def main(config, stamp):
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['data_type'] if 'data_type' in config else (
config['contexts'] if 'contexts' in config else 'plain')
bad_tagging = config[
'bad_tagging'] if 'bad_tagging' in config else 'pessimistic'
logger.info("data_type -- {}, bad_tagging -- {}".format(
data_type, bad_tagging))
# time_stamp = str(time.time())
time_stamp = stamp
workers = config['workers']
tmp_dir = config['tmp_dir']
# one generator
train_data_generator = build_object(config['datasets']['training'][0])
train_data = train_data_generator.generate()
# 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]]))
# 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
logger.info('here are the keys in your representations: {}'.format(
train_data.keys()))
bad_tagging = config[
'bad_tagging'] if 'bad_tagging' in config else 'pessimistic'
# test_contexts = create_contexts_ngram(test_data, data_type=data_type, test=True, bad_tagging=bad_tagging)
test_contexts = create_contexts_ngram(test_data,
data_type=data_type,
test=True,
bad_tagging=bad_tagging,
tags_format=config['tags_format'])
print("Objects in the train data: {}".format(len(train_data['target'])))
print("UNAMBIGUOUS: ", config['unambiguous'])
# train_contexts = create_contexts_ngram(train_data, data_type=data_type, bad_tagging=bad_tagging, unambiguous=config['unambiguous'])
train_contexts = create_contexts_ngram(train_data,
data_type=data_type,
bad_tagging=bad_tagging,
unambiguous=config['unambiguous'],
tags_format=config['tags_format'])
#print("Train contexts: {}".format(len(train_contexts)))
#print("1st context:", train_contexts[0])
# the list of context objects' 'target' field lengths
# to restore the word-level tags from the phrase-level
#test_context_correspondence = get_contexts_words_number(test_contexts)
if data_type == 'sequential':
test_context_correspondence = flatten(
[get_contexts_words_number(cont) for cont in test_contexts])
#print(test_context_correspondence)
for idx, cont in enumerate(test_contexts):
get_cont = get_contexts_words_number(cont)
count_cont = [len(c['token']) for c in cont]
assert (all([
get_cont[i] == count_cont[i] for i in range(len(cont))
])), "Sum doesn't match at line {}:\n{}\n{}".format(
idx, ' '.join([str(c) for c in get_cont]),
' '.join([str(c) for c in count_cont]))
assert (sum(test_context_correspondence) == sum([
len(c['token']) for cont in test_contexts for c in cont
])), "Sums don't match: {} and {}".format(
sum(test_context_correspondence) == sum(
[len(c['token']) for cont in test_contexts for c in cont]))
else:
test_context_correspondence = get_contexts_words_number(test_contexts)
assert (sum(test_context_correspondence) == sum([
len(c['token']) for c in test_contexts
])), "Sums don't match: {} and {}".format(
sum(test_context_correspondence),
sum([len(c['token']) for c in test_contexts]))
# print("Token lengths:", sum([len(c['token']) for c in test_contexts]))
# assert(sum(test_context_correspondence) == 9613), "GOLAKTEKO OPASNOSTE!!!, {}".format(sum(test_context_correspondence))
# sys.exit()
# if data_type == 'sequential':
# test_context_correspondence = flatten(test_context_correspondence)
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_true = test_data['tags']
tag_idx = 0
seg_idx = 0
# test_context_correspondence_seq = [get_contexts_words_number(cont) for cont in test_contexts]
# for idx, (tag_seq, phr_seq) in enumerate(zip(test_data['tags'], test_context_correspondence_seq)):
# assert(len(tag_seq) == sum(phr_seq)),"Something wrong in line {}:\n{}\n{}".format(idx, ' '.join(tag_seq), ' '.join([str(p) for p in phr_seq]))
# tag_idx = 0
# for d in phr_seq:
# first_tag = tag_seq[tag_idx]
# assert(all([t == first_tag for t in tag_seq[tag_idx:tag_idx+d]])), "Something wrong in line {}:\n{}\n{}".format(idx, ' '.join(tag_seq), ' '.join([str(p) for p in phr_seq]))
# try:
# indicator = [t == first_tag for t in test_data['tags'][seg_idx][tag_idx:tag_idx+d]]
# assert(all(indicator))
# tags_cnt += d
# if tags_cnt == len(test_data['tags'][seg_idx]):
# tags_cnt = 0
# seg_idx += 1
# elif tags_cnt > len(test_data['tags'][seg_idx]):
# raise
# except:
# print("No correspondence in line {}, tag {}: \n{}\n{}".format(seg_idx, tag_idx, ' '.join(test_data['tags'][seg_idx]), d))
# sys.exit()
#assert(sum(test_context_correspondence) == len(flatten(test_data['tags']))), "Sums don't match for phrase contexts and test data object: {} and {}".format(sum(test_context_correspondence), len(flatten(test_data['tags'])))
# flat_cont = flatten(test_contexts)
# flat_tags = flatten(test_data['tags'])
# for ii in range(len(flat_cont)):
if data_type == 'plain':
assert (
len(test_context_correspondence) == len(test_tags)
), "Lengths don't match for phrase contexts and test tags: {} and {}".format(
len(test_context_correspondence), len(test_tags))
# 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
from sklearn.metrics import f1_score, precision_score, recall_score
from sklearn.cross_validation import permutation_test_score
import numpy as np
tag_map = {u'OK': 1, u'BAD': 0}
if data_type == 'sequential':
# TODO: save features for CRFSuite, call it
logger.info('training sequential model...')
