def prepare_dev(prefix, dev_filename, vocab, download = False):
print("Downloading {}".format(dev_filename))
# Don't check file size, since we could be using other datasets
if download:
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
else:
dev_dataset = data_from_json(dev_filename)
context_data, question_data, question_uuid_data = read_dataset(dev_data, 'dev', vocab)
return context_data, question_data, question_uuid_data
def get_json_data(data_filename):
"""
Read the contexts and questions from a .json file (like dev-v1.1.json)
Returns:
qn_uuid_data: list (length equal to dev set size) of unicode strings like '56be4db0acb8001400a502ec'
context_token_data, qn_token_data: lists (length equal to dev set size) of lists of strings (no UNKs, unpadded)
"""
# Check the data file exists
if not os.path.exists(data_filename):
raise Exception("JSON input file does not exist: %s" % data_filename)
# Read the json file
print("Reading data from %s..." % data_filename)
data = data_from_json(data_filename)
# Get the tokenized contexts and questions, and unique question identifiers
print("Preprocessing data from %s..." % data_filename)
qn_uuid_data, context_token_data, qn_token_data = preprocess_dataset(data)
data_size = len(qn_uuid_data)
assert len(context_token_data) == data_size
assert len(qn_token_data) == data_size
print("Finished preprocessing. Got %i examples from %s" %
(data_size, data_filename))
return qn_uuid_data, context_token_data, qn_token_data
def process_dev_json_to_files():
# dev_path example data/squad/dev-v1.1.json
download_prefix = os.path.dirname(os.path.abspath(
FLAGS.dev_path)) # data/squad/
dev_filename = os.path.basename(FLAGS.dev_path) # "dev-v1.1.json"
# relative path to save the data
print("Downloading datasets into {}".format(download_prefix))
print("Preprocessing datasets into {}".format(FLAGS.data_dir))
if not os.path.exists(download_prefix):
os.makedirs(download_prefix)
if not os.path.exists(FLAGS.data_dir):
os.makedirs(FLAGS.data_dir)
maybe_download(squad_base_url, dev_filename, download_prefix, None)
# Read data from dev json file
dev_data = data_from_json(os.path.join(download_prefix, dev_filename))
# write data out to FLAGS.data_dir location
dev_num_questions, dev_num_answers = read_write_dataset(
dev_data, 'dev', FLAGS.data_dir)
dev_path = os.path.join(FLAGS.data_dir, "dev")
## generate tokens
x_dev_dis_path = dev_path + ".ids.context"
y_dev_ids_path = dev_path + ".ids.question"
qa_data.data_to_token_ids(dev_path + ".context", x_dev_dis_path,
FLAGS.vocab_path)
qa_data.data_to_token_ids(dev_path + ".question", y_dev_ids_path,
FLAGS.vocab_path)
def prepare_dev(prefix, dev_filename, vocab):
# Don't check file size, since we could be using other datasets
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
context_data, question_data, question_uuid_data, context_text = read_dataset(
dev_data, 'dev', vocab)
return context_data, question_data, question_uuid_data, context_text
def get_json_data(data_filename):
"""
Read the contexts and questions from a .json file (like dev-v1.1.json)
Returns:
qn_uuid_data: list (length equal to dev set size) of unicode strings like '56be4db0acb8001400a502ec'
context_token_data, qn_token_data: lists (length equal to dev set size) of lists of strings (no UNKs, unpadded)
"""
# Check the data file exists
if not os.path.exists(data_filename):
raise Exception("JSON input file does not exist: %s" % data_filename)
# Read the json file
print "Reading data from %s..." % data_filename
data = data_from_json(data_filename)
# Get the tokenized contexts and questions, and unique question identifiers
print "Preprocessing data from %s..." % data_filename
qn_uuid_data, context_token_data, qn_token_data = preprocess_dataset(data)
data_size = len(qn_uuid_data)
assert len(context_token_data) == data_size
assert len(qn_token_data) == data_size
print "Finished preprocessing. Got %i examples from %s" % (data_size, data_filename)
return qn_uuid_data, context_token_data, qn_token_data
def prepare_dev(prefix, dev_filename, vocab):
# Don't check file size, since we could be using other datasets
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
context_data, question_data, question_uuid_data = read_dataset(dev_data, 'dev', vocab)
return context_data, question_data, question_uuid_data
def prepare_dev(prefix, dev_filename, vocab):
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
context_data, question_data, question_uuid_data = read_dataset(
dev_data, 'dev', vocab)
def normalize(dat):
return map(lambda tok: map(int, tok.split()), dat)
context_data = normalize(context_data)
question_data = normalize(question_data)
return context_data, question_data, question_uuid_data
def prepare_dev(prefix, dev_filename, vocab):
# Don't check file size, since we could be using other datasets
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
