def prepare_data(model, train_config, dataset_oversampling, n_processes):
extract = ExtractMultiParagraphsPerQuestion(
MergeParagraphs(train_config.n_tokens),
ShallowOpenWebRanker(train_config.num_paragraphs),
model.preprocessor, intern=True
)
trivia_qa_test = RandomParagraphSetDatasetBuilder(
train_config.test_batch_size,
"merge" if train_config.trivia_qa_mode == "merge" else "group", True,
train_config.oversample
)
trivia_qa_train = StratifyParagraphSetsBuilder(
train_config.train_batch_size,
train_config.trivia_qa_mode == "merge",
True, train_config.oversample
)
datas = []
for name, sampling in dataset_oversampling.items():
for s in range(sampling):
ds = TriviaQaSpanCorpus(name)
ds.corpus_name = ds.corpus_name + '_{}'.format(s)
datas.append(ds)
data = MultiDataset(datas)
data = PreprocessedData(data, extract, trivia_qa_train, trivia_qa_test, eval_on_verified=False)
data.preprocess(n_processes, 1000)
return data
async def setup_qa(app, loop):
# To play nice with iohttp's async ClientSession objects, we need to construct the QaSystem
# inside the event loop.
if args.debug == "dummy_qa":
qa = DummyQa()
else:
qa = QaSystem(
args.wiki_cache,
MergeParagraphs(args.tokens),
ShallowOpenWebRanker(args.n_paragraphs),
args.voc,
model,
loader,
bing_api_key,
bing_version=args.bing_version,
tagme_api_key=tagme_api_key,
n_dl_threads=args.n_dl_threads,
blacklist_trivia_sites=args.blacklist_trivia_sites,
download_timeout=args.download_timeout,
span_bound=span_bound,
tagme_threshold=None if
(tagme_api_key is None) else args.tagme_thresh,
n_web_docs=args.n_web,
)
app.qa = qa
def show_open_paragraphs(start: int, end: int):
splitter = MergeParagraphs(400)
stop = NltkPlusStopWords(True)
ranker = ShallowOpenWebRanker(6)
stop_words = stop.words
print("Loading train")
corpus = TriviaQaOpenDataset()
train = corpus.get_dev()
np.random.shuffle(train)
for q in train:
q_words = {strip_accents_unicode(w.lower()) for w in q.question}
q_words = {x for x in q_words if x not in stop_words}
para = []
for d in q.all_docs:
doc = corpus.evidence.get_document(d.doc_id)
para += splitter.split_annotated(doc, d.answer_spans)
ranked = ranker.prune(q.question, para)
if len(ranked) < start:
continue
ranked = ranked[start:end]
print(" ".join(q.question))
print(q.answer.all_answers)
for i in range(start, end):
para = ranked[i]
text = flatten_iterable(para.text)
print("Start=%d, Rank=%d" % (para.start, i))
if len(para.answer_spans) == 0:
# print("No Answer!")
continue
for s, e in para.answer_spans:
text[s] = bcolors.CYAN + text[s]
text[e] = text[e] + bcolors.ENDC
for i, w in enumerate(text):
if strip_accents_unicode(w.lower()) in q_words:
text[i] = bcolors.ERROR + text[i] + bcolors.ENDC
print(" ".join(text))
input()
def get_para_filter(filter_name, per_document, n_paragraphs):
filter_name = ('tfidf' if per_document else
'linear') if filter_name is None else filter_name
if filter_name == "tfidf":
para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True),
n_paragraphs)
elif filter_name == "truncate":
para_filter = FirstN(n_paragraphs)
elif filter_name == "linear":
para_filter = ShallowOpenWebRanker(n_paragraphs)
else:
raise ValueError()
return para_filter
def prepro(ds,
fold,
num_tokens_per_group,
num_paragraphs,
pad=True,
n_samples=None):
fold_funcs = {
'train': lambda: ds.get_train(),
'dev': lambda: ds.get_dev(),
'test': lambda: ds.get_test()
}
qs = fold_funcs[fold]()
if n_samples is not None:
qs = qs[:n_samples]
evidence = ds.evidence
prep = None
extract = ExtractMultiParagraphsPerQuestion(
MergeParagraphs(num_tokens_per_group),
ShallowOpenWebRanker(num_paragraphs),
prep,
intern=True)
answers = {}
batches = {}
for q in tqdm(qs, ncols=80, desc='preprocessing'):
pre = extract.preprocess([q], evidence)
if len(pre.data) == 0:
continue
assert len(pre.data) < 2
assert q.question_id not in answers
assert q.question_id not in batches
mpq = pre.data[0]
pq_batch = [
ParagraphAndQuestion(p.get_context(), q.question, None,
q.question_id, p.doc_id)