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')
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',
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'] if 'crfsuite_algorithm' in config else 'arow'
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']))
sys.exit()
sequential_true = [[]]
sequential_predictions = [[]]
flat_true = []
flat_predictions = []
for line in open(test_file + '.tagged'):
# end of tagging, statistics reported
if line.startswith('Performance'):
break
if line == '\n':
sequential_predictions.append([])
continue
chunks = line[:-1].decode('utf-8').split()
flat_true.append(chunks[-2])
sequential_true[-1].append(chunks[-2])
flat_predictions.append(chunks[-1])
sequential_predictions[-1].append(chunks[-1])
# restoring the word-level tags
test_predictions_word, test_tags_word = [], []
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
test_predictions_word.append(flat_predictions[idx])
test_tags_word.append(flat_true[idx])
print(f1_score(test_predictions_word, test_tags_word, average=None))
print(
f1_score(test_predictions_word,
test_tags_word,
average='weighted',
pos_label=None))
print("Precision: {}, recall: {}".format(
precision_score(test_predictions_word,
test_tags_word,
average=None),
recall_score(test_predictions_word, test_tags_word, average=None)))
else:
train_tags = [tag_map[tag] for tag in train_tags]
#print(test_tags)
test_tags = [tag_map[tag] for tag in test_tags]
#print(test_tags)
#sys.exit()
# data_type is 'token' or 'plain'
logger.info('start training...')
classifier_type = import_class(
config['learning']['classifier']['module'])
# train the classifier(s)
classifier_map = map_classifiers(train_features,
train_tags,
classifier_type,
data_type=data_type)
logger.info('classifying the test instances')
test_predictions = predict_all(test_features,
classifier_map,
data_type=data_type)
# assert(len(test_predictions) == len(flatten(test_tags_seq))), "long predictions: {}, sequential: {}".format(len(test_predictions), len(flatten(test_tags_seq)))
cnt = 0
test_predictions_seq = []
test_tags_seq_num = []
tag_map = {'OK': 1, 'BAD': 0, 1: 1, 0: 0}
long_test = True if 'multiply_data_test' in config and (
config['multiply_data_test'] == 'ngrams'
or config['multiply_data_test'] == '1ton') else False
# restoring the word-level tags
test_predictions_word, test_tags_word = [], []
logger.info("Test predictions lenght: {}".format(
len(test_predictions)))
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
test_predictions_word.append(test_predictions[idx])
test_tags_word.append(test_tags[idx])
test_tags_true_flat = flatten(test_tags_true)
test_tags_true_flat = [tag_map[t] for t in test_tags_true_flat]
# print(f1_score(test_tags_word, test_predictions_word, average=None))
# print(f1_score(test_tags_word, test_predictions_word, average='weighted', pos_label=None))
print(
f1_score(test_tags_true_flat, test_predictions_word, average=None))
print(
f1_score(test_tags_true_flat,
test_predictions_word,
average='weighted',
pos_label=None))
print("Precision: {}, recall: {}".format(
precision_score(test_tags_true_flat,
test_predictions_word,
average=None),
recall_score(test_tags_true_flat,
test_predictions_word,
average=None)))
# TODO: remove the hard coding of the tags here
bad_count = sum(1 for t in test_tags if t == u'BAD' or t == 0)
good_count = sum(1 for t in test_tags if t == u'OK' or t == 1)
total = len(test_tags)
assert (total == bad_count +
good_count), 'tag counts should be correct'
percent_good = good_count / total
logger.info('percent good in test set: {}'.format(percent_good))
logger.info('percent bad in test set: {}'.format(1 - percent_good))
random_class_results = []
random_weighted_results = []
for i in range(20):
random_tags_phrase = list(
np.random.choice([1, 0], total,
[percent_good, 1 - percent_good]))
random_tags = []
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
random_tags.append(random_tags_phrase[idx])
# random_tags = [u'GOOD' for i in range(total)]
random_class_f1 = f1_score(test_tags_true_flat,
random_tags,
average=None)
random_class_results.append(random_class_f1)
logger.info('two class f1 random score ({}): {}'.format(
i, random_class_f1))
# random_average_f1 = f1_score(random_tags, test_tags, average='weighted')
random_average_f1 = f1_score(test_tags_true_flat,
random_tags,
average='weighted',
pos_label=None)
random_weighted_results.append(random_average_f1)
# logger.info('average f1 random score ({}): {}'.format(i, random_average_f1))
avg_random_class = np.average(random_class_results, axis=0)