# remove answer
# if FLAGS.eval_on_train:
# context_tokens_data, context_data, question_tokens_data, question_data, question_uuid_data, s_labels, e_labels, true_answers = read_dataset(dev_data, 'train', vocab)
# return context_tokens_data, context_data, question_tokens_data, question_data, question_uuid_data, s_labels, e_labels, true_answers
context_tokens_data, context_data, question_tokens_data, question_data, question_uuid_data = read_dataset(
dev_data, 'dev', vocab)
return context_tokens_data, context_data, question_tokens_data, question_data, question_uuid_data
def prepare_dev(prefix, dev_filename, vocab):
# Don't check file size, since we could be using other datasets
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
context_data, question_data, question_uuid_data = read_dataset(
dev_data, 'dev', vocab)
def normalize(dat):
return list(map(lambda tok: list(map(int, tok.split())), dat))
context_data = normalize(context_data)
question_data = normalize(question_data)
return context_data, question_data, question_uuid_data
def get_question_context_data(question_string, context_json_file):
context_string = data_from_json(context_json_file)['context']
context = str(context_string) # string
# The following replacements are suggested in the paper
# BidAF (Seo et al., 2016)
context = context.replace("''", '" ')
context = context.replace("``", '" ')
context_tokens = tokenize(context) # list of strings (lowercase)
context = context.lower()
question = str(question_string) # string
question_tokens = tokenize(question) # list of strings
# also get the question_uuid
question_uuid = len(question_tokens)
return [question_uuid], [context_tokens], [question_tokens]
def get_json_data(data_filename):
"""
Read the contexts and questions from a .json file (like dev-v1.1.json)
"""
if not os.path.exists(data_filename):
raise Exception("JSON input file does not exist: %s" % data_filename)
print("Reading data from %s..." % data_filename)
data = data_from_json(data_filename)
print("Preprocessing data from %s..." % data_filename)
qn_uuid_data, context_token_data, qn_token_data = preprocess_dataset(data)
data_size = len(qn_uuid_data)
assert len(context_token_data) == data_size
assert len(qn_token_data) == data_size
print("Finished preprocessing. Got %i examples from %s" %
(data_size, data_filename))
return qn_uuid_data, context_token_data, qn_token_data
def main(_):
vocab, rev_vocab = initialize_vocab(FLAGS.vocab_path)
embed_path = FLAGS.embed_path or pjoin("data", "squad", "glove.trimmed.{}.npz".format(FLAGS.embedding_size))
global_train_dir = '/tmp/cs224n-squad-train'
# Adds symlink to {train_dir} from /tmp/cs224n-squad-train to canonicalize the
# file paths saved in the checkpoint. This allows the model to be reloaded even
# if the location of the checkpoint files has moved, allowing usage with CodaLab.
# This must be done on both train.py and qa_answer.py in order to work.
if not os.path.exists(FLAGS.train_dir):
os.makedirs(FLAGS.train_dir)
if os.path.exists(global_train_dir):
os.unlink(global_train_dir)
#os.symlink(os.path.abspath(FLAGS.train_dir), global_train_dir)
train_dir = global_train_dir
if not os.path.exists(FLAGS.log_dir):
os.makedirs(FLAGS.log_dir)
file_handler = logging.FileHandler(pjoin(FLAGS.log_dir, "log.txt"))
logging.getLogger().addHandler(file_handler)
print(vars(FLAGS))
with open(os.path.join(FLAGS.log_dir, "flags.json"), 'w') as fout:
json.dump(FLAGS.__flags, fout)
# ========= Download Dataset json =========
# You can change this code to load dataset in your own way
#dev_dirname = os.path.dirname(os.path.abspath(FLAGS.dev_path))
#dev_filename = os.path.basename(FLAGS.dev_path)
#_, _, _ = prepare_dev(dev_dirname, dev_filename, vocab)
# ========= Process input json =========
# for codalab
prefix = os.path.join("data", "squad")
# writes dev.answer, dev.context, dev.question, dev.span
dev_path = FLAGS.dev_path
dev_filename = FLAGS.dev_path.split("/")[-1]
if FLAGS.download:
dev_data = data_from_json(os.path.join(prefix, dev_filename))
else:
dev_data = data_from_json(dev_filename)
dev_num_questions, dev_num_answers = read_write_dataset(dev_data, 'dev', prefix="")
print("Processed {} questions and {} answers in dev".format(dev_num_questions, dev_num_answers))
# writes dev.ids.context, dev.ids.question
vocab_path = pjoin(os.path.join("data", "squad"), "vocab.dat")
dev_deposit_path = pjoin(os.path.join("", ""), "dev") #pjoin(os.path.join("data", "squad"), "dev")
x_dis_path = dev_deposit_path + ".ids.context"
y_ids_path = dev_deposit_path + ".ids.question"
data_to_token_ids(dev_deposit_path + ".context", x_dis_path, vocab_path)
data_to_token_ids(dev_deposit_path + ".question", y_ids_path, vocab_path)
# load data sets
#Q_test, P_test, A_start_test, A_end_test, A_len_test, P_raw_test, A_raw_test, Q_len_test, P_len_test = load_data(os.path.join("data", "squad"), "dev") # for our purposes this is as test set.
