def main():
parser = argparse.ArgumentParser(description="take text feature")
parser.add_argument("-t", "--type", type=str, choices=("db", "file"), default="file", help="db/file")
parser.add_argument("-s", "--source", type=str, help="file path/sql script")
parser.add_argument("-n", "--name", type=str, help="output file name")
parser.add_argument("-k", "--topk", type=int, default=500, help="top k words")
parser.add_argument("-w", "--word_category", default="v,vd,vn,vf,a,ad,an,ag,al", type=str, help="word category")
args = parser.parse_args()
source_from = args.type
source = args.source
name = args.name
k_num = args.topk
word_category = args.word_category.split(",")
print word_category
if source_from == "db":
comments_df = preprocess.get_data_from_db(source)
elif source_from == "file":
comments_df = preprocess.read_comment_from_file(source)
else:
return
comments_list = list(comments_df["comment"].values)
cutted, word_category_list = utils.word_cut(comments_list)
word_weight_flag = utils.tfidf(cutted, word_category_list, "tfidf_" + name)
key_word = utils.get_topK(word_weight_flag, "top_k_" + name, k=k_num, category_list=word_category)
def prune_on_keywords(self, thres):
data_words, note_ids, id2word, corpus = utils.preprocess(
self.df, 5, ['NOUN', 'VERB'], STOP_WORDS, 'tokens_phrases')
tfidf_matrix, tf_dicts, post_appear_dict = utils.tfidf(data_words)
keywords = {
i: utils.get_tfidfs_thres(tfidf_matrix[i], thres)
for i, m in enumerate(tfidf_matrix)
}
word2id = {v: k for k, v in id2word.items()}
tfidf_corpus = [[(word2id[pair[0]], pair[1]) for pair in post.items()]
for post in keywords]
def load_data(data_name):
timer = utils.timer(name='main')
data_path = './data/' + data_name
user_pref_file = data_path + '/U_BPR.npy'
item_pref_file = data_path + '/V_BPR.npy'
item_content_file = data_path + '/item_features.txt'
train_file = data_path + '/train.csv'
test_file = data_path + '/test.csv'
vali_file = data_path + '/vali.csv'
dat = {}
# load preference data
timer.tic()
dat['u_pref'] = np.load(user_pref_file)
dat['v_pref'] = np.load(item_pref_file)
timer.toc('loaded U:%s,V:%s' %
(str(dat['u_pref'].shape), str(dat['v_pref'].shape))).tic()
# pre-process preference data
_, dat['u_pref'] = utils.standardize(dat['u_pref'])
_, dat['v_pref'] = utils.standardize_2(dat['v_pref'])
timer.toc('standardized U,V').tic()
# load item(article) content data
# load_svmlight_file(file): 读取svmlight格式的数据文件，文件存放格式
# <label> <feature-id>:<feature-value> <feature-id>:<feature-value> ...
# 其中 zero_based 选项，如果为 False 的话会将所有的 indices 减 1
# 返回 (X, y)，其中 X 是 scipy.sparse matrix，y 是 numpy.ndarray
item_content, _ = datasets.load_svmlight_file(item_content_file,
zero_based=True,
dtype=np.float32)
# tfidf 文本特征化
item_content = tfidf(item_content)
# svd 特征降维
u, s, _ = randomized_svd(item_content, n_components=300, n_iter=5)
item_content = u * s
# 特征标准化
_, item_content = utils.standardize(item_content)
dat['item_content'] = item_content
timer.toc('loaded item feature sparse matrix: %s' %
(str(item_content.shape))).tic()
# load split
train = pd.read_csv(train_file, dtype=np.int32)
dat['user_list'] = train['uid'].values
dat['item_list'] = train['iid'].values
timer.toc('read train triplets %s' % str(train.shape))
dat['test_eval'] = data.load_eval_data(test_file)
dat['vali_eval'] = data.load_eval_data(vali_file)
return dat
def get_nps(data):
def parse_np(index):
np = ''
closing = 0
for elem in tree[index:]:
if elem[0] == '(':
closing += 1
else:
match = re.findall("\)", elem)
np += elem.replace(')', '').strip() + ' '
closing -= len(match)
if closing <= 0:
break
return np.replace('-LRB- ', '(').replace(' -RRB-', ')').replace('-LRB-', '(').replace('-RRB-', ')').strip().lower()
nps = []
nps_condition = {}