avg_weighted = np.average(random_weighted_results)
logger.info(
'two class f1 random average score: {}'.format(avg_random_class))
logger.info(
'weighted f1 random average score: {}'.format(avg_weighted))
# print("Cross-validation:")
# print(permutation_test_score())
# logger.info("Sequence correlation: ")
# print(sequence_correlation_weighted(test_tags_seq_num, test_predictions_seq, verbose=True)[1])
label_test_hyp_ref(test_predictions_word, test_tags_true_flat,
os.path.join(tmp_dir, config['output_name']),
config["output_test"])
def main(config):
workers = config['workers']
# REPRESENTATION GENERATION
# main representations (source, target, tags)
# training
train_data_generator = build_object(config['datasets']['training'][0])
train_data = train_data_generator.generate()
# 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()
#logger.info("Alignment file: {}".format(train_data['alignments_file']))
#logger.info("Alignment file: {}".format(test_data['alignments_file']))
# 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':
logger.info("Multiply data: {} and {}".format(
config['multiply_data_train'], config['multiply_data_test']))
train_data = multiply_data_ngrams(train_data, borders=borders)
logger.info("Sequences: {}, tag sequences: {}".format(
len(train_data['target']), len(train_data['tags'])))
elif config['multiply_data_train'] == '1ton':
logger.info("Multiply data: {} and {}".format(
config['multiply_data_train'], config['multiply_data_test']))
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("Train data example: {}".format(train_data['target'][:10]))
logger.info("Train tags example: {}".format(train_data['tags'][:10]))
logger.info("Extended train representations: {}".format(
len(train_data['target'])))
# print(train_data[:2])
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'
data_type = config['data_type'] if 'data_type' in config else 'sequential'
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('train features sample: {}'.format(train_features[:5]))
logger.info('train tags sample: {}'.format(train_tags[:5]))
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['persist_dir']:
persist_dir = config['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)
sys.exit()
# 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
tag_map = {u'OK': 1, u'BAD': 0, 0: 0, 1: 1}
if data_type == 'sequential':
logger.info('training sequential model...')
train_tags = [[tag_map[tag] for tag in seq] for seq in train_tags]
test_tags = [[tag_map[tag] for tag in seq] for seq in test_tags]
x_train = np.array([np.array(xi) for xi in train_features])
y_train = np.array([np.array(xi) for xi in train_tags])
x_test = np.array([numpy.array(xi) for xi in test_features])
y_test = np.array([numpy.array(xi) for xi in test_tags])
# pystruct
from marmot.learning.pystruct_sequence_learner import PystructSequenceLearner
sequence_learner = PystructSequenceLearner()
sequence_learner.fit(x_train, y_train)
structured_hyp = sequence_learner.predict(x_test)
# only the last word in every sequence should be counted
flattened_hyp = []
flattened_ref = []
if long_test:
for idx, seq in enumerate(structured_hyp):
flattened_hyp.append(seq[-1])
flattened_ref.append(y_test[idx][-1])
else:
flattened_hyp = flatten(structured_hyp)
flattened_ref = flatten(y_test)
logger.info('scoring sequential model...')
# TODO: the flattening is currently a hack to let us use the same evaluation code for structured and plain tasks
# flattened_hyp = flatten(structured_hyp)
# end pystruct
# for idx, seq in enumerate(test_tags_seq):
# cnt += len(seq)
# if cnt >= len(test_predictions):
# print("long predictions: {}, sequential: {}, sequence #{}".format(len(test_predictions), len(flatten(test_tags_seq)), idx))
# print("Sequence: ", test_contexts_seq[idx])
# if long_test:
# cnt = -1
# new_predictions = []
# new_true = []
# for seq in test_tags_seq:
# cnt += len(seq)
# new_predictions.append(tag_map[test_predictions[cnt]])
# new_true.append(tag_map[seq[-1]])
# test_predictions = new_predictions
# test_tags = new_true
#
# print(f1_score(test_predictions, test_tags, average=None))
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: ")
print(
sequence_correlation_weighted(y_test, structured_hyp,
verbose=True)[1])
else:
train_tags = [tag_map[tag] for tag in train_tags]
test_tags = [tag_map[tag] for tag in test_tags]
# data_type is 'token' or 'plain'
logger.info('start training...')