Q_test, P_test, A_start_test, A_end_test, A_len_test, P_raw_test, A_raw_test, Q_len_test, P_len_test = load_data_home(dev_deposit_path) # for our purposes this is as test set.
question_uuid_data = []
with open(dev_deposit_path + ".quid") as f:
for line in f:
question_uuid_data.append((line))
# pad the data at load-time. So, we don't need to do any masking later!!!
# ref: https://keras.io/preprocessing/sequence/
# if len < maxlen, pad with specified val
# elif len > maxlen, truncate
QMAXLEN = FLAGS.QMAXLEN
PMAXLEN = FLAGS.PMAXLEN
Q_test = pad_sequences(Q_test, maxlen=QMAXLEN, value=PAD_ID, padding='post')
P_test = pad_sequences(P_test, maxlen=PMAXLEN, value=PAD_ID, padding='post')
A_start_test = pad_sequences(A_start_test, maxlen=PMAXLEN, value=0, padding='post')
A_end_test = pad_sequences(A_end_test, maxlen=PMAXLEN, value=0, padding='post')
test_data = zip(P_test, Q_test, P_len_test, Q_len_test, A_start_test, A_end_test, A_len_test, P_raw_test, A_raw_test, question_uuid_data)
# ========= Model-specific =========
# You must change the following code to adjust to your model
"""models = [ 'MPCM', 'COATT', 'COATT_fixed', 'COATT_mix','COATT_fixed_mix', 'COATT_fixed_200_mix'] # 'COATT_fixed_200', leave out to save time
predictions_start = {}; predictions_end = {}
with open("preds_dev.txt", "a") as f:
f.write("model" + "," + "pred_raw" + "," + "a_raw")
for model in models:
FLAGS.model_type = model
FLAGS.train_dir = "train/ensemble_train_" + model
train_dir = "train/ensemble_train_" + model
# define sizes etc. for different models.
if model == 'COATT_fixed_200' or model == 'COATT_fixed_200_mix' :
FLAGS.embedding_size = 200
FLAGS.lstm_units = 200
elif model == "MPCM_p100":
FLAGS.embedding_size = 100
FLAGS.lstm_units = 100
FLAGS.perspective_units = 100
else:
FLAGS.embedding_size = 100
FLAGS.lstm_units = 100
FLAGS.perspective_units = 50
with tf.Graph().as_default():
with tf.Session() as sess:
embeddings = np.load(FLAGS.data_dir + '/glove.trimmed.' + str(FLAGS.embedding_size) + '.npz')
pretrained_embeddings = embeddings['glove']
qa = QASystem(FLAGS, pretrained_embeddings, vocab_dim=len(vocab.keys()))
initialize_model(sess, qa, train_dir)
# get predicted start-end indices
a_s_l = []
a_e_l = []
f1 = exact_match = total = 0; answers = {}; prob_start = {}; prob_end = {}; p_raw_mapping= {}
prog = Progbar(target=1 + int(len(test_data) / FLAGS.batch_size))
for i, batch in enumerate(minibatches(test_data, FLAGS.batch_size, shuffle = False)):
batch_test = batch[:4]
(ys, ye) = qa.predict_on_batch(sess, *batch_test)
a_s = (np.argmax(ys, axis=1))
a_e = (np.argmax(ye, axis=1))
a_s_l = a_s_l + list(a_s)
a_e_l = a_e_l + list(a_e)
print(len(a_s))
for j in range(len(a_s)):
p_raw = batch[7][j]
a_raw = batch[8][j]
s = a_s[j]
e = a_e[j]
pred_raw = ' '.join(p_raw.split()[s:e + 1])
p_raw_mapping[batch[9][j].strip("\n")] = p_raw
#answers[batch[9][j].strip("\n")] = pred_raw.strip("\n")
prob_start[batch[9][j].strip("\n")] = ys[j]
prob_end[batch[9][j].strip("\n")] = ye[j]
f.write(model + "," + pred_raw + "," + a_raw )
prog.update(i + 1, [("processed", i + 1)])
predictions_start[model] = prob_start
predictions_end[model] = prob_end
f.close()
# save
dropPickle(predictions_start, "preds_start.pkl")
dropPickle(predictions_end, "preds_end.pkl")
dropPickle(p_raw_mapping, "p_raw_mapping.pkl")"""
predictions_start = loadPickle("preds_start.pkl")
predictions_end = loadPickle("preds_end.pkl")
p_raw_mapping = loadPickle("p_raw_mapping.pkl")
models = ['COATT_fixed_200']
#predictions_start = {}; predictions_end = {}
with open("preds_dev.txt", "a") as f:
f.write("model" + "," + "pred_raw" + "," + "a_raw")
for model in models:
FLAGS.model_type = model
FLAGS.train_dir = "train/ensemble_train_" + model
train_dir = "train/ensemble_train_" + model
if model == 'COATT_fixed_200' or model == 'COATT_fixed_200_mix' :