for p in mpq.paragraphs
# document paragraph question?
]
if pad:
for i in range(num_paragraphs - len(pq_batch)):
pq_batch.append(
ParagraphAndQuestion([], q.question, None, q.question_id,
None))
answers[q.question_id] = mpq.answer_text
batches[q.question_id] = pq_batch
voc = {w for bs in batches.values() for b in bs for w in b.question}
voc.update({w for bs in batches.values() for b in bs for w in b.context})
return answers, batches, voc
def find_answer(documents, raw_question):
raw_question = raw_question.lower()
documents = [d.lower() for d in documents]
global best_spans, conf
documents = [re.split("\s*\n\s*", doc) for doc in documents]
tokenizer = NltkAndPunctTokenizer()
question = tokenizer.tokenize_paragraph_flat(raw_question)
documents = [[tokenizer.tokenize_paragraph(p) for p in doc]
for doc in documents]
splitter = MergeParagraphs(400)
documents = [splitter.split(doc) for doc in documents]
if len(documents) == 1:
selector = TopTfIdf(NltkPlusStopWords(True), n_to_select=5)
context = selector.prune(question, documents[0])
else:
selector = ShallowOpenWebRanker(n_to_select=10)
context = selector.prune(question, flatten_iterable(documents))
context = [flatten_iterable(x.text) for x in context]
data = [
ParagraphAndQuestion(x, question, None, "user-question%d" % i)
for i, x in enumerate(context)
]
encoded = model.encode(data, is_train=False)
with sess.as_default():
spans, confid = sess.run([best_spans, conf], feed_dict=encoded)
best_para = np.argmax(confid)
ans = " ".join(context[best_para][spans[best_para][0]:spans[best_para][1] +
1])
confidence = confid[best_para]
return ans, confidence
def main():
parser = argparse.ArgumentParser()
parser.add_argument("corpus", choices=["en", "en_trans_de", "en_trans_zh"])
parser.add_argument(
'mode',
choices=["confidence", "merge", "shared-norm", "sigmoid", "paragraph"])
# Note I haven't tested modes other than `shared-norm` on this corpus, so
# some things might need adjusting
parser.add_argument("name", help="Where to store the model")
parser.add_argument("-t",
"--n_tokens",
default=400,
type=int,
help="Paragraph size")
parser.add_argument(
'-n',
'--n_processes',
type=int,
default=2,
help="Number of processes (i.e., select which paragraphs to train on) "
"the data with")
args = parser.parse_args()
mode = args.mode
corpus = args.corpus
out = args.name + "-" + datetime.now().strftime("%m%d-%H%M%S")
model = get_model(100, 140, mode, WithIndicators())
extract = ExtractMultiParagraphsPerQuestion(MergeParagraphs(args.n_tokens),
ShallowOpenWebRanker(16),
model.preprocessor,
intern=True)
eval = [
LossEvaluator(),
MultiParagraphSpanEvaluator(8,
"triviaqa",
mode != "merge",
per_doc=False)
]
oversample = [
1
] * 2 # Sample the top two answer-containing paragraphs twice
if mode == "paragraph":
n_epochs = 120
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(ClusteredBatcher(
60, ContextLenBucketedKey(3), True),
oversample,
only_answers=True)
elif mode == "confidence" or mode == "sigmoid":
if mode == "sigmoid":
n_epochs = 640
else:
n_epochs = 160
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(
ClusteredBatcher(60, ContextLenBucketedKey(3), True), oversample)
else:
n_epochs = 80
test = RandomParagraphSetDatasetBuilder(
120, "merge" if mode == "merge" else "group", True, oversample)
train = StratifyParagraphSetsBuilder(30, mode == "merge", True,
oversample)
data = XQADataset(corpus)
params = TrainParams(SerializableOptimizer("Adadelta",
dict(learning_rate=1)),
num_epochs=n_epochs,
ema=0.999,
max_checkpoints_to_keep=2,
async_encoding=10,
log_period=30,
eval_period=1800,
save_period=1800,
best_weights=("dev", "b8/question-text-f1"),
eval_samples=dict(dev=None, train=6000))
data = PreprocessedData(data, extract, train, test, eval_on_verified=False)
data.preprocess(args.n_processes, 1000)
with open(__file__, "r") as f:
notes = f.read()
notes = "Mode: " + args.mode + "\n" + notes
trainer.start_training(data, model, params, eval, model_dir.ModelDir(out),
notes)
def main():
parser = argparse.ArgumentParser(description='Evaluate a model on TriviaQA data')
parser.add_argument('model', help='model directory')
parser.add_argument('-p', '--paragraph_output', type=str,
help="Save fine grained results for each paragraph in csv format")
parser.add_argument('-o', '--official_output', type=str, help="Build an offical output file with the model's"
" most confident span for each (question, doc) pair")
parser.add_argument('--no_ema', action="store_true", help="Don't use EMA weights even if they exist")
parser.add_argument('--n_processes', type=int, default=None,
help="Number of processes to do the preprocessing (selecting paragraphs+loading context) with")
parser.add_argument('-i', '--step', type=int, default=None, help="checkpoint to load, default to latest")