classifier_type = import_class(
config['learning']['classifier']['module'])
# train the classifier(s)
classifier_map = map_classifiers(train_features,
train_tags,
classifier_type,
data_type=data_type)
logger.info('classifying the test instances')
test_predictions = predict_all(test_features,
classifier_map,
data_type=data_type)
# assert(len(test_predictions) == len(flatten(test_tags_seq))), "long predictions: {}, sequential: {}".format(len(test_predictions), len(flatten(test_tags_seq)))
cnt = 0
test_predictions_seq = []
test_tags_seq_num = []
tag_map = {'OK': 1, 'BAD': 0, 1: 1, 0: 0}
long_test = True if 'multiply_data_test' in config and (
config['multiply_data_test'] == 'ngrams'
or config['multiply_data_test'] == '1ton') else False
for idx, seq in enumerate(test_tags_seq):
test_predictions_seq.append([])
test_tags_seq_num.append([])
for w in seq:
test_predictions_seq[-1].append(tag_map[test_predictions[cnt]])
test_tags_seq_num[-1].append(tag_map[w])
cnt += 1
# cnt += len(seq)
# if cnt >= len(test_predictions):
# print("long predictions: {}, sequential: {}, sequence #{}".format(len(test_predictions), len(flatten(test_tags_seq)), idx))
# print("Sequence: ", test_contexts_seq[idx])
if long_test:
cnt = -1
new_predictions = []
new_true = []
for seq in test_tags_seq:
cnt += len(seq)
new_predictions.append(tag_map[test_predictions[cnt]])
new_true.append(tag_map[seq[-1]])
test_predictions = new_predictions
test_tags = new_true
print(f1_score(test_predictions, test_tags, average=None))
print(
f1_score(test_predictions,
test_tags,
average='weighted',
pos_label=None))
print("Precision: {}, recall: {}".format(
precision_score(test_predictions, test_tags, average=None),
recall_score(test_predictions, test_tags, average=None)))
logger.info("Sequence correlation: ")
print(
sequence_correlation_weighted(test_tags_seq_num,
test_predictions_seq,
verbose=True)[1])
def main(config):
workers = config['workers']
# 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'])))
# print(train_data[:2])
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
tag_map = {u'OK': 1, u'BAD': 0, 0: 0, 1: 1}
if data_type == 'sequential':
logger.info('training sequential model...')
train_tags = [[tag_map[tag] for tag in seq] for seq in train_tags]
test_tags = [[tag_map[tag] for tag in seq] for seq in test_tags]
x_train = np.array([np.array(xi) for xi in train_features])
y_train = np.array([np.array(xi) for xi in train_tags])
x_test = np.array([numpy.array(xi) for xi in test_features])
y_test = np.array([numpy.array(xi) for xi in test_tags])
# pystruct
from marmot.learning.pystruct_sequence_learner import PystructSequenceLearner
sequence_learner = PystructSequenceLearner()
sequence_learner.fit(x_train, y_train)
structured_hyp = sequence_learner.predict(x_test)
# only the last word in every sequence should be counted
flattened_hyp = []
flattened_ref = []
if long_test:
for idx, seq in enumerate(structured_hyp):
flattened_hyp.append(seq[-1])
flattened_ref.append(y_test[idx][-1])
else:
flattened_hyp = flatten(structured_hyp)
flattened_ref = flatten(y_test)
logger.info('scoring sequential model...')
# TODO: the flattening is currently a hack to let us use the same evaluation code for structured and plain tasks
# flattened_hyp = flatten(structured_hyp)
# end pystruct
# for idx, seq in enumerate(test_tags_seq):
# cnt += len(seq)
# if cnt >= len(test_predictions):
# print("long predictions: {}, sequential: {}, sequence #{}".format(len(test_predictions), len(flatten(test_tags_seq)), idx))
# print("Sequence: ", test_contexts_seq[idx])
# if long_test:
# cnt = -1
# new_predictions = []
# new_true = []
# for seq in test_tags_seq:
# cnt += len(seq)
# new_predictions.append(tag_map[test_predictions[cnt]])
# new_true.append(tag_map[seq[-1]])
# test_predictions = new_predictions
# test_tags = new_true
#
# print(f1_score(test_predictions, test_tags, average=None))
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: ")
print(sequence_correlation_weighted(y_test, structured_hyp, verbose=True)[1])
else:
train_tags = [tag_map[tag] for tag in train_tags]
test_tags = [tag_map[tag] for tag in test_tags]
# data_type is 'token' or 'plain'
logger.info('start training...')