FLAGS.embedding_size = 200
FLAGS.lstm_units = 200
elif model == "MPCM_p100":
FLAGS.embedding_size = 100
FLAGS.lstm_units = 100
FLAGS.perspective_units = 100
else:
FLAGS.embedding_size = 100
FLAGS.lstm_units = 100
FLAGS.perspective_units = 50
with tf.Graph().as_default():
with tf.Session() as sess:
embeddings = np.load(FLAGS.data_dir + '/glove.trimmed.' + str(FLAGS.embedding_size) + '.npz')
pretrained_embeddings = embeddings['glove']
qa = QASystem(FLAGS, pretrained_embeddings, vocab_dim=len(vocab.keys()))
initialize_model(sess, qa, train_dir)
# get predicted start-end indices
a_s_l = []
a_e_l = []
f1 = exact_match = total = 0; answers = {}; prob_start = {}; prob_end = {}; p_raw_mapping= {}
prog = Progbar(target=1 + int(len(test_data) / FLAGS.batch_size))
for i, batch in enumerate(minibatches(test_data, FLAGS.batch_size, shuffle = False)):
batch_test = batch[:4]
(ys, ye) = qa.predict_on_batch(sess, *batch_test)
a_s = (np.argmax(ys, axis=1))
a_e = (np.argmax(ye, axis=1))
a_s_l = a_s_l + list(a_s)
a_e_l = a_e_l + list(a_e)
print(len(a_s))
for j in range(len(a_s)):
p_raw = batch[7][j]
a_raw = batch[8][j]
s = a_s[j]
e = a_e[j]
print(s,e)# comment this out
pred_raw = ' '.join(p_raw.split()[s:e + 1])
p_raw_mapping[batch[9][j].strip("\n")] = p_raw
#answers[batch[9][j].strip("\n")] = pred_raw.strip("\n")
prob_start[batch[9][j].strip("\n")] = ys[j]
prob_end[batch[9][j].strip("\n")] = ye[j]
f.write(model + "," + pred_raw + "," + a_raw )
prog.update(i + 1, [("processed", i + 1)])
predictions_start[model] = prob_start
predictions_end[model] = prob_end
f.close()
dropPickle(predictions_start, "preds_start.pkl")
dropPickle(predictions_end, "preds_end.pkl")
dropPickle(p_raw_mapping, "p_raw_mapping.pkl")
# combine the predictions of the two models (while making independent start, end predictions)
"""answers = {}
for qkey in predictions_start['MPCM'].keys():
ys = predictions_start['MPCM'][qkey]*predictions_start['COATT'][qkey]*predictions_start['COATT_fixed'][qkey]
ye = predictions_end['MPCM'][qkey]*predictions_end['COATT'][qkey]*predictions_end['COATT_fixed'][qkey]
s = (np.argmax(ys))
arr = ye.copy()
arr[0:s] = 0
e = (np.argmax(arr))
#e = (np.argmax(ye))
pred_raw = ' '.join(p_raw_mapping[qkey].split()[s:e + 1])
answers[qkey] = pred_raw.strip("\n")"""
# predict span with max predicted probability (make joint prediction rather than indepenedntly predicitng start and end indices)
answers = {}
for qkey in predictions_start['MPCM'].keys():
ys = predictions_start['MPCM'][qkey]*predictions_start['COATT'][qkey]*predictions_start['COATT_fixed'][qkey]\
*predictions_start['COATT_mix'][qkey]*predictions_start['COATT_fixed_mix'][qkey]\
*predictions_start['COATT_fixed_200_mix'][qkey]*predictions_start['COATT_fixed_200'][qkey] #to save time
ye = predictions_end['MPCM'][qkey]*predictions_end['COATT'][qkey]*predictions_end['COATT_fixed'][qkey]\
*predictions_end['COATT_mix'][qkey]*predictions_end['COATT_fixed_mix'][qkey]\
*predictions_end['COATT_fixed_200_mix'][qkey]*predictions_end['COATT_fixed_200'][qkey] #to save time
s = 0; e = 0; prodmax = 0
for si in range(0, len(ys)):
for ei in range(si, len(ye)):
prod = ys[si]*ye[ei]
if prod > prodmax:
s = si
e = ei
prodmax = prod
print(s,e, prodmax)
pred_raw = ' '.join(p_raw_mapping[qkey].split()[s:e + 1]); print(pred_raw)
answers[qkey] = pred_raw.strip("\n")
# write to json file to root dir
with io.open('dev-prediction.json', 'w', encoding='utf-8') as f:
f.write(unicode(json.dumps(answers, ensure_ascii=False)))
def expand_vocab(prefix, dev_filename, vocab, embd, raw_glove,
raw_glove_vocab):
# Don't check file size, since we could be using other datasets
dev_dataset = maybe_download(squad_base_url, dev_filename, prefix)
dev_data = data_from_json(os.path.join(prefix, dev_filename))