for guess in data:
tree = guess['parse'].split()
for i, elem in enumerate(tree):
if elem == '(NP':
np = parse_np(i)
nps.append(np)
if guess['condition'] not in nps_condition:
nps_condition[guess['condition']] = []
nps_condition[guess['condition']].append(np)
# print 'Most frequent descriptions'
# print 10 * '-'
nps = nltk.FreqDist(nps)
# v = sorted(freq.items(), key=operator.itemgetter(1), reverse=True)[:30]
# for np in v:
# print np[0], np[1]
print 10 * '-'
print 'Most distinctive descriptions per condition'
nps_condition = utils.tfidf(nps_condition, 10)
for condition in nps_condition:
print 'Condition: ', condition
print 10 * '-'
for np in nps_condition[condition]:
print np[0], np[1], nps[np[0]]
print 10 * '-'
def main():
parser = argparse.ArgumentParser(description='take text feature')
parser.add_argument('-t',
'--type',
type=str,
choices=('db', 'file'),
default='file',
help='db/file')
parser.add_argument('-s',
'--source',
type=str,
help='file path/sql script')
parser.add_argument('-n', '--name', type=str, help='output file name')
parser.add_argument('-k',
'--topk',
type=int,
default=500,
help='top k words')
parser.add_argument('-w',
'--word_category',
default='v,vd,vn,vf,a,ad,an,ag,al',
type=str,
help='word category')
args = parser.parse_args()
source_from = args.type
source = args.source
name = args.name
k_num = args.topk
word_category = args.word_category.split(',')
print word_category
if source_from == 'db':
comments_df = preprocess.get_data_from_db(source)
elif source_from == 'file':
comments_df = preprocess.read_comment_from_file(source)
else:
return
comments_list = list(comments_df['comment'].values)
cutted, word_category_list = utils.word_cut(comments_list)
word_weight_flag = utils.tfidf(cutted, word_category_list, 'tfidf_' + name)
key_word = utils.get_topK(word_weight_flag,
'top_k_' + name,
k=k_num,
category_list=word_category)
def get_nps_attractiveness(faces):
def parse_np(index):
np = ''
closing = 0
for elem in tree[index:]:
if elem[0] == '(':
closing += 1
else:
match = re.findall("\)", elem)
np += elem.replace(')', '').strip() + ' '
closing -= len(match)
if closing <= 0:
break
return np.replace('-LRB- ', '(').replace(' -RRB-', ')').replace('-LRB-', '(').replace('-RRB-', ')').strip().lower()
nps = []
nps_attractiveness = {}
for face in faces:
tree = face['parse'].split()
for i, elem in enumerate(tree):
if elem == '(NP':
np = parse_np(i)
nps.append(np)
attract = face['responses']['attractive'].lower()
if attract not in nps_attractiveness:
nps_attractiveness[attract] = []
nps_attractiveness[attract].append(np)
print 10 * '-'
print 'Most frequent descriptions per attractiveness'
nps_attractiveness = utils.tfidf(nps_attractiveness, 10)
nps = nltk.FreqDist(nps)
for attract in nps_attractiveness:
print 'Race: ', attract
print 10 * '-'
for np in nps_attractiveness[attract]:
print np[0], np[1], nps[np[0]]
print 10 * '-'
def common_words_faces_typicality(data):
typicality = set(map(lambda face: face['responses']['typical'], data))
voc, gvoc = {}, []
for typical in typicality:
voc[typical] = []
for face in filter(lambda face: face['responses']['typical'] == typical, data):
for i, word in enumerate(face['tokens']):
if 'NN' in face['pos_tag'][i] or 'JJ' in face['pos_tag'][i]:
voc[typical].append(word.lower())
gvoc.append(word.lower())
tfidf = utils.tfidf(voc, 10)
gvoc = nltk.FreqDist(gvoc)
print 'Most common words in Faces per typicality:'
for typical in typicality:
print typical
for word in tfidf[typical]:
print word, gvoc[word[0]]
print 20 * '-'
def common_words_faces_attractiveness(data):
attractiveness = set(map(lambda face: face['responses']['attractive'], data))
voc, gvoc = {}, []
for attract in attractiveness:
voc[attract] = []