classifier_type = import_class(config['learning']['classifier']['module'])
# train the classifier(s)
classifier_map = map_classifiers(train_features, train_tags, classifier_type, data_type=data_type)
logger.info('classifying the test instances')
test_predictions = predict_all(test_features, classifier_map, data_type=data_type)
# assert(len(test_predictions) == len(flatten(test_tags_seq))), "long predictions: {}, sequential: {}".format(len(test_predictions), len(flatten(test_tags_seq)))
cnt = 0
test_predictions_seq = []
test_tags_seq_num = []
tag_map = {'OK': 1, 'BAD': 0, 1: 1, 0: 0}
long_test = True if 'multiply_data_test' in config and (config['multiply_data_test'] == 'ngrams' or config['multiply_data_test'] == '1ton') else False
for idx, seq in enumerate(test_tags_seq):
test_predictions_seq.append([])
test_tags_seq_num.append([])
for w in seq:
test_predictions_seq[-1].append(tag_map[test_predictions[cnt]])
test_tags_seq_num[-1].append(tag_map[w])
cnt += 1
# cnt += len(seq)
# if cnt >= len(test_predictions):
# print("long predictions: {}, sequential: {}, sequence #{}".format(len(test_predictions), len(flatten(test_tags_seq)), idx))
# print("Sequence: ", test_contexts_seq[idx])
if long_test:
cnt = -1
new_predictions = []
new_true = []
for seq in test_tags_seq:
cnt += len(seq)
new_predictions.append(tag_map[test_predictions[cnt]])
new_true.append(tag_map[seq[-1]])
test_predictions = new_predictions
test_tags = new_true
print(f1_score(test_predictions, test_tags, average=None))
print(f1_score(test_predictions, test_tags, average='weighted', pos_label=None))
print("Precision: {}, recall: {}".format(precision_score(test_predictions, test_tags, average=None), recall_score(test_predictions, test_tags, average=None)))
logger.info("Sequence correlation: ")
print(sequence_correlation_weighted(test_tags_seq_num, test_predictions_seq, verbose=True)[1])
def main(config, stamp):
# the data_type is the format corresponding to the model of the data that the user wishes to learn
data_type = config['data_type'] if 'data_type' in config else (config['contexts'] if 'contexts' in config else 'plain')
bad_tagging = config['bad_tagging'] if 'bad_tagging' in config else 'pessimistic'
logger.info("data_type -- {}, bad_tagging -- {}".format(data_type, bad_tagging))
# time_stamp = str(time.time())
time_stamp = stamp
workers = config['workers']
tmp_dir = config['tmp_dir']
# one generator
train_data_generator = build_object(config['datasets']['training'][0])
train_data = train_data_generator.generate()
# 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]]))
# 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
logger.info('here are the keys in your representations: {}'.format(train_data.keys()))
bad_tagging = config['bad_tagging'] if 'bad_tagging' in config else 'pessimistic'
# test_contexts = create_contexts_ngram(test_data, data_type=data_type, test=True, bad_tagging=bad_tagging)
test_contexts = create_contexts_ngram(test_data, data_type=data_type, test=True, bad_tagging=bad_tagging, tags_format=config['tags_format'])
print("Objects in the train data: {}".format(len(train_data['target'])))
print("UNAMBIGUOUS: ", config['unambiguous'])
# train_contexts = create_contexts_ngram(train_data, data_type=data_type, bad_tagging=bad_tagging, unambiguous=config['unambiguous'])
train_contexts = create_contexts_ngram(train_data, data_type=data_type, bad_tagging=bad_tagging, unambiguous=config['unambiguous'], tags_format=config['tags_format'])
#print("Train contexts: {}".format(len(train_contexts)))
#print("1st context:", train_contexts[0])
# the list of context objects' 'target' field lengths
# to restore the word-level tags from the phrase-level
#test_context_correspondence = get_contexts_words_number(test_contexts)
if data_type == 'sequential':
test_context_correspondence = flatten([get_contexts_words_number(cont) for cont in test_contexts])
#print(test_context_correspondence)
for idx, cont in enumerate(test_contexts):
get_cont = get_contexts_words_number(cont)
count_cont = [len(c['token']) for c in cont]
assert(all([get_cont[i] == count_cont[i] for i in range(len(cont))])), "Sum doesn't match at line {}:\n{}\n{}".format(idx, ' '.join([str(c) for c in get_cont]), ' '.join([str(c) for c in count_cont]))