parser.add_argument('-n', '--n_sample', type=int, default=None, help="Number of questions to evaluate on")
parser.add_argument('-a', '--async', type=int, default=10)
parser.add_argument('-t', '--tokens', type=int, default=400,
help="Max tokens per a paragraph")
parser.add_argument('-g', '--n_paragraphs', type=int, default=15,
help="Number of paragraphs to run the model on")
parser.add_argument('-f', '--filter', type=str, default=None, choices=["tfidf", "truncate", "linear"],
help="How to select paragraphs")
parser.add_argument('-b', '--batch_size', type=int, default=200,
help="Batch size, larger sizes might be faster but wll take more memory")
parser.add_argument('--max_answer_len', type=int, default=8,
help="Max answer span to select")
parser.add_argument('-c', '--corpus',
choices=["web-dev", "web-test", "web-verified-dev", "web-train",
"open-dev", "open-train"],
default="web-verified-dev")
args = parser.parse_args()
model_dir = ModelDir(args.model)
model = model_dir.get_model()
if args.corpus.startswith('web'):
dataset = TriviaQaWebDataset()
corpus = dataset.evidence
if args.corpus == "web-dev":
test_questions = dataset.get_dev()
elif args.corpus == "web-test":
test_questions = dataset.get_test()
elif args.corpus == "web-verified-dev":
test_questions = dataset.get_verified()
elif args.corpus == "web-train":
test_questions = dataset.get_train()
else:
raise RuntimeError()
else:
dataset = TriviaQaOpenDataset()
corpus = dataset.evidence
if args.corpus == "open-dev":
test_questions = dataset.get_dev()
elif args.corpus == "open-train":
test_questions = dataset.get_train()
else:
raise RuntimeError()
splitter = MergeParagraphs(args.tokens)
per_document = not args.corpus.startswith("open")
filter_name = args.filter
if filter_name is None:
if args.corpus.startswith("open"):
filter_name = "linear"
else:
filter_name = "tfidf"
print("Selecting %d paragraphs using %s method per %s" % (args.n_paragraphs, filter_name,
("question-document pair" if per_document else "question")))
if filter_name == "tfidf":
para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True), args.n_paragraphs)
elif filter_name == "truncate":
para_filter = FirstN(args.n_paragraphs)
elif filter_name == "linear":
para_filter = ShallowOpenWebRanker(args.n_paragraphs)
else:
raise ValueError()
n_questions = args.n_sample
if n_questions is not None:
test_questions.sort(key=lambda x:x.question_id)
np.random.RandomState(0).shuffle(test_questions)
test_questions = test_questions[:n_questions]
print("Building question/paragraph pairs...")
# Loads the relevant questions/documents, selects the right paragraphs, and runs the model's preprocessor
if per_document:
prep = ExtractMultiParagraphs(splitter, para_filter, model.preprocessor, require_an_answer=False)
else:
prep = ExtractMultiParagraphsPerQuestion(splitter, para_filter, model.preprocessor, require_an_answer=False)
prepped_data = preprocess_par(test_questions, corpus, prep, args.n_processes, 1000)
data = []
for q in prepped_data.data:
for i, p in enumerate(q.paragraphs):
if q.answer_text is None:
ans = None
else:
ans = TokenSpans(q.answer_text, p.answer_spans)
data.append(DocumentParagraphQuestion(q.question_id, p.doc_id,
(p.start, p.end), q.question, p.text,
ans, i))
# Reverse so our first batch will be the largest (so OOMs happen early)
questions = sorted(data, key=lambda x: (x.n_context_words, len(x.question)), reverse=True)
print("Done, starting eval")
if args.step is not None:
if args.step == "latest":
checkpoint = model_dir.get_latest_checkpoint()
else:
checkpoint = model_dir.get_checkpoint(int(args.step))
else:
checkpoint = model_dir.get_best_weights()
if checkpoint is not None:
print("Using best weights")
else:
print("Using latest checkpoint")
checkpoint = model_dir.get_latest_checkpoint()
test_questions = ParagraphAndQuestionDataset(questions, FixedOrderBatcher(args.batch_size, True))
evaluation = trainer.test(model,
[RecordParagraphSpanPrediction(args.max_answer_len, True)],
{args.corpus:test_questions}, ResourceLoader(), checkpoint, not args.no_ema, args.async)[args.corpus]
if not all(len(x) == len(data) for x in evaluation.per_sample.values()):
raise RuntimeError()
df = pd.DataFrame(evaluation.per_sample)
if args.official_output is not None:
print("Saving question result")
# I didn't store the unormalized filenames exactly, so unfortunately we have to reload
# the source data to get exact filename to output an official test script
fns = {}
print("Loading proper filenames")
if args.corpus == 'web-test':
source = join(TRIVIA_QA, "qa", "web-test-without-answers.json")
elif args.corpus == "web-dev":
source = join(TRIVIA_QA, "qa", "web-dev.json")
else:
raise NotImplementedError()
with open(join(source)) as f:
data = json.load(f)["Data"]
for point in data:
for doc in point["EntityPages"]:
filename = doc["Filename"]
fn = join("wikipedia", filename[:filename.rfind(".")])
