in numpy arrays')
logger.info('training and test sets successfully generated')
# persisting features
logger.info('training and test sets successfully generated')
experiment_datasets = [{
'name': 'train',
'features': train_features,
'tags': train_tags
}]
if test:
experiment_datasets.append({
'name': 'test',
'features': test_features,
'tags': test_tags
})
if dev:
experiment_datasets.append({
'name': 'dev',
'features': dev_features,
'tags': dev_tags
})
feature_names = [
f for extractor in feature_extractors
for f in extractor.get_feature_names()
]
persist_dir = config['persist_dir'] if 'persist_dir' in config else config[
'features']['persist_dir']
persist_dir = mk_tmp_dir(persist_dir)
persist_format = config[
'persist_format'] if 'persist_format' in config else config[
'features']['persist_format']
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
for dataset_obj in experiment_datasets:
# persist_features(dataset_obj['name'], dataset_obj['features'], persist_dir, feature_names=feature_names, tags=dataset_obj['tags'], file_format=persist_format)
persist_features(dataset_obj['name'],
dataset_obj['features'],
persist_dir,
feature_names=feature_names,
tags=None,
file_format=persist_format)
# generate a template for CRF++ feature extractor
feature_num = len(feature_names)
if persist_format == 'crf++':
generate_crf_template(feature_num, 'template', persist_dir)
logger.info('Features persisted to: {}'.format(', '.join([
os.path.join(persist_dir, nn)
for nn in [obj['name'] for obj in experiment_datasets]
])))
def main(config):
workers = config['workers']
tmp_dir = config['tmp_dir'] if 'tmp_dir' in config else None
tmp_dir = mk_tmp_dir(tmp_dir)
time_stamp = str(time.time())
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
train_data_generators = build_objects(config['datasets']['training'])
train_data = {}
for gen in train_data_generators:
data = gen.generate()
for key in data:
if key not in train_data:
train_data[key] = []
train_data[key].extend(data[key])
# test
test_data_generator = build_object(config['datasets']['test'][0])
test_data = test_data_generator.generate()
logger.info("Train data keys: {}".format(train_data.keys()))
logger.info("Train data sequences: {}".format(len(train_data['target'])))
logger.info("Sample sequence: {}".format(
[w.encode('utf-8') for w in train_data['target'][0]]))
# logger.info("Sample sequence: {}".format(train_data['similarity'][0]))
# sys.exit()
# additional representations
if 'representations' in config:
representation_generators = build_objects(config['representations'])
else:
representation_generators = []
for r in representation_generators:
train_data = r.generate(train_data)
test_data = r.generate(test_data)
# borders = config['borders'] if 'borders' in config else False
# if 'multiply_data_train' not in config:
# pass
# elif config['multiply_data_train'] == 'ngrams':
# train_data = multiply_data_ngrams(train_data, borders=borders)
# elif config['multiply_data_train'] == '1ton':
# train_data = multiply_data(train_data, borders=borders)
# elif config['multiply_data_train'] == 'duplicate':
# train_data = multiply_data_base(train_data)
# elif config['multiply_data_train'] == 'all':
# train_data = multiply_data_all(train_data, borders=borders)
# else:
# print("Unknown 'multiply data train' value: {}".format(config['multiply_data_train']))
# logger.info("Extended train representations: {}".format(len(train_data['target'])))
# logger.info("Simple test representations: {}".format(len(test_data['target'])))
# if 'multiply_data_test' not in config:
# pass
# elif config['multiply_data_test'] == 'ngrams':
# test_data = multiply_data_ngrams(test_data, borders=borders)
# elif config['multiply_data_test'] == '1ton':
# test_data = multiply_data(test_data, borders=borders)
# else:
# print("Unknown 'multiply data test' value: {}".format(config['multiply_data_test']))
# logger.info("Extended test representations: {}".format(len(test_data['target'])))
logger.info('here are the keys in your representations: {}'.format(
train_data.keys()))
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['contexts'] if 'contexts' in config else 'plain'
test_contexts = create_contexts(test_data, data_type=data_type)
test_contexts_seq = create_contexts(test_data, data_type='sequential')
train_contexts = create_contexts(train_data, data_type=data_type)
logger.info('Vocabulary comparison -- coverage for each dataset: ')
logger.info(compare_vocabulary([train_data['target'],
test_data['target']]))
# END REPRESENTATION GENERATION
# FEATURE EXTRACTION
train_tags = call_for_each_element(train_contexts,
tags_from_contexts,
data_type=data_type)
test_tags = call_for_each_element(test_contexts,
tags_from_contexts,
data_type=data_type)
test_tags_seq = call_for_each_element(test_contexts_seq,
tags_from_contexts,
data_type='sequential')
logger.info('creating feature extractors...')
feature_extractors = build_objects(config['feature_extractors'])
logger.info('mapping the feature extractors over the contexts for test...')
test_features = call_for_each_element(test_contexts,
contexts_to_features,
[feature_extractors, workers],
data_type=data_type)
logger.info(
'mapping the feature extractors over the contexts for train...')