#context_data, question_data, question_uuid_data = read_dataset(dev_data, 'dev', vocab)
dataset = dev_data
context_data = []
query_data = []
question_uuid_data = []
tier = 'dev'
new_vocab = {}
found = 0
notfound = 0
for articles_id in tqdm(range(len(dataset['data'])),
desc="Preprocessing {}".format(tier)):
article_paragraphs = dataset['data'][articles_id]['paragraphs']
for pid in range(len(article_paragraphs)):
context = article_paragraphs[pid]['context']
# The following replacements are suggested in the paper
# BidAF (Seo et al., 2016)
context = context.replace("''", '" ')
context = context.replace("``", '" ')
context_tokens = tokenize(context)
qas = article_paragraphs[pid]['qas']
for qid in range(len(qas)):
question = qas[qid]['question']
question_tokens = tokenize(question)
question_uuid = qas[qid]['id']
#context_ids = [str(vocab.get(w, qa_data.UNK_ID)) for w in context_tokens]
#qustion_ids = [str(vocab.get(w, qa_data.UNK_ID)) for w in question_tokens]
#print(context_ids)
for w in context_tokens:
if not w in vocab:
if not w in new_vocab:
new_vocab[w] = 1
else:
new_vocab[w] += 1
notfound += 1
else:
found += 1
for w in question_tokens:
if not w in vocab:
if not w in new_vocab:
new_vocab[w] = 1
else:
new_vocab[w] += 1
notfound += 1
else:
found += 1
print('found/not found: {}/{}, {}% not found'.format(
found, notfound, 100 * notfound / float(found + notfound)))
print('New vocabulary:', len(new_vocab))
vocab_list = list(vocab.items())
vn = len(vocab_list)
for i in range((len(new_vocab))):
vocab_list.append((new_vocab.keys()[i], vn + i))
vocab = dict(vocab_list)
rev_vocab = dict([(x, y) for (y, x) in vocab_list])
#context_data.append(' '.join(context_ids))
#query_data.append(' '.join(qustion_ids))
#question_uuid_data.append(question_uuid)
#return context_data, question_data, question_uuid_data
_, dim = embd.shape
new_glove = np.random.randn(len(vocab), dim)
new_glove[:vn, :] = embd
found = 0
for i in range(vn, vn + (len(new_vocab))):
word = vocab_list[i][0]
if word in raw_glove_vocab:
found += 1
idx = raw_glove_vocab[word]
new_glove[i, :] = raw_glove[idx, :]
if word.capitalize() in raw_glove_vocab:
found += 1
idx = raw_glove_vocab[word.capitalize()]
new_glove[i, :] = raw_glove[idx, :]
if word.upper() in raw_glove_vocab:
found += 1
idx = raw_glove_vocab[word.upper()]
new_glove[i, :] = raw_glove[idx, :]
#from IPython import embed; embed()
print("{} unseen words found embeddings".format(found))
return vocab, rev_vocab, new_glove
def main(_):
vocab, rev_vocab = initialize_vocab(FLAGS.vocab_path)
embed_path = FLAGS.embed_path or pjoin("data", "squad", "glove.trimmed.{}.npz".format(FLAGS.embedding_size))
if not os.path.exists(FLAGS.log_dir):
os.makedirs(FLAGS.log_dir)
file_handler = logging.FileHandler(pjoin(FLAGS.log_dir, "log.txt"))
logging.getLogger().addHandler(file_handler)
print(vars(FLAGS))
with open(os.path.join(FLAGS.log_dir, "flags.json"), 'w') as fout:
json.dump(FLAGS.__flags, fout)
# ========= Load Dataset =========
# You can change this code to load dataset in your own way
# # Old version. Encoding issue
# dev_dirname = os.path.dirname(os.path.abspath(FLAGS.dev_path))
# dev_filename = os.path.basename(FLAGS.dev_path)
# context_data, question_data, question_uuid_data = prepare_dev(dev_dirname, dev_filename, vocab)
# dataset = (context_data, question_data, question_uuid_data)
#
# dataset = adjust_dataset(dataset, 'dev')
# New version. To match the preprocessing provided to train.py
# As in squad_preprocessing.py:
tt = time.time()
download_prefix = os.path.join("download", "squad")
data_prefix = os.path.join("data", "squad")
if not os.path.exists(download_prefix):
os.makedirs(download_prefix)
if not os.path.exists(data_prefix):
os.makedirs(data_prefix)
dev_filename = "dev-v1.1.json"
dev_data = data_from_json(os.path.join(download_prefix, dev_filename))
(dev_num_questions,