for face in filter(lambda face: face['responses']['attractive'] == attract, data):
for i, word in enumerate(face['tokens']):
if 'NN' in face['pos_tag'][i] or 'JJ' in face['pos_tag'][i]:
voc[attract].append(word.lower())
gvoc.append(word.lower())
tfidf = utils.tfidf(voc, 10)
gvoc = nltk.FreqDist(gvoc)
print 'Most common words in Faces per attractiveness:'
for attract in attractiveness:
print attract
for word in tfidf[attract]:
print word, gvoc[word[0]]
print 20 * '-'
def common_words_guesses(data):
conditions = map(lambda x: x['condition'], data)
voc, gvoc = {}, []
for condition in set(conditions):
voc[condition] = []
f = filter(lambda guess: guess['condition'] == condition, data)
for guess in f:
for i, word in enumerate(guess['tokens']):
if 'NN' in guess['pos_tag'][i] or 'NN' in guess['pos_tag'][i]:
voc[condition].append(word.lower())
gvoc.append(word.lower())
# voc[condition] = nltk.FreqDist(voc[condition])
tfidf = utils.tfidf(voc, 10)
gvoc = nltk.FreqDist(gvoc)
print 'Most common words in Guesses per condition:'
for condition in tfidf:
print 'Condition:', condition
for word in tfidf[condition]:
print word, gvoc[word[0]]
print 20 * '-'
# add ratio features
data['ratio_title'] = data['word_in_title']/data['len_of_query']
data['ratio_description'] = data['word_in_description']/data['len_of_query']
data['attribute'] = data['search_term']+"\t"+data['brand']
data['ratio_brand'] = data['word_in_brand']/data['len_of_query']
data['ratio_attr'] = data['word_in_attr']/data['len_of_query']
data['ratio_attr_title'] = data['word_in_attr_title']/data['len_of_query']
data['brand_ratio'] = data['word_in_brand']/data['len_of_brand']
data['attr_ratio'] = data['word_in_attr']/data['len_of_attr']
data['attr_title_ratio'] = data['word_in_attr_title']/data['len_of_attr_title']
data['title_ratio'] = data['word_in_title']/data['len_of_title']
data['description_ratio'] = data['word_in_description']/data['len_of_description']
# add bm25 features
desc_tf, desc_idf, desc_length, desc_ave_length = utils.tfidf(data, 'product_description')
data['desc_BM25'] = data.apply(lambda x: utils.BM25_score(
x, desc_tf, desc_idf, desc_length, desc_ave_length), axis=1)
attr_tf, attr_idf, attr_length, attr_ave_length = utils.tfidf(data, 'attr')
data['attr_BM25'] = data.apply(lambda x: utils.BM25_score(
x, attr_tf, attr_idf, attr_length, attr_ave_length), axis=1)
title_tf, title_idf, title_length, title_ave_length = utils.tfidf(data, 'product_title')
data['title_BM25'] = data.apply(lambda x: utils.BM25_score(
x, title_tf, title_idf, title_length, title_ave_length), axis=1)
attr_title_tf, attr_title_idf, attr_title_length, attr_title_ave_length = utils.tfidf(data, 'attr_title')
data['attr_title_BM25'] = data.apply(lambda x: utils.BM25_score(
x, attr_title_tf, attr_title_idf, attr_title_length, attr_title_ave_length), axis=1)
brand_tf, brand_idf, brand_length, brand_ave_length = utils.tfidf(data, 'brand')
data['brand_BM25'] = data.apply(lambda x: utils.BM25_score(
x, brand_tf, brand_idf, brand_length, brand_ave_length), axis=1)
def get_data():
node_information = pd.read_csv(
'node_information.csv',
header=None,
names=['ID', 'Year', 'Title', 'Authors', 'Journal', 'Abstract'])
node_information = pd.read_csv(
'node_information.csv',
header=None,
names=['ID', 'Year', 'Title', 'Authors', 'Journal', 'Abstract'])
training_set = pd.read_csv('training_set.txt',
header=None,
names=['Target', 'Source', 'Edge'],
delim_whitespace=True)
#testing_set = pd.read_csv('testing_set.txt', header=None, names=['Target', 'Source'], delim_whitespace=True)
print("Get valid IDs")
valid_ids = set()
for element in training_set.values:
valid_ids.add(element[0])
valid_ids.add(element[1])
print("Select valid indices from valid IDs")