assert(sum(test_context_correspondence) == sum([len(c['token']) for cont in test_contexts for c in cont])), "Sums don't match: {} and {}".format(sum(test_context_correspondence) == sum([len(c['token']) for cont in test_contexts for c in cont]))
else:
test_context_correspondence = get_contexts_words_number(test_contexts)
assert(sum(test_context_correspondence) == sum([len(c['token']) for c in test_contexts])), "Sums don't match: {} and {}".format(sum(test_context_correspondence), sum([len(c['token']) for c in test_contexts]))
# print("Token lengths:", sum([len(c['token']) for c in test_contexts]))
# assert(sum(test_context_correspondence) == 9613), "GOLAKTEKO OPASNOSTE!!!, {}".format(sum(test_context_correspondence))
# sys.exit()
# if data_type == 'sequential':
# test_context_correspondence = flatten(test_context_correspondence)
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_true = test_data['tags']
tag_idx = 0
seg_idx = 0
# test_context_correspondence_seq = [get_contexts_words_number(cont) for cont in test_contexts]
# for idx, (tag_seq, phr_seq) in enumerate(zip(test_data['tags'], test_context_correspondence_seq)):
# assert(len(tag_seq) == sum(phr_seq)),"Something wrong in line {}:\n{}\n{}".format(idx, ' '.join(tag_seq), ' '.join([str(p) for p in phr_seq]))
# tag_idx = 0
# for d in phr_seq:
# first_tag = tag_seq[tag_idx]
# assert(all([t == first_tag for t in tag_seq[tag_idx:tag_idx+d]])), "Something wrong in line {}:\n{}\n{}".format(idx, ' '.join(tag_seq), ' '.join([str(p) for p in phr_seq]))
# try:
# indicator = [t == first_tag for t in test_data['tags'][seg_idx][tag_idx:tag_idx+d]]
# assert(all(indicator))
# tags_cnt += d
# if tags_cnt == len(test_data['tags'][seg_idx]):
# tags_cnt = 0
# seg_idx += 1
# elif tags_cnt > len(test_data['tags'][seg_idx]):
# raise
# except:
# print("No correspondence in line {}, tag {}: \n{}\n{}".format(seg_idx, tag_idx, ' '.join(test_data['tags'][seg_idx]), d))
# sys.exit()
assert(sum(test_context_correspondence) == len(flatten(test_data['tags']))), "Sums don't match for phrase contexts and test data object: {} and {}".format(sum(test_context_correspondence), len(flatten(test_data['tags'])))
# flat_cont = flatten(test_contexts)
# flat_tags = flatten(test_data['tags'])
# for ii in range(len(flat_cont)):
if data_type == 'plain':
assert(len(test_context_correspondence) == len(test_tags)), "Lengths don't match for phrase contexts and test tags: {} and {}".format(len(test_context_correspondence), len(test_tags))
# 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
from sklearn.metrics import f1_score, precision_score, recall_score
from sklearn.cross_validation import permutation_test_score
import numpy as np
tag_map = {u'OK': 1, u'BAD': 0}
if data_type == 'sequential':
# TODO: save features for CRFSuite, call it
logger.info('training sequential model...')
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')
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', 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'] if 'crfsuite_algorithm' in config else 'arow'
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']))
sequential_true = [[]]
sequential_predictions = [[]]
flat_true = []
flat_predictions = []
for line in open(test_file+'.tagged'):
# end of tagging, statistics reported
if line.startswith('Performance'):
break
if line == '\n':
sequential_predictions.append([])
continue
chunks = line[:-1].decode('utf-8').split()
flat_true.append(chunks[-2])
sequential_true[-1].append(chunks[-2])
flat_predictions.append(chunks[-1])
sequential_predictions[-1].append(chunks[-1])
# restoring the word-level tags
test_predictions_word, test_tags_word = [], []
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
test_predictions_word.append(flat_predictions[idx])
test_tags_word.append(flat_true[idx])
print(f1_score(test_predictions_word, test_tags_word, average=None))
print(f1_score(test_predictions_word, test_tags_word, average='weighted', pos_label=None))
print("Precision: {}, recall: {}".format(precision_score(test_predictions_word, test_tags_word, average=None), recall_score(test_predictions_word, test_tags_word, average=None)))
else:
train_tags = [tag_map[tag] for tag in train_tags]
#print(test_tags)
test_tags = [tag_map[tag] for tag in test_tags]
#print(test_tags)
#sys.exit()
# data_type is 'token' or 'plain'
logger.info('start training...')