dev_num_answers,
uuid) = read_write_dataset_(dev_data, 'dev', data_prefix)
print("Processed {} questions and {} answers in dev".format(
dev_num_questions, dev_num_answers))
print(time.time()-tt, 'part: squar_preprocessing.py')
# As in qa_data.py:
tt = time.time()
args = qa_data.setup_args()
vocab_path = pjoin(args.vocab_dir, "vocab.dat")
dev_path = pjoin(args.source_dir, "dev")
x_dev_dis_path = dev_path + ".ids.context"
y_dev_ids_path = dev_path + ".ids.question"
data_to_token_ids(dev_path + ".context", x_dev_dis_path, vocab_path)
data_to_token_ids(dev_path + ".question", y_dev_ids_path, vocab_path)
print(time.time()-tt, 'part: qa_data.py')
# As in train.py
tt = time.time()
dataset = {}
load_data_dq(dataset, 'dev', FLAGS.data_dir)
indices = trim_empty(dataset['dev'])
print(time.time()-tt, 'part: train.py')
# uuid from read_write_dataset_
uuid = [i for j, i in enumerate(uuid) if j not in indices]
dataset['dev']['uuid'] = uuid
# sanity check
keys = dataset['dev'].keys()
for i in xrange(len(keys)-1):
print(i, keys[i], len(dataset['dev'][keys[i]]),
i+1, keys[i+1], len(dataset['dev'][keys[i+1]]))
assert len(dataset['dev'][keys[i]]) == len(dataset['dev'][keys[i+1]])
# ========= Model-specific =========
# You must change the following code to adjust to your model
encoder = Encoder(size=FLAGS.state_size, vocab_dim=FLAGS.embedding_size)
decoder = Decoder(output_size=FLAGS.output_size)
with tf.Session() as sess:
pass
local_device_protos = device_lib.list_local_devices() # 38559755
for x in local_device_protos:
if x.device_type == 'GPU':
FLAGS.ifgpu = True
break
qa = QASystem(encoder, decoder, embed_path, rev_vocab)
#with tf.Session() as sess:
# pass
train_dir = get_normalized_train_dir(FLAGS.train_dir)
initialize_model(sess, qa, train_dir)
answers = generate_answers(sess, qa, dataset, rev_vocab)
# write to json file to root dir
with io.open('dev-prediction.json', 'w', encoding='utf-8') as f:
f.write(unicode(json.dumps(answers, ensure_ascii=False)))
def main(unused_argv):
# Print an error message if you've entered flags incorrectly
if len(unused_argv) != 1:
raise Exception("There is a problem with how you entered flags: %s" %
unused_argv)
# Define train_dir
if not FLAGS.name and not FLAGS.train_dir and FLAGS.mode != EVAL_MODE:
raise Exception("You need to specify either --name or --train_dir")
FLAGS.train_dir = FLAGS.train_dir or os.path.join(LOGS_DIR, FLAGS.name)
# If not specified, set d_ff to match d_model
if FLAGS.d_ff == 0:
FLAGS.d_ff = FLAGS.d_model
# Initialize best model directory
best_model_dir = os.path.join(FLAGS.train_dir, "best_checkpoint")
# Define path for glove vecs
FLAGS.glove_path = FLAGS.glove_path or os.path.join(
FLAGS.data_dir, "glove.840B.{}d.txt".format(FLAGS.word_emb_size))
FLAGS.char_emb_path = os.path.join(FLAGS.data_dir, "char_emb_file.txt")
FLAGS.word_emb_path = os.path.join(FLAGS.data_dir, "word_emb_file.txt")
# Get file paths to train/dev/test datafiles for tokenized queries, contexts and answers
FLAGS.train_rec_path = os.path.join(FLAGS.data_dir, "train.tfrecord")
FLAGS.train_ans_path = os.path.join(FLAGS.data_dir, "train_ans.json")
FLAGS.train_info_path = os.path.join(FLAGS.data_dir, "train_info.json")
FLAGS.dev_rec_path = os.path.join(FLAGS.data_dir, "dev.tfrecord")
FLAGS.dev_ans_path = os.path.join(FLAGS.data_dir, "dev_ans.json")
FLAGS.dev_info_path = os.path.join(FLAGS.data_dir, "dev_info.json")
# Load word embedding matrix and char embedding matrix.
word_emb_matrix, word2id = get_word_embs(FLAGS.word_emb_path,
FLAGS.word_emb_size)
char_emb_matrix, char2id = get_char_embs(FLAGS.char_emb_path,
FLAGS.char_emb_size)
# Some GPU settings
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
# Split by mode
if FLAGS.mode == TRAIN_MODE:
# Load dataset info and answer files
print("Loading train and dev datasets...")