index_valid = [
i for i, element in enumerate(node_information.values)
if element[0] in valid_ids
]
node_info = node_information.iloc[index_valid]
print("Get index for nodes")
IDs = []
ID_pos = {}
for element in node_info.values:
ID_pos[element[0]] = len(IDs)
IDs.append(element[0])
print("Add ID column for merging")
training_set['Target_ID'] = training_set.apply(lambda row: ID_pos[row[0]],
axis=1)
training_set['Source_ID'] = training_set.apply(lambda row: ID_pos[row[1]],
axis=1)
print("Merge")
train = pd.merge(training_set,
node_information,
how='left',
left_on='Target_ID',
right_index=True)
train = pd.merge(train,
node_information,
how='left',
left_on='Source_ID',
right_index=True,
suffixes=['_target', '_source'])
#train.to_csv('train_blank.csv', index=False)
#train = pd.read_csv('train_blank.csv')
#train.to_csv('train.csv', index=False)
t = time()
print("Add overlapping titles")
train['Overlap_title'] = train.apply(lambda row: overlap(row, 'Title'),
axis=1)
print("Add common_authors")
train['Common_authors'] = train.apply(lambda row: common(row, 'Authors'),
axis=1)
print("Add overlapping abstract")
train['Overlap_abstract'] = train.apply(
lambda row: overlap(row, 'Abstract'), axis=1)
print("Date difference")
train['Date_diff'] = (train['Year_source'] - train['Year_target']).abs()
print(time() - t)
#train.to_csv('train_basic.csv', index=False)
#print("Loading set")
#train = pd.read_csv('train_basic.csv')
#print("Loaded")
t = time()
print("Tfidf")
tfidf_vect = TfidfVectorizer(stop_words="english")
abstracts_source = train['Abstract_source'].values
abstracts_target = train['Abstract_target'].values
all_abstracts = np.concatenate((abstracts_source, abstracts_target))
tfidf_vect.fit(all_abstracts)
print("tf_idf fitted")
vect_source = tfidf_vect.transform(abstracts_source)
print("source transformed")
vect_target = tfidf_vect.transform(abstracts_target)
print("target transformed")
train['Tfidf_cosine_abstracts_nolim'] = tfidf(vect_source, vect_target)
print(time() - t)
#train.to_csv('train_basic_tfidf.csv', index=False)
#train = pd.read_csv('train_basic_tfidf.csv')
t = time()
print("Tfidf")
tfidf_vect = TfidfVectorizer(stop_words="english")
titles_source = train['Title_source'].values
titles_target = train['Title_target'].values
all_abstracts = np.concatenate((titles_source, titles_target))
tfidf_vect.fit(all_abstracts)
print("tf_idf fitted")
vect_source = tfidf_vect.transform(titles_source)
print("source transformed")
vect_target = tfidf_vect.transform(titles_target)
print("target transformed")
train['Tfidf_cosine_titles'] = tfidf(vect_source, vect_target)
print(time() - t)
#train.to_csv('train_basic_tfidf_title.csv', index=False)
#train = pd.read_csv('train_basic_tfidf_title.csv')
return train
def embed_posts(self, min_count, allowed_pos, stopwords,
preprocess_option):
if self.option == 'tfidf+lsi':
logging.info(
'CBF - Using TFIDF vectors, LSI for dimension reduction')
data_words, note_ids, id2word, corpus = utils.preprocess(
self.all_note_contents, min_count, allowed_pos, stopwords,
preprocess_option)
#self.post_bows = pd.DataFrame(data={'NoteID':note_ids,'BoW':data_words}).set_index('NoteID')
logging.debug('[CBF] - %d non-empty posts', len(corpus))
logging.debug('[CBF] - %s extracted %d tokens/phrases',
preprocess_option, len(id2word))
tfidf_matrix, tf_dicts, post_appear_dict = utils.tfidf(data_words)
word2id = {v: k for k, v in id2word.items()}
tfidf_corpus = [[(word2id[pair[0]], pair[1])
for pair in post.items()]
for post in tfidf_matrix]
model = LsiModel(tfidf_corpus,
num_topics=self.feature_size,
id2word=id2word)
for i, post_tfidf in enumerate(tfidf_corpus):
note_id = note_ids[i]
if not note_id in self.items:
post_repr = model[post_tfidf]