fn = normalize_wiki_filename(fn)
fns[(point["QuestionId"], fn)] = filename
answers = {}
scores = {}
for q_id, doc_id, start, end, txt, score in df[["question_id", "doc_id", "para_start", "para_end",
"text_answer", "predicted_score"]].itertuples(index=False):
filename = dataset.evidence.file_id_map[doc_id]
if filename.startswith("web"):
true_name = filename[4:] + ".txt"
else:
true_name = fns[(q_id, filename)]
key = q_id + "--" + true_name
prev_score = scores.get(key)
if prev_score is None or prev_score < score:
scores[key] = score
answers[key] = txt
with open(args.official_output, "w") as f:
json.dump(answers, f)
if per_document:
group_by = ["question_id", "doc_id"]
else:
group_by = ["question_id"]
# Print a table of scores as more paragraphs are used
df.sort_values(group_by + ["rank"], inplace=True)
f1 = compute_model_scores(df, "predicted_score", "text_f1", group_by)
em = compute_model_scores(df, "predicted_score", "text_em", group_by)
table = [["N Paragraphs", "EM", "F1"]]
table += list([str(i+1), "%.4f" % e, "%.4f" % f] for i, (e, f) in enumerate(zip(em, f1)))
print_table(table)
output_file = args.paragraph_output
if output_file is not None:
print("Saving paragraph result")
if output_file.endswith("json"):
with open(output_file, "w") as f:
json.dump(evaluation.per_sample, f)
elif output_file.endswith("pkl"):
with open(output_file, "wb") as f:
pickle.dump(evaluation.per_sample, f)
elif output_file.endswith("csv"):
df.to_csv(output_file, index=False)
else:
raise ValueError("Unrecognized file format")
def main():
parser = argparse.ArgumentParser(description="Run an ELMo model on user input")
# parser.add_argument("model", type=int, help="Model directory")
parser.add_argument("question", help="Question to answer")
parser.add_argument("documents", help="List of text documents to answer the question with", nargs='+')
args = parser.parse_args()
# Models path
SQUAD_MODEL_DIRECTORY_PATH = 'docqa/models-cpu/squad'
SQUAD_SHARED_NORM_MODEL_DIRECTORY_PATH = 'docqa/models-cpu/squad-shared-norm'
TRIVIAQA_MODEL_DIRECTORY_PATH = 'docqa/models-cpu/triviaqa-unfiltered-shared-norm'
TRIVIAQA_SHARED_NORM_MODEL_DIRECTORY_PATH = 'docqa/models-cpu/triviaqa-web-shared-norm'
models_directory = [
SQUAD_MODEL_DIRECTORY_PATH,
SQUAD_SHARED_NORM_MODEL_DIRECTORY_PATH,
TRIVIAQA_MODEL_DIRECTORY_PATH,
TRIVIAQA_SHARED_NORM_MODEL_DIRECTORY_PATH
]
print("Preprocessing...")
# Load the model
# model_dir = ModelDir(args.model)
model_dir = ModelDir(models_directory[0])
model = model_dir.get_model()
if not isinstance(model, ParagraphQuestionModel):
raise ValueError("This script is built to work for ParagraphQuestionModel models only")
# Read the documents
documents = []
for doc in args.documents:
if not isfile(doc):
raise ValueError(doc + " does not exist")
with open(doc, "r") as f:
documents.append(f.read())
print("Loaded %d documents" % len(documents))
# Split documents into lists of paragraphs
documents = [re.split("\s*\n\s*", doc) for doc in documents]
# Tokenize the input, the models expects data to be tokenized using `NltkAndPunctTokenizer`
# Note the model expects case-sensitive input
tokenizer = NltkAndPunctTokenizer()
question = tokenizer.tokenize_paragraph_flat(args.question) # List of words
# Now list of document->paragraph->sentence->word
documents = [[tokenizer.tokenize_paragraph(p) for p in doc] for doc in documents]
# Now group the document into paragraphs, this returns `ExtractedParagraph` objects
# that additionally remember the start/end token of the paragraph within the source document
splitter = MergeParagraphs(400)
# splitter = PreserveParagraphs() # Uncomment to use the natural paragraph grouping
documents = [splitter.split(doc) for doc in documents]
# Now select the top paragraphs using a `ParagraphFilter`
if len(documents) == 1:
# Use TF-IDF to select top paragraphs from the document
selector = TopTfIdf(NltkPlusStopWords(True), n_to_select=5)
context = selector.prune(question, documents[0])
else:
# Use a linear classifier to select top paragraphs among all the documents
selector = ShallowOpenWebRanker(n_to_select=10)
context = selector.prune(question, flatten_iterable(documents))
print("Select %d paragraph" % len(context))
if model.preprocessor is not None:
# Models are allowed to define an additional pre-processing step
# This will turn the `ExtractedParagraph` objects back into simple lists of tokens
context = [model.preprocessor.encode_text(question, x) for x in context]
else:
# Otherwise just use flattened text
context = [flatten_iterable(x.text) for x in context]
print("Setting up model")
# Tell the model the batch size (can be None) and vocab to expect, This will load the
# needed word vectors and fix the batch size to use when building the graph / encoding the input
voc = set(question)
for txt in context:
voc.update(txt)
model.set_input_spec(ParagraphAndQuestionSpec(batch_size=len(context)), voc)
# Now we build the actual tensorflow graph, `best_span` and `conf` are
# tensors holding the predicted span (inclusive) and confidence scores for each
# element in the input batch, confidence scores being the pre-softmax logit for the span
print("Build tf graph")
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# We need to use sess.as_default when working with the cuNND stuff, since we need an active