train_answers = data_from_json(FLAGS.train_ans_path)
train_info = data_from_json(FLAGS.train_info_path)
dev_answers = data_from_json(FLAGS.dev_ans_path)
dev_info = data_from_json(FLAGS.dev_info_path)
# Initialize data pipeline
loader = get_data_loader(FLAGS, is_training=True)
train_dataset = load_dataset(FLAGS,
FLAGS.train_rec_path,
loader,
shuffle=True)
train_iterator = train_dataset.make_one_shot_iterator()
dev_dataset = load_dataset(FLAGS,
FLAGS.dev_rec_path,
loader,
shuffle=True)
dev_iterator = dev_dataset.make_one_shot_iterator()
# Initialize the model
input_handle = tf.placeholder(tf.string, shape=())
input_iterator = tf.data.Iterator.from_string_handle(
input_handle, train_dataset.output_types,
train_dataset.output_shapes)
model = SQuADTransformer(FLAGS, input_iterator, input_handle,
word_emb_matrix, char_emb_matrix)
# Setup train dir and logfile
if not os.path.exists(FLAGS.train_dir):
os.makedirs(FLAGS.train_dir)
file_handler = logging.FileHandler(
os.path.join(FLAGS.train_dir, "log.txt"))
logging.getLogger().addHandler(file_handler)
# Make best model dir if necessary
if not os.path.exists(best_model_dir):
os.makedirs(best_model_dir)
with tf.Session(config=config) as sess:
# Load most recent model
initialize_model(sess, model, FLAGS.train_dir, expect_exists=False)
# Train
model.train(sess, train_iterator, train_answers, train_info,
dev_iterator, dev_answers, dev_info)
elif FLAGS.mode == EVAL_MODE:
if FLAGS.json_in_path == "":
raise Exception(
"For {} mode, you need to specify --json_in_path".format(
EVAL_MODE))
if FLAGS.checkpoint_dir == "" and FLAGS.ensemble_path == "":
raise Exception(
"For {} mode, you need to specify --checkpoint_dir or --ensemble_path"
.format(EVAL_MODE))
FLAGS.is_training = False
# Read the JSON data from file
print("Loading test dataset from {}...".format(FLAGS.json_in_path))
test_data = data_from_json(FLAGS.json_in_path)
test_examples, test_answers, test_info, _, _ = preprocess(test_data)
# Get formatted examples in memory for creating a TF Dataset
formatted_examples, output_types, output_shapes = get_formatted_examples(
FLAGS, test_examples, word2id, char2id)
# Construct a generator function for building TF dataset
def gen():
infinite_idx = 0
while True:
yield formatted_examples[infinite_idx]
infinite_idx = (infinite_idx + 1) % len(formatted_examples)
# Initialize data pipeline (repeat so we can use this multiple times in an ensemble).
test_dataset = tf.data.Dataset.from_generator(
gen, output_types, output_shapes).repeat().batch(FLAGS.batch_size)
test_iterator = test_dataset.make_one_shot_iterator()
input_handle = tf.placeholder(tf.string, shape=())
input_iterator = tf.data.Iterator.from_string_handle(
input_handle, test_dataset.output_types,
test_dataset.output_shapes)
# Ensemble or single eval.
is_ensemble = FLAGS.ensemble_path != ""
if is_ensemble: # Path to file with a list of directories for ensemble
with open(FLAGS.ensemble_path, 'r') as fh:
checkpoint_paths = [
line.strip() for line in fh.readlines() if line
]
if len(checkpoint_paths) == 0:
raise Exception(
"Ensemble path {} did not contain any checkpoint paths."
.format(FLAGS.ensemble_path))
else:
checkpoint_paths = [FLAGS.checkpoint_dir]
# Make predictions using all checkpoints specified in checkpoint_paths
model = SQuADTransformer(FLAGS, input_iterator, input_handle,
word_emb_matrix, char_emb_matrix)
all_answers = defaultdict(
list) # Maps from UUID to list of (answer text, prob) pairs.
for i in range(len(checkpoint_paths)):
if is_ensemble:
print("Ensemble model {} / {}...".format(
i + 1, len(checkpoint_paths)))
with tf.Session(config=config) as sess:
# Load model from checkpoint_dir
initialize_model(sess,
model,
checkpoint_paths[i],
expect_exists=True,
is_training=False)
# Get a predicted answer for each example in the data
num_batches = test_info['num_examples'] // FLAGS.batch_size + 1
answers_dict = model.get_answers(sess, test_iterator,
test_answers, num_batches)
# Add it to the combined answers
for k, v in answers_dict.items():
all_answers[k].append(v)
# Combine the results into a final prediction
if is_ensemble:
print("Combining answers with max-vote...")
answers_dict = {}
for k, v in tqdm(all_answers.items()):
answers_dict[k] = ensemble_max_vote(all_answers[k])
# Write the uuid->answer mapping a to json file in root dir
print("Writing predictions to %s..." % FLAGS.json_out_path)
with io.open(FLAGS.json_out_path, 'w', encoding='utf-8') as f:
f.write(json.dumps(answers_dict, ensure_ascii=False))
print("Wrote predictions to %s" % FLAGS.json_out_path)
else:
raise Exception("Unsupported mode: %s" % FLAGS.mode)
def main(_):
vocab, rev_vocab = initialize_vocab(FLAGS.vocab_path)
embed_path = FLAGS.embed_path or pjoin("data", "squad", "glove.trimmed.{}.npz".format(FLAGS.embedding_size))
global_train_dir = '/tmp/cs224n-squad-train'