self.items[note_id] = [
p[1] for p in post_repr
if len(post_repr) == self.feature_size
]
self.model = model
return True
elif self.option == 'tfidf+keywords+lsi':
logging.info(
'CBF - Using TFIDF vectors on only 1/3 keywords of each post, LSI for dimension reduction'
)
data_words, note_ids, id2word, corpus = utils.preprocess(
self.all_note_contents, min_count, allowed_pos, stopwords,
preprocess_option)
#self.post_bows = pd.DataFrame(data={'NoteID':note_ids,'BoW':data_words}).set_index('NoteID')
print('CBF - %d non-empty posts' % len(corpus))
print('CBF - %s BoW extracted %d tokens/phrases' %
(preprocess_option, len(id2word)))
tfidf_matrix, tf_dicts, post_appear_dict = utils.tfidf(data_words)
keywords = {
i: utils.get_top_tfidfs(
tfidf_matrix[i],
len(tfidf_matrix[i]) //
3) # TODO: have over-threshold phrases as the keyword
for i, m in enumerate(tfidf_matrix)
}
word2id = {v: k for k, v in id2word.items()}
tfidf_corpus = [[(word2id[pair[0]], pair[1])
for pair in post.items()] for post in keywords]
model = LsiModel(tfidf_corpus,
num_topics=self.feature_size,
id2word=id2word)
for i, post_tfidf in enumerate(tfidf_corpus):
note_id = note_ids[i]
self.items[note_id] = model[post_tfidf]
self.model = model
return True
elif self.option == 'KCB':
from gensim import models
data_words, note_ids, id2word, corpus = utils.preprocess(
self.all_note_contents, min_count, allowed_pos, stopwords,
preprocess_option)
tfidf = models.TfidfModel(corpus)
corpus_tfidf = tfidf[corpus]
corpus_tfidf_lst = []
for doc in corpus_tfidf:
doc.sort(key=operator.itemgetter(1))
doc = doc[-len(doc) // self.top_ratio:]
corpus_tfidf_lst.append(doc)
# print('kt',corpus_tfidf_lst)
lsi_model = models.LsiModel(corpus_tfidf_lst,
id2word=id2word,
num_topics=self.feature_size
) # initialize an LSI transformation
corpus_lsi = lsi_model[corpus_tfidf_lst]
for i, post_repr in enumerate(corpus_lsi):
note_id = note_ids[i]
self.items[note_id] = [
p[1] for p in post_repr
if len(post_repr) == self.feature_size
]
self.model = lsi_model
return True
elif self.option == 'word_emb+wmd':
# Load pretrained FastText embeddings
self.model = FastText.load('cleaned_data/all_notes_model')
# print('using model:',self.model)
# Cannot get post embeddings from word embeddings
# It cannot stand alone as a CBF method
return False
elif self.option == 'keyword+word_emb+wmd':
# Load pretrained FastText embeddings
self.model = FastText.load('cleaned_data/all_notes_model')
# print('using model:',self.model)
# Cannot get post embeddings from word embeddings
# It cannot stand alone as a CBF method
return False
elif self.option == 'keyword+ft_word_emb+sif': # Using SIF on keyword --> sentence embedding
data_words, note_ids, id2word, corpus = utils.preprocess(
self.all_note_contents, min_count, allowed_pos, stopwords,
preprocess_option)
self.post_bows = pd.DataFrame(data={
'NoteID': note_ids,
'BoW': data_words
}).set_index('NoteID')
logging.debug('CBF - %d non-empty posts', len(corpus))
logging.debug('CBF - %s BoW extracted %d tokens/phrases',
preprocess_option, len(id2word))
sentence_list = []
note_ids_lookup = []
for note_id, post in self.post_bows.iterrows():
word_list = []
for word in post:
word_emd = self.model[word]
word_list.append(Word(word, word_emd))
if len(word_list
) > 0: # did we find any words (not an empty set)
sentence_list.append(Sentence(word_list))
note_ids_lookup.append(
note_id
) # in case there are some posts of 0 length, thus not included in this
sentence_embs = {}
sentence_vectors = sentence_to_vec(
sentence_list,
self.feature_size) # all vectors converted together
if len(sentence_vectors) == len(sentence_list):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[note_ids_lookup[i]] = sentence_vectors[i]