classifier_type = import_class(config['learning']['classifier']['module'])
# train the classifier(s)
classifier_map = map_classifiers(train_features, train_tags, classifier_type, data_type=data_type)
logger.info('classifying the test instances')
test_predictions = predict_all(test_features, classifier_map, data_type=data_type)
# assert(len(test_predictions) == len(flatten(test_tags_seq))), "long predictions: {}, sequential: {}".format(len(test_predictions), len(flatten(test_tags_seq)))
cnt = 0
test_predictions_seq = []
test_tags_seq_num = []
tag_map = {'OK': 1, 'BAD': 0, 1: 1, 0: 0}
long_test = True if 'multiply_data_test' in config and (config['multiply_data_test'] == 'ngrams' or config['multiply_data_test'] == '1ton') else False
# restoring the word-level tags
test_predictions_word, test_tags_word = [], []
logger.info("Test predictions lenght: {}".format(len(test_predictions)))
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
test_predictions_word.append(test_predictions[idx])
test_tags_word.append(test_tags[idx])
test_tags_true_flat = flatten(test_tags_true)
test_tags_true_flat = [tag_map[t] for t in test_tags_true_flat]
# print(f1_score(test_tags_word, test_predictions_word, average=None))
# print(f1_score(test_tags_word, test_predictions_word, average='weighted', pos_label=None))
print(f1_score(test_tags_true_flat, test_predictions_word, average=None))
print(f1_score(test_tags_true_flat, test_predictions_word, average='weighted', pos_label=None))
print("Precision: {}, recall: {}".format(precision_score(test_tags_true_flat, test_predictions_word, average=None), recall_score(test_tags_true_flat, test_predictions_word, average=None)))
# TODO: remove the hard coding of the tags here
bad_count = sum(1 for t in test_tags if t == u'BAD' or t == 0)
good_count = sum(1 for t in test_tags if t == u'OK' or t == 1)
total = len(test_tags)
assert (total == bad_count+good_count), 'tag counts should be correct'
percent_good = good_count / total
logger.info('percent good in test set: {}'.format(percent_good))
logger.info('percent bad in test set: {}'.format(1 - percent_good))
random_class_results = []
random_weighted_results = []
for i in range(20):
random_tags_phrase = list(np.random.choice([1, 0], total, [percent_good, 1-percent_good]))
random_tags = []
for idx, n in enumerate(test_context_correspondence):
for i in range(n):
random_tags.append(random_tags_phrase[idx])
# random_tags = [u'GOOD' for i in range(total)]
random_class_f1 = f1_score(test_tags_true_flat, random_tags, average=None)
random_class_results.append(random_class_f1)
logger.info('two class f1 random score ({}): {}'.format(i, random_class_f1))
# random_average_f1 = f1_score(random_tags, test_tags, average='weighted')
random_average_f1 = f1_score(test_tags_true_flat, random_tags, average='weighted', pos_label=None)
random_weighted_results.append(random_average_f1)
# logger.info('average f1 random score ({}): {}'.format(i, random_average_f1))
avg_random_class = np.average(random_class_results, axis=0)
avg_weighted = np.average(random_weighted_results)
logger.info('two class f1 random average score: {}'.format(avg_random_class))
logger.info('weighted f1 random average score: {}'.format(avg_weighted))
# print("Cross-validation:")
# print(permutation_test_score())
# logger.info("Sequence correlation: ")
# print(sequence_correlation_weighted(test_tags_seq_num, test_predictions_seq, verbose=True)[1])
label_test_hyp_ref(test_predictions_word, test_tags_true_flat, os.path.join(tmp_dir, config['output_name']), config["output_test"])
def main(config):
workers = config['workers']
# 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()
# 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)
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)
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
# make sure the test_context and train_context keys are in sync
# TODO: this is important when we are learning token-level classifiers
# experiment_utils.sync_keys(train_contexts, test_contexts)
# TODO: this is important when we are learning token-level classifiers
# test_contexts = filter_contexts(test_contexts, min_total=min_total)
# assert set(test_contexts.keys()) == set(train_contexts.keys())
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)
# all of the feature extraction should be parallelizable
# note that a feature extractor MUST be able to parse the context exchange format, or it should throw an error:
# { 'token': <token>, index: <idx>, 'source': [<source toks>]', 'target': [<target toks>], 'tag': <tag>}
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())
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)
# TODO: we should only learn and evaluate the model if this is what the user wants
# TODO: we should be able to dump the features for each of the user's datasets to a file specified by the user
# 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
import numpy as np
if data_type == 'sequential':
logger.info('training sequential model...')