# session to figure out the # of parameters needed for each layer. The cpu-compatible models don't need this.
with sess.as_default():
# 8 means to limit the span to size 8 or less
best_spans, conf = model.get_prediction().get_best_span(10)
# Loads the saved weights
model_dir.restore_checkpoint(sess)
# Now the model is ready to run
# The model takes input in the form of `ContextAndQuestion` objects, for example:
data = [ParagraphAndQuestion(x, question, None, "user-question%d"%i)
for i, x in enumerate(context)]
print("Starting run")
# The model is run in two steps, first it "encodes" a batch of paragraph/context pairs
# into numpy arrays, then we use `sess` to run the actual model get the predictions
encoded = model.encode(data, is_train=False) # batch of `ContextAndQuestion` -> feed_dict
best_spans, conf = sess.run([best_spans, conf], feed_dict=encoded) # feed_dict -> predictions
best_para = np.argmax(conf) # We get output for each paragraph, select the most-confident one to print
print("Best Paragraph: " + str(best_para))
para_id = int(str(best_para))
# print("Best Paragraph: \n" + (" ".join((paras[para_id].text)[0])))
print("Best Paragraph: \n" + " ".join(context[para_id]))
print("Best span: " + str(best_spans[best_para]))
print("Answer text: " + " ".join(context[best_para][best_spans[best_para][0]:best_spans[best_para][1]+1]))
print("Confidence: " + str(conf[best_para]))
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'--n_processes',
type=int,
default=1,
help=
"Number of processes to do the preprocessing (selecting paragraphs+loading context) with"
)
parser.add_argument('-a', '--async', type=int, default=10)
parser.add_argument('-t',
'--tokens',
type=int,
default=400,
help="Max tokens per a paragraph")
parser.add_argument('-n',
'--n_sample',
type=int,
default=None,
help="Number of questions to evaluate on")
parser.add_argument('-g',
'--n_paragraphs',
type=int,
default=15,
help="Number of paragraphs to run the model on")
parser.add_argument('-f',
'--filter',
type=str,
default=None,
choices=["tfidf", "truncate", "linear"],
help="How to select paragraphs")
parser.add_argument(
'-c',
'--corpus',
choices=[
"en_dev", "en_test", "fr_dev", "fr_test", "de_dev", "de_test",
"ru_dev", "ru_test", "pt_dev", "pt_test", "zh_dev", "zh_test",
"pl_dev", "pl_test", "uk_dev", "uk_test", "ta_dev", "ta_test",
"fr_trans_en_dev", "fr_trans_en_test", "de_trans_en_dev",
"de_trans_en_test", "ru_trans_en_dev", "ru_trans_en_test",
"pt_trans_en_dev", "pt_trans_en_test", "zh_trans_en_dev",
"zh_trans_en_test", "pl_trans_en_dev", "pl_trans_en_test",
"uk_trans_en_dev", "uk_trans_en_test", "ta_trans_en_dev",
"ta_trans_en_test"
],
required=True)
args = parser.parse_args()
corpus_name = args.corpus[:args.corpus.rfind("_")]
eval_set = args.corpus[args.corpus.rfind("_") + 1:]
dataset = XQADataset(corpus_name)
if eval_set == "dev":
test_questions = dataset.get_dev()
elif eval_set == "test":
test_questions = dataset.get_test()
else:
raise AssertionError()
corpus = dataset.evidence
splitter = MergeParagraphs(args.tokens)
per_document = args.corpus.startswith(
"web") # wiki and web are both multi-document
filter_name = args.filter
if filter_name is None:
# Pick default depending on the kind of data we are using
if per_document:
filter_name = "tfidf"
else:
filter_name = "linear"
print("Selecting %d paragraphs using method \"%s\" per %s" %
(args.n_paragraphs, filter_name,
("question-document pair" if per_document else "question")))
if filter_name == "tfidf":
para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True),
args.n_paragraphs)
elif filter_name == "truncate":
para_filter = FirstN(args.n_paragraphs)
elif filter_name == "linear":
para_filter = ShallowOpenWebRanker(args.n_paragraphs)
else:
raise ValueError()
n_questions = args.n_sample
if n_questions is not None:
test_questions.sort(key=lambda x: x.question_id)
np.random.RandomState(0).shuffle(test_questions)
test_questions = test_questions[:n_questions]
preprocessor = WithIndicators()
print("Building question/paragraph pairs...")
# Loads the relevant questions/documents, selects the right paragraphs, and runs the model's preprocessor
if per_document:
prep = ExtractMultiParagraphs(splitter,
para_filter,
preprocessor,
require_an_answer=False)
else:
prep = ExtractMultiParagraphsPerQuestion(splitter,
para_filter,
preprocessor,
require_an_answer=False)
prepped_data = preprocess_par(test_questions, corpus, prep,
args.n_processes, 1000)
data = []
for q in prepped_data.data:
for i, p in enumerate(q.paragraphs):
if q.answer_text is None:
ans = None
else:
ans = TokenSpans(q.answer_text, p.answer_spans)
data.append(
DocumentParagraphQuestion(q.question_id, p.doc_id,
(p.start, p.end), q.question, p.text,
ans, i))
# Reverse so our first batch will be the largest (so OOMs happen early)
questions = sorted(data,
key=lambda x: (x.n_context_words, len(x.question)),
reverse=True)
# dump eval data for bert
import pickle
pickle.dump(questions,
open("%s_%d.pkl" % (args.corpus, args.n_paragraphs), "wb"))
def predict():
json_data = {"success": False, "predictions": []}
print("Preprocessing...")