self.items = sentence_embs
return True
elif self.option == 'ft_word_emb+sif': # Using SIF on whole text --> sentence embedding
data_words, note_ids, id2word, corpus = utils.preprocess_raw(
self.all_note_contents)
self.post_bows = pd.DataFrame(data={
'NoteID': note_ids,
'BoW': data_words
}).set_index('NoteID')
sentence_list = []
note_ids_lookup = []
for note_id, post in self.post_bows.iterrows():
word_list = []
for word in post:
word_emd = self.model[word]
word_list.append(Word(word, word_emd))
if len(word_list
) > 0: # did we find any words (not an empty set)
sentence_list.append(Sentence(word_list))
note_ids_lookup.append(
note_id
) # in case there are some posts of 0 length, thus not included in this
sentence_embs = {}
sentence_vectors = sentence_to_vec(
sentence_list,
self.feature_size) # all vectors converted together
if len(sentence_vectors) == len(sentence_list):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[note_ids_lookup[i]] = sentence_vectors[i]
self.items = sentence_embs
return True
elif self.option == 'bert_word_emb+sif':
tokenizer = BertTokenizer.from_pretrained('bert-base-uncased',
max_len=512)
#nids = [nid for nid in self.all_note_contents.NoteID.values if nid not in self.items.keys()]
note_ids = self.all_note_contents.NoteID.to_list()
MAX_LEN = 512
tokenized_texts_list = []
indexed_tokens_list = []
attention_masks = []
for text in self.all_note_contents.Contents.values:
marked_text = "[CLS] " + text + " [SEP]"
tokenized_text = tokenizer.tokenize(marked_text)
tokenized_texts_list.append(tokenized_text)
indexed_tokens_list.append(
tokenizer.convert_tokens_to_ids(tokenized_text))
input_ids_list = pad_sequences(indexed_tokens_list,
maxlen=MAX_LEN,
dtype="long",
truncating="post",
padding="post")
for seq in input_ids_list:
seq_mask = [int(float(i > 0)) for i in seq]
attention_masks.append(seq_mask)
# Convert inputs to PyTorch tensors
tokens_tensor = torch.tensor(input_ids_list)
segments_tensors = torch.tensor(attention_masks)
# Put the model in "evaluation" mode, meaning feed-forward operation.
self.model.eval()
with torch.no_grad():
encoded_layers, _ = model(tokens_tensor, segments_tensors)
emb_layers = encoded_layers[-4:]
sum_layers = torch.stack(emb_layers, dim=0).sum(dim=0)
sentence_word_embs = {}
for i in range(len(tokenized_texts_list)):
sentence_word_embs[
note_ids[i]] = sum_layers[i][:len(tokenized_texts_list[i])]
tokenized_texts_ = {
nid: tokenized_texts_list[i]
for i, nid in enumerate(note_ids)
}
sentence_list = []
note_ids_lookup = []
for note_id in note_ids:
#print(note_id)
word_list = []
for j in range(len(sentence_word_embs[note_id])):
word_emb = sentence_word_embs[note_id][j]
# Add here if to use only keywords
word_text = tokenized_texts_[note_id][j]
word_list.append(Word(word_text, word_emb.numpy()))
if len(word_list
) > 0: # did we find any words (not an empty set)
sentence_list.append(Sentence(word_list))
note_ids_lookup.append(
note_id
) # in case there are some posts of 0 length, thus not included in this
#print('wordlist',len(word_list))
sentence_embs = {}
sentence_vectors = sentence_to_vec(
sentence_list,
self.feature_size) # all vectors converted together
if len(sentence_vectors) == len(sentence_list):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[note_ids_lookup[i]] = sentence_vectors[i]
self.items = sentence_embs
return True
elif self.option == 'sentence_emb':
note_ids = self.all_note_contents.NoteID.to_list()
all_note_contents = self.all_note_contents['Contents'].to_list()
sentence_embs = {}
sentence_vectors = self.model[all_note_contents]
if len(sentence_vectors) == len(all_note_contents):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[
note_ids_lookup[i]] = sentence_vectors[i].numpy()