# Adds symlink to {train_dir} from /tmp/cs224n-squad-train to canonicalize the
# file paths saved in the checkpoint. This allows the model to be reloaded even
# if the location of the checkpoint files has moved, allowing usage with CodaLab.
# This must be done on both train.py and qa_answer.py in order to work.
if not os.path.exists(FLAGS.train_dir):
os.makedirs(FLAGS.train_dir)
if os.path.exists(global_train_dir):
os.unlink(global_train_dir)
os.symlink(os.path.abspath(FLAGS.train_dir), global_train_dir)
train_dir = global_train_dir
if not os.path.exists(FLAGS.log_dir):
os.makedirs(FLAGS.log_dir)
file_handler = logging.FileHandler(pjoin(FLAGS.log_dir, "log.txt"))
logging.getLogger().addHandler(file_handler)
print(vars(FLAGS))
with open(os.path.join(FLAGS.log_dir, "flags.json"), 'w') as fout:
json.dump(FLAGS.__flags, fout)
# ========= Download Dataset json =========
# You can change this code to load dataset in your own way
dev_dirname = os.path.dirname(os.path.abspath(FLAGS.dev_path))
dev_filename = os.path.basename(FLAGS.dev_path)
_, _, _ = prepare_dev(dev_dirname, dev_filename, vocab)
# ========= Process input json =========
prefix = os.path.join("data", "squad")
# writes dev.answer, dev.context, dev.question, dev.span
dev_path = FLAGS.dev_path
dev_filename = FLAGS.dev_path.split("/")[-1]
dev_data = data_from_json(os.path.join(prefix, dev_filename))
dev_num_questions, dev_num_answers = read_write_dataset(dev_data, 'dev', prefix)
print("Processed {} questions and {} answers in dev".format(dev_num_questions, dev_num_answers))
# writes dev.ids.context, dev.ids.question
vocab_path = pjoin(os.path.join("data", "squad"), "vocab.dat")
dev_deposit_path = pjoin(os.path.join("data", "squad"), "dev")
x_dis_path = dev_deposit_path + ".ids.context"
y_ids_path = dev_deposit_path + ".ids.question"
data_to_token_ids(dev_deposit_path + ".context", x_dis_path, vocab_path)
data_to_token_ids(dev_deposit_path + ".question", y_ids_path, vocab_path)
# load data sets
Q_test, P_test, A_start_test, A_end_test, A_len_test, P_raw_test, A_raw_test, Q_len_test, P_len_test = load_data(os.path.join("data", "squad"), "dev") # for our purposes this is as test set.
question_uuid_data = []
with open(os.path.join("data", "squad") + "/dev.quid") as f:
for line in f:
question_uuid_data.append((line))
# pad the data at load-time. So, we don't need to do any masking later!!!
# ref: https://keras.io/preprocessing/sequence/
# if len < maxlen, pad with specified val
# elif len > maxlen, truncate
QMAXLEN = FLAGS.QMAXLEN
PMAXLEN = FLAGS.PMAXLEN
Q_test = pad_sequences(Q_test, maxlen=QMAXLEN, value=PAD_ID, padding='post')
P_test = pad_sequences(P_test, maxlen=PMAXLEN, value=PAD_ID, padding='post')
A_start_test = pad_sequences(A_start_test, maxlen=PMAXLEN, value=0, padding='post')
A_end_test = pad_sequences(A_end_test, maxlen=PMAXLEN, value=0, padding='post')
test_data = zip(P_test, Q_test, P_len_test, Q_len_test, A_start_test, A_end_test, A_len_test, P_raw_test, A_raw_test, question_uuid_data)
# ========= Model-specific =========
# You must change the following code to adjust to your model
with tf.Graph().as_default():
with tf.Session() as sess:
embeddings = np.load(FLAGS.data_dir + '/glove.trimmed.' + str(FLAGS.embedding_size) + '.npz')
pretrained_embeddings = embeddings['glove']
qa = QASystem(FLAGS, pretrained_embeddings, vocab_dim=len(vocab.keys()))
initialize_model(sess, qa, train_dir)
# get predicted start-end indices
a_s = [] # store all start index preds
a_e = [] # store all end index preds
a_s_l = []
a_e_l = []
f1 = exact_match = total = 0; answers = {}
prog = Progbar(target=1 + int(len(test_data) / FLAGS.batch_size))
for i, batch in enumerate(minibatches(test_data, FLAGS.batch_size, shuffle = False)):
batch_test = batch[:4]
(ys, ye) = qa.predict_on_batch(sess, *batch_test)
a_s = (np.argmax(ys, axis=1))
a_e = (np.argmax(ye, axis=1))
a_s_l = a_s_l + list(a_s)
a_e_l = a_e_l + list(a_e)
for j in range(len(a_s)):
p_raw = batch[7][j]
a_raw = batch[8][j]
s = a_s[j]
e = a_e[j]
pred_raw = ' '.join(p_raw.split()[s:e + 1])
f1 += f1_score(pred_raw, a_raw)
exact_match += exact_match_score(pred_raw, a_raw)
total += 1
answers[batch[9][j].strip("\n")] = pred_raw.strip("\n")
prog.update(i + 1, [("processed", i + 1)])
exact_match = 100.0 * exact_match / total
f1 = 100.0 * f1 / total
print(("First Answer Entity level F1/EM: %.2f/%.2f", f1, exact_match))
#answers = generate_answers(question_uuid_data, a_s_l, a_e_l, context_data, rev_vocab)
# write to json file to root dir
with io.open('dev-prediction.json', 'w', encoding='utf-8') as f:
f.write(unicode(json.dumps(answers, ensure_ascii=False)))