# TODO: move the tag and array conversion code to the utils of this module
# TODO: check if X and y are in the format we expect
# TODO: don't hardcode the dictionary
tag_map = {u'OK': 1, u'BAD': 0}
train_tags = [[tag_map[tag] for tag in seq] for seq in train_tags]
test_tags = [[tag_map[tag] for tag in seq] for seq in test_tags]
# make sure that everything is numpy
# cast the dataset to numpy array (ndarrays)
# note that these are _NOT_ matrices, because the inner sequences have different lengths
x_train = np.array([np.array(xi) for xi in train_features])
y_train = np.array([np.array(xi) for xi in train_tags])
x_test = np.array([numpy.array(xi) for xi in test_features])
y_test = np.array([numpy.array(xi) for xi in test_tags])
# SEQLEARN
# from seqlearn.perceptron import StructuredPerceptron
#
# # seqlearn needs a flat list of instances
# x_train = np.array([i for seq in x_train for i in seq])
# y_train = np.array([i for seq in y_train for i in seq])
# x_test = np.array([i for seq in x_test for i in seq])
# y_test = np.array([i for seq in y_test for i in seq])
#
# # seqlearn requires the lengths of each sequence
# lengths_train = [len(seq) for seq in train_features]
# lengths_test = [len(seq) for seq in test_features]
#
# clf = StructuredPerceptron(verbose=True, max_iter=400)
# clf.fit(x_train, y_train, lengths_train)
#
# structured_predictions = clf.predict(x_test, lengths_test)
# logger.info('f1 from seqlearn: {}'.format(f1_score(y_test, structured_predictions, average=None)))
# END SEQLEARN
# pystruct
from marmot.learning.pystruct_sequence_learner import PystructSequenceLearner
sequence_learner = PystructSequenceLearner()
sequence_learner.fit(x_train, y_train)
structured_hyp = sequence_learner.predict(x_test)
logger.info('scoring sequential model...')
# print('score: ' + str(structured_predictor.score(x_test, y_test)))
# TODO: implement this in the config
# classifier_type = import_class(config['learning']['classifier']['module'])
# TODO: the flattening is currently a hack to let us use the same evaluation code for structured and plain tasks
flattened_hyp = flatten(structured_hyp)
# end pystruct
test_predictions = flattened_hyp
flattened_ref = flatten(y_test)
test_tags = flattened_ref
logger.info('Structured prediction f1: ')
print(f1_score(flattened_ref, flattened_hyp, average=None))
else:
# data_type is 'token' or 'plain'
logger.info('start training...')
classifier_type = import_class(config['learning']['classifier']['module'])
# train the classifier(s)
classifier_map = map_classifiers(train_features, train_tags, classifier_type, data_type=data_type)
logger.info('classifying the test instances')
test_predictions = predict_all(test_features, classifier_map, data_type=data_type)
# TODO: this section only works for 'plain'
print(f1_score(test_predictions, test_tags, average=None))
# EVALUATION
logger.info('evaluating your results')
# TODO: remove the hard coding of the tags here
bad_count = sum(1 for t in test_tags if t == u'BAD' or t == 0)
good_count = sum(1 for t in test_tags if t == u'OK' or t == 1)
total = len(test_tags)
assert (total == bad_count+good_count), 'tag counts should be correct'
percent_good = good_count / total
logger.info('percent good in test set: {}'.format(percent_good))
logger.info('percent bad in test set: {}'.format(1 - percent_good))
import numpy as np
random_class_results = []
random_weighted_results = []
for i in range(20):
random_tags = list(np.random.choice([1, 0], total, [percent_good, 1-percent_good]))
# random_tags = [u'GOOD' for i in range(total)]
random_class_f1 = f1_score(test_tags, random_tags, average=None)
random_class_results.append(random_class_f1)
logger.info('two class f1 random score ({}): {}'.format(i, random_class_f1))
# random_average_f1 = f1_score(random_tags, test_tags, average='weighted')
random_average_f1 = weighted_fmeasure(test_tags, random_tags)
random_weighted_results.append(random_average_f1)
# logger.info('average f1 random score ({}): {}'.format(i, random_average_f1))
avg_random_class = np.average(random_class_results, axis=0)
avg_weighted = np.average(random_weighted_results)
logger.info('two class f1 random average score: {}'.format(avg_random_class))
logger.info('weighted f1 random average score: {}'.format(avg_weighted))
actual_class_f1 = f1_score(test_tags, test_predictions, average=None)
actual_average_f1 = weighted_fmeasure(test_tags, test_predictions)
logger.info('two class f1 ACTUAL SCORE: {}'.format(actual_class_f1))
logger.info('weighted f1 ACTUAL SCORE: {}'.format(actual_average_f1))
if data_type == 'token':
f1_map = {}
for token, predicted in test_predictions.iteritems():
logger.info("Evaluating results for token = " + token)
actual = test_tags_actual[token]
# print('Actual: ', actual)
# print('Predicted: ', predicted)
# logger.info("\ttotal instances: " + str(len(predicted)))
f1_map[token] = weighted_fmeasure(actual, predicted)
logger.info('Printing the map of f1 scores by token: ')
print(f1_map)
elif data_type == 'plain':
f1 = weighted_fmeasure(test_tags, test_predictions)