# Load the model
model_dir = ModelDir(
"/home/antriv/conversation_ai/Transfer_Learning/ALLENAI_DocumentQA/document-qa/pretrained_models/models/triviaqa-unfiltered-shared-norm"
)
model = model_dir.get_model()
if not isinstance(model, ParagraphQuestionModel):
raise ValueError(
"This script is built to work for ParagraphQuestionModel models only"
)
# Load the question
question = (flask.request.data).decode("utf-8")
# Read the documents
documents = []
doclist = ["/home/antriv/data/The-Future-Computed.txt"]
for doc in doclist:
if not isfile(doc):
raise ValueError(doc + " does not exist")
with open(doc, "r") as f:
documents.append(f.read())
print("Loaded %d documents" % len(documents))
# Split documents into lists of paragraphs
documents = [re.split("\s*\n\s*", doc) for doc in documents]
# Tokenize the input, the models expects data to be tokenized using `NltkAndPunctTokenizer`
# Note the model expects case-sensitive input
tokenizer = NltkAndPunctTokenizer()
question = tokenizer.tokenize_paragraph_flat(question) # List of words
# Now list of document->paragraph->sentence->word
documents = [[tokenizer.tokenize_paragraph(p) for p in doc]
for doc in documents]
# Now group the document into paragraphs, this returns `ExtractedParagraph` objects
# that additionally remember the start/end token of the paragraph within the source document
splitter = MergeParagraphs(400)
#splitter = PreserveParagraphs() # Uncomment to use the natural paragraph grouping
documents = [splitter.split(doc) for doc in documents]
# Now select the top paragraphs using a `ParagraphFilter`
if len(documents) == 1:
# Use TF-IDF to select top paragraphs from the document
selector = TopTfIdf(NltkPlusStopWords(True), n_to_select=1000)
context = selector.prune(question, documents[0])
else:
# Use a linear classifier to select top paragraphs among all the documents
selector = ShallowOpenWebRanker(n_to_select=1000)
context = selector.prune(question, flatten_iterable(documents))
print("Select %d paragraph" % len(context))
if model.preprocessor is not None:
# Models are allowed to define an additional pre-processing step
# This will turn the `ExtractedParagraph` objects back into simple lists of tokens
context = [
model.preprocessor.encode_text(question, x) for x in context
]
else:
# Otherwise just use flattened text
context = [flatten_iterable(x.text) for x in context]
print("Setting up model")
# Tell the model the batch size (can be None) and vocab to expect, This will load the
# needed word vectors and fix the batch size to use when building the graph / encoding the input
voc = set(question)
for txt in context:
voc.update(txt)
model.set_input_spec(ParagraphAndQuestionSpec(batch_size=len(context)),
voc)
# Now we build the actual tensorflow graph, `best_span` and `conf` are
# tensors holding the predicted span (inclusive) and confidence scores for each
# element in the input batch, confidence scores being the pre-softmax logit for the span
print("Build tf graph")
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# We need to use sess.as_default when working with the cuNND stuff, since we need an active
# session to figure out the # of parameters needed for each layer. The cpu-compatible models don't need this.
with sess.as_default():
# 8 means to limit the span to size 8 or less
best_spans, conf = model.get_prediction().get_best_span(8)
# Loads the saved weights
model_dir.restore_checkpoint(sess)
# Now the model is ready to run
# The model takes input in the form of `ContextAndQuestion` objects, for example:
data = [
ParagraphAndQuestion(x, question, None, "user-question%d" % i)
for i, x in enumerate(context)
]
print("Starting run")
# The model is run in two steps, first it "encodes" a batch of paragraph/context pairs
# into numpy arrays, then we use `sess` to run the actual model get the predictions
encoded = model.encode(
data, is_train=False) # batch of `ContextAndQuestion` -> feed_dict
best_spans, conf = sess.run([best_spans, conf],
feed_dict=encoded) # feed_dict -> predictions
best_para = np.argmax(
conf
) # We get output for each paragraph, select the most-confident one to print
print("Best Paragraph: " + str(best_para))
print("Best span: " + str(best_spans[best_para]))
print("Answer text: " +
" ".join(context[best_para]
[best_spans[best_para][0]:best_spans[best_para][1] + 1]))
print("Confidence: " + str(conf[best_para]))
y_output = " ".join(
context[best_para][best_spans[best_para][0]:best_spans[best_para][1] +
1])
print(y_output)