train_features = call_for_each_element(train_contexts,
contexts_to_features,
[feature_extractors, workers],
data_type=data_type)
logger.info('number of training instances: {}'.format(len(train_features)))
logger.info('number of testing instances: {}'.format(len(test_features)))
logger.info(
'All of your features now exist in their raw representation, but they may not be numbers yet'
)
# END FEATURE EXTRACTION
# BEGIN CONVERTING FEATURES TO NUMBERS
logger.info('binarization flag: {}'.format(config['features']['binarize']))
# flatten so that we can properly binarize the features
if config['features']['binarize'] is True:
logger.info('Binarizing your features...')
all_values = []
if data_type == 'sequential':
all_values = flatten(train_features)
elif data_type == 'plain':
all_values = train_features
elif data_type == 'token':
all_values = flatten(train_features.values())
feature_names = [
f for extractor in feature_extractors
for f in extractor.get_feature_names()
]
features_num = len(feature_names)
true_features_num = len(all_values[0])
logger.info('fitting binarizers...')
binarizers = fit_binarizers(all_values)
logger.info('binarizing test data...')
test_features = call_for_each_element(test_features,
binarize, [binarizers],
data_type=data_type)
logger.info('binarizing training data...')
# TODO: this line hangs with alignment+w2v
train_features = call_for_each_element(train_features,
binarize, [binarizers],
data_type=data_type)
logger.info('All of your features are now scalars in numpy arrays')
logger.info('training and test sets successfully generated')
# the way that we persist depends upon the structure of the data (plain/sequence/token_dict)
# TODO: remove this once we have a list containing all datasets
if config['features']['persist']:
if 'persist_format' in config['features']:
persist_format = config['features']['persist_format']
else:
persist_format = 'crf++'
experiment_datasets = [{
'name': 'test',
'features': test_features,
'tags': test_tags
}, {
'name': 'train',
'features': train_features,
'tags': train_tags
}]
feature_names = [
f for extractor in feature_extractors
for f in extractor.get_feature_names()
]
if config['features']['persist_dir']:
persist_dir = config['features']['persist_dir']
else:
persist_dir = os.path.getcwd()
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
for dataset_obj in experiment_datasets:
persist_features(dataset_obj['name'],
dataset_obj['features'],
persist_dir,
feature_names=feature_names,
tags=dataset_obj['tags'],
file_format=persist_format)
# BEGIN LEARNING
# TODO: different sequence learning modules need different representation, we should wrap them in a class
# TODO: create a consistent interface to sequence learners, will need to use *args and **kwargs because APIs are very different
from sklearn.metrics import f1_score, precision_score, recall_score
import numpy as np
experiment_datasets = [{
'name': 'test',
'features': test_features,
'tags': test_tags
}, {
'name': 'train',
'features': train_features,
'tags': train_tags
}]
feature_names = [
f for extractor in feature_extractors
for f in extractor.get_feature_names()
]
print("FEATURE NAMES: ", feature_names)
persist_dir = tmp_dir
logger.info('persisting your features to: {}'.format(persist_dir))
# for each dataset, write a file and persist the features
if 'persist_format' not in config:
config['persist_format'] = 'crf_suite'
for dataset_obj in experiment_datasets:
persist_features(dataset_obj['name'] + time_stamp,
dataset_obj['features'],
persist_dir,
feature_names=feature_names,
tags=dataset_obj['tags'],
file_format=config['persist_format'])
feature_num = len(train_features[0][0])
train_file = os.path.join(tmp_dir, 'train' + time_stamp + '.crf')
test_file = os.path.join(tmp_dir, 'test' + time_stamp + '.crf')
tag_map = {u'OK': 1, u'BAD': 0, 0: 0, 1: 1}
if config['persist_format'] == 'crf++':
# generate a template for CRF++ feature extractor
generate_crf_template(feature_num, 'template', tmp_dir)
# train a CRF++ model
call([
'crf_learn', '-a', 'MIRA',
os.path.join(tmp_dir, 'template'), train_file,
os.path.join(tmp_dir, 'crfpp_model_file' + time_stamp)
])
# tag a test set
call([
'crf_test', '-m',
os.path.join(tmp_dir, 'crfpp_model_file' + time_stamp), '-o',
test_file + '.tagged', test_file
])
elif config['persist_format'] == 'crf_suite':
crfsuite_algorithm = config['crfsuite_algorithm']
call([
'crfsuite', 'learn', '-a', crfsuite_algorithm, '-m',
os.path.join(tmp_dir, 'crfsuite_model_file' + time_stamp),
train_file
])
test_out = open(test_file + '.tagged', 'w')
call([
'crfsuite', 'tag', '-tr', '-m',
os.path.join(tmp_dir, 'crfsuite_model_file' + time_stamp),
test_file
],
stdout=test_out)
test_out.close()
else:
print("Unknown persist format: {}".format(config['persist_format']))
# parse CRFSuite output
flattened_ref, flattened_hyp = [], []
tag_map = {'OK': 1, 'BAD': 0}
for line in open(test_file + '.tagged'):
if line == "\n":
continue
chunks = line.strip('\n').split('\t')
if len(chunks) != 2:
continue
try:
flattened_ref.append(tag_map[chunks[-2]])
flattened_hyp.append(tag_map[chunks[-1]])
except KeyError:
continue
print("Ref, hyp: ", len(flattened_ref), len(flattened_hyp))
logger.info('Structured prediction f1: ')
print(f1_score(flattened_ref, flattened_hyp, average=None))
print(
f1_score(flattened_ref,
flattened_hyp,
average='weighted',
pos_label=None))
logger.info("Sequence correlation: ")