self.items = sentence_embs
return True
elif self.option == 'sentence_emb_precomputed':
return True
def precompute_similarity(self, model_path, option, feature_size):
all_note_contents = self.all_note_contents.Contents.to_list()
all_note_nids = self.all_note_contents.NoteID.to_list()
similarity_matrix = {}
if option == 'ft_word_emd+sif':
#'cleaned_data/ft_model_incr'
# Load pretrained FastText embeddings
model = FastText.load(model_path)
logging.info('[Preprocessor] Using model: %s', str(model))
similarity_matrix = {}
nlp = spacy.load("en_core_web_sm")
note_ids = all_note_contents['NoteID'].values
contents = all_note_contents['Contents'].values
data_words = [[token.text for token in nlp(content)]
for note_id, content in zip(note_ids, contents)]
post_tokens = pd.DataFrame(data={
'NoteID': note_ids,
'Tokens': data_words
}).set_index('NoteID')
sentence_list = []
sentence_embs = {}
for note_id, post in post_tokens.iterrows():
word_list = []
for word in post.values[0]:
word_emd = model[word]
word_list.append(Word(word, word_emd))
if len(word_list
) > 0: # did we find any words (not an empty set)
sentence_list.append(Sentence(word_list))
sentence_embs[note_id] = sentence_to_vec(
sentence_list, feature_size)
# Compute post-wise cosine similarities
for note_id1, emb1 in sentence_embs.items():
for note_id2, emb2 in sentence_embs.items():
if note_id1 != note_id2 and (
note_id2, note_id1) not in similarity_matrix:
# apply l2-distance
#utils.l2_sim()
# apply cosine distance
sim = utils.cosine_sim(emb1[0], emb2[0])
similarity_matrix[(note_id1, note_id2)] = sim
similarity_matrix[(note_id2, note_id1)] = sim
return similarity_matrix
elif option == 'bert_word_emb+sif':
# for BERT
import torch
from pytorch_pretrained_bert import BertTokenizer, BertModel, BertForMaskedLM
from keras.preprocessing.sequence import pad_sequences
tokenizer = BertTokenizer.from_pretrained('bert-base-uncased',
max_len=128)
MAX_LEN = 512
tokenized_texts_list = []
indexed_tokens_list = []
attention_masks = []
for text in all_note_contents.Contents.values:
marked_text = "[CLS] " + text + " [SEP]"
tokenized_text = tokenizer.tokenize(marked_text)
tokenized_texts_list.append(tokenized_text)
indexed_tokens_list.append(
tokenizer.convert_tokens_to_ids(tokenized_text))
input_ids_list = pad_sequences(indexed_tokens,
maxlen=MAX_LEN,
dtype="long",
truncating="post",
padding="post")
for seq in input_ids:
seq_mask = [int(float(i > 0)) for i in seq]
attention_masks.append(seq_mask)
# Convert inputs to PyTorch tensors
tokens_tensor = torch.tensor(input_ids_list)
segments_tensors = torch.tensor(attention_masks)
# Load pre-trained model (weights)
model = BertModel.from_pretrained('bert-base-uncased')
# Put the model in "evaluation" mode, meaning feed-forward operation.
model.eval()
with torch.no_grad():
encoded_layers, _ = model(tokens_tensor, segments_tensors)
emb_layers = encoded_layers[-4:]
sum_layers = torch.stack(emb_layers,
dim=0).sum(dim=0) # 434*512*768
sentence_word_embs = {}
for i in range(len(tokenized_texts_list)):
sentence_word_embs[
nids[i]] = sum_layers[i][:len(tokenized_texts_list[i])]
# Keep a look up dictionary [note id] --> text content
tokenized_texts_ = {
nid: tokenized_texts_list[i]
for i, nid in enumerate(nids)
}
embedding_size = feature_size # Set the shape of the sentence/post embeddings
sentence_list = []
note_ids_lookup = []
for note_id in nids:
#print(note_id)
word_list = []
for j in range(len(sentence_word_embs[note_id])):
word_emb = sentence_word_embs[note_id][j]
# Add here if to use only keywords
word_text = tokenized_texts_[note_id][j]
word_list.append(Word(word_text, word_emb.numpy()))
if len(word_list) > 0:
sentence_list.append(Sentence(word_list))
note_ids_lookup.append(