json_data["predictions"].append(str(y_output))
#indicate that the request was a success
json_data["success"] = True
#return the data dictionary as a JSON response
return flask.jsonify(json_data)
def main():
parser = argparse.ArgumentParser(
description='Evaluate a model on TriviaQA data')
parser.add_argument('model', help='model directory')
parser.add_argument(
'-p',
'--paragraph_output',
type=str,
help="Save fine grained results for each paragraph in csv format")
parser.add_argument('-o',
'--official_output',
type=str,
help="Build an offical output file with the model's"
" most confident span for each (question, doc) pair")
parser.add_argument('--no_ema',
action="store_true",
help="Don't use EMA weights even if they exist")
parser.add_argument(
'--n_processes',
type=int,
default=None,
help=
"Number of processes to do the preprocessing (selecting paragraphs+loading context) with"
)
parser.add_argument('-i',
'--step',
type=int,
default=None,
help="checkpoint to load, default to latest")
parser.add_argument('-n',
'--n_sample',
type=int,
default=None,
help="Number of questions to evaluate on")
parser.add_argument('-a', '--async', type=int, default=10)
parser.add_argument('-t',
'--tokens',
type=int,
default=400,
help="Max tokens per a paragraph")
parser.add_argument('-g',
'--n_paragraphs',
type=int,
default=15,
help="Number of paragraphs to run the model on")
parser.add_argument('-f',
'--filter',
type=str,
default=None,
choices=["tfidf", "truncate", "linear"],
help="How to select paragraphs")
parser.add_argument(
'-b',
'--batch_size',
type=int,
default=200,
help="Batch size, larger sizes might be faster but wll take more memory"
)
parser.add_argument('--max_answer_len',
type=int,
default=8,
help="Max answer span to select")
parser.add_argument('-c',
'--corpus',
choices=[
"web-dev", "web-test", "web-verified-dev",
"web-train", "open-dev", "open-train", "wiki-dev",
"wiki-test"
],
default="web-verified-dev")
parser.add_argument("-s",
"--source_dir",
type=str,
default=None,
help="where to take input files")
parser.add_argument("--n_span_per_q",
type=int,
default=1,
help="where to take input files")
args = parser.parse_args()
dataset_name = args.source_dir.split('/')[-1]
model_name = args.model.split('/')[-1]
ElasticLogger().write_log('INFO',
'Start Evaluation',
context_dict={
'model': model_name,
'dataset': dataset_name
})
model_dir = ModelDir(args.model)
model = model_dir.get_model()
if args.corpus.startswith('web'):
dataset = TriviaQaWebDataset()
if args.corpus == "web-dev":
test_questions = dataset.get_dev()
elif args.corpus == "web-test":
test_questions = dataset.get_test()
elif args.corpus == "web-verified-dev":
test_questions = dataset.get_verified()
elif args.corpus == "web-train":
test_questions = dataset.get_train()
else:
raise AssertionError()
elif args.corpus.startswith("wiki"):
dataset = TriviaQaWikiDataset()
if args.corpus == "wiki-dev":
test_questions = dataset.get_dev()
elif args.corpus == "wiki-test":
test_questions = dataset.get_test()
else:
raise AssertionError()
else:
dataset = TriviaQaOpenDataset(args.source_dir)
if args.corpus == "open-dev":
# just loading the pkl that was saved in build_span_corpus
test_questions = dataset.get_dev()
elif args.corpus == "open-train":
test_questions = dataset.get_train()
else:
raise AssertionError()
### ALON debuging
#test_questions = test_questions[0:5]
corpus = dataset.evidence
splitter = MergeParagraphs(args.tokens)
per_document = args.corpus.startswith(
"web") # wiki and web are both multi-document
#per_document = True
filter_name = args.filter
if filter_name is None:
# Pick default depending on the kind of data we are using
if per_document:
filter_name = "tfidf"
else:
filter_name = "linear"
print("Selecting %d paragraphs using method \"%s\" per %s" %
(args.n_paragraphs, filter_name,
("question-document pair" if per_document else "question")))
if filter_name == "tfidf":
para_filter = TopTfIdf(NltkPlusStopWords(punctuation=True),
args.n_paragraphs)
elif filter_name == "truncate":
para_filter = FirstN(args.n_paragraphs)
elif filter_name == "linear":
para_filter = ShallowOpenWebRanker(args.n_paragraphs)
else:
raise ValueError()
n_questions = args.n_sample
docqa.config.SPANS_PER_QUESTION = args.n_span_per_q
#n_questions = 1
if n_questions is not None:
test_questions.sort(key=lambda x: x.question_id)
np.random.RandomState(0).shuffle(test_questions)
test_questions = test_questions[:n_questions]
print("Building question/paragraph pairs...")