note_id
) # in case there are some posts of 0 length, thus not included in this
# Encode sentences/posts with embeddigns
sentence_embs = {}
sentence_vectors = sentence_to_vec(
sentence_list,
embedding_size) # all vectors converted together
if len(sentence_vectors) == len(sentence_list):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[note_ids_lookup[i]] = sentence_vectors[i]
# Compute post-wise cosine similarities
for note_id1, emb1 in sentence_embs.items():
for note_id2, emb2 in sentence_embs.items():
if note_id1 != note_id2 and (
note_id2, note_id1) not in similarity_matrix:
# apply l2-distance
#utils.l2_sim()
# apply cosine distance
sim = utils.cosine_sim(emb1[0], emb2[0])
similarity_matrix[(note_id1, note_id2)] = sim
similarity_matrix[(note_id2, note_id1)] = sim
return similarity_matrix, sentence_embs
elif option == 'sentence_emb':
import tensorflow as tf
import tensorflow_hub as hub
embed = hub.load(model_path)
logging.info(
'[Preprocessor] using model: universal-sentence-encoder-1')
sentence_embs = {}
sentence_vectors = embed(all_note_contents)
if len(sentence_vectors) == len(all_note_contents):
for i in range(len(sentence_vectors)):
# map: note_id -> vector
sentence_embs[
all_note_nids[i]] = sentence_vectors[i].numpy()
#corr = np.inner(sentence_vectors, sentence_vectors)
#cosine_similarities = tf.reduce_sum(tf.multiply(sentence_vectors, sentence_vectors), axis=1)
#clip_cosine_similarities = tf.clip_by_value(cosine_similarities, -1.0, 1.0)
#sim_scores = 1.0 - tf.acos(clip_cosine_similarities)
#print(sim_scores)
#for i, sims in enumerate(sim_scores):
# for j, sim in enumerate(sims):
## note_id1 = all_note_nids[i]
# note_id2 = all_note_nids[j]
# if not note_id1==note_id2:
# similarity_matrix[(note_id1, note_id2)] = sim
# Compute post-wise cosine similarities
for note_id1, emb1 in sentence_embs.items():
for note_id2, emb2 in sentence_embs.items():
if note_id1 != note_id2 and (
note_id2, note_id1) not in similarity_matrix:
# apply l2-distance
#utils.l2_sim()
# apply cosine distance
sim = utils.cosine_sim(emb1, emb2)
similarity_matrix[(note_id1, note_id2)] = sim
similarity_matrix[(note_id2, note_id1)] = sim
return similarity_matrix, sentence_embs
elif option == 'tfidf+lsi':
logging.info(
'[Preprocessor] using TFIDF vectors, LSI for dimension reduction'
)
data_words, note_ids, id2word, corpus = utils.preprocess(
self.all_note_contents, 10, ['NOUN', 'VERB'], STOP_WORDS,
'tokens_phrases')
#self.post_bows = pd.DataFrame(data={'NoteID':note_ids,'BoW':data_words}).set_index('NoteID')
logging.debug('[Preprocessor] - %d non-empty posts', len(corpus))
logging.debug('[Preprocessor] - %s extracted %d tokens/phrases',
'tokens_phrases', len(id2word))
tfidf_matrix, tf_dicts, post_appear_dict = utils.tfidf(data_words)
word2id = {v: k for k, v in id2word.items()}
tfidf_corpus = [[(word2id[pair[0]], pair[1])
for pair in post.items()]
for post in tfidf_matrix]
model = LsiModel(tfidf_corpus,
num_topics=feature_size,
id2word=id2word)
sentence_embs = {}
for i, post_tfidf in enumerate(tfidf_corpus):
note_id = note_ids[i]
if not note_id in sentence_embs:
post_repr = model[post_tfidf]
#print(post_repr)
#print(i)
sentence_embs[note_id] = np.array([
p[1] for p in post_repr
if len(post_repr) == feature_size
])
# Compute post-wise cosine similarities
for note_id1, emb1 in sentence_embs.items():
for note_id2, emb2 in sentence_embs.items():
if note_id1 != note_id2 and (
note_id2, note_id1) not in similarity_matrix:
if len(emb1) and len(emb2):
# apply l2-distance
#utils.l2_sim()
# apply cosine distance
sim = utils.cosine_sim(emb1, emb2)
similarity_matrix[(note_id1, note_id2)] = sim
similarity_matrix[(note_id2, note_id1)] = sim
return similarity_matrix, sentence_embs