# Loads the relevant questions/documents, selects the right paragraphs, and runs the model's preprocessor
if per_document:
prep = ExtractMultiParagraphs(splitter,
para_filter,
model.preprocessor,
require_an_answer=False)
else:
prep = ExtractMultiParagraphsPerQuestion(splitter,
para_filter,
model.preprocessor,
require_an_answer=False)
prepped_data = preprocess_par(test_questions, corpus, prep,
args.n_processes, 1000)
data = []
for q in prepped_data.data:
for i, p in enumerate(q.paragraphs):
if q.answer_text is None:
ans = None
else:
ans = TokenSpans(q.answer_text, p.answer_spans)
data.append(
DocumentParagraphQuestion(q.question_id, p.doc_id,
(p.start, p.end), q.question, p.text,
ans, i))
# Reverse so our first batch will be the largest (so OOMs happen early)
questions = sorted(data,
key=lambda x: (x.n_context_words, len(x.question)),
reverse=True)
print("Done, starting eval")
if args.step is not None:
if args.step == "latest":
checkpoint = model_dir.get_latest_checkpoint()
else:
checkpoint = model_dir.get_checkpoint(int(args.step))
else:
checkpoint = model_dir.get_best_weights()
if checkpoint is not None:
print("Using best weights")
else:
print("Using latest checkpoint")
checkpoint = model_dir.get_latest_checkpoint()
test_questions = ParagraphAndQuestionDataset(
questions, FixedOrderBatcher(args.batch_size, True))
evaluation = trainer.test(
model, [RecordParagraphSpanPrediction(args.max_answer_len, True)],
{args.corpus: test_questions}, ResourceLoader(), checkpoint,
not args.no_ema, args. async)[args.corpus]
if not all(len(x) == len(data) for x in evaluation.per_sample.values()):
raise RuntimeError()
df = pd.DataFrame(evaluation.per_sample)
if args.official_output is not None:
print("Saving question result")
fns = {}
if per_document:
# I didn't store the unormalized filenames exactly, so unfortunately we have to reload
# the source data to get exact filename to output an official test script
print("Loading proper filenames")
if args.corpus == 'web-test':
source = join(TRIVIA_QA, "qa", "web-test-without-answers.json")
elif args.corpus == "web-dev":
source = join(TRIVIA_QA, "qa", "web-dev.json")
else:
raise AssertionError()
with open(join(source)) as f:
data = json.load(f)["Data"]
for point in data:
for doc in point["EntityPages"]:
filename = doc["Filename"]
fn = join("wikipedia", filename[:filename.rfind(".")])
fn = normalize_wiki_filename(fn)
fns[(point["QuestionId"], fn)] = filename
answers = {}
scores = {}
for q_id, doc_id, start, end, txt, score in df[[
"question_id", "doc_id", "para_start", "para_end",
"text_answer", "predicted_score"
]].itertuples(index=False):
filename = dataset.evidence.file_id_map[doc_id]
if per_document:
if filename.startswith("web"):
true_name = filename[4:] + ".txt"
else:
true_name = fns[(q_id, filename)]
# Alon Patch for triviaqa test results
true_name = true_name.replace('TriviaQA_Org/', '')
key = q_id + "--" + true_name
else:
key = q_id
prev_score = scores.get(key)
if prev_score is None or prev_score < score:
scores[key] = score
answers[key] = txt
with open(args.official_output, "w") as f:
json.dump(answers, f)
output_file = args.paragraph_output
if output_file is not None:
print("Saving paragraph result")
df.to_csv(output_file, index=False)
print("Computing scores")
if per_document:
group_by = ["question_id", "doc_id"]
else:
group_by = ["question_id"]
# Print a table of scores as more paragraphs are used
df.sort_values(group_by + ["rank"], inplace=True)
df_scores = df.copy(deep=True)
df_scores['predicted_score'] = df_scores['predicted_score'].apply(
lambda x: pd.Series(x).max())
em = compute_ranked_scores(df_scores, "predicted_score", "text_em",
group_by)
f1 = compute_ranked_scores(df_scores, "predicted_score", "text_f1",
group_by)
table = [["N Paragraphs", "EM", "F1"]]
table += list([str(i + 1), "%.4f" % e, "%.4f" % f]
for i, (e, f) in enumerate(zip(em, f1)))
table_df = pd.DataFrame(table[1:], columns=table[0]).drop(['N Paragraphs'],
axis=1)
ElasticLogger().write_log('INFO', 'Results', context_dict={'model': model_name, 'dataset': dataset_name, \
'max_EM':table_df.max().ix['EM'], \
'max_F1':table_df.max().ix['F1'], \
'result_table': str(table_df)})
df_flat = []
for id, question in df.iterrows():
for text_answer, predicted_span, predicted_score in zip(
question['text_answer'], question['predicted_span'],
question['predicted_score']):
new_question = dict(question.copy())
new_question.update({
'text_answer': text_answer,
'predicted_span': predicted_span,
'predicted_score': predicted_score
})
df_flat.append(new_question)
results_df = pd.DataFrame(df_flat)
#Alon: outputing the estimates for all the
#results_df = results_df.groupby(['question_id', 'text_answer']).apply(lambda df: df.ix[df['predicted_score'].argmax()]).reset_index(drop=True)
results_df.sort_values(by=['question_id', 'predicted_score'],
ascending=False).set_index([
'question_id', 'text_answer'
])[['question', 'predicted_score',
'text_em']].to_csv('results.csv')
print_table(table)
def main():
parser = argparse.ArgumentParser(
description='Train a model on TriviaQA unfiltered')
parser.add_argument(
'mode',
choices=["confidence", "merge", "shared-norm", "sigmoid", "paragraph"])
parser.add_argument("name", help="Where to store the model")
parser.add_argument("-t",
"--n_tokens",
default=400,
type=int,
help="Paragraph size")
parser.add_argument(
'-n',
'--n_processes',
type=int,
default=2,
help="Number of processes (i.e., select which paragraphs to train on) "
"the data with")
parser.add_argument("-s",
"--source_dir",
type=str,
default=None,
help="where to take input files")
parser.add_argument("--n_epochs",
type=int,
default=None,
help="Max number of epoches to train on ")
parser.add_argument("--char_th",
type=int,
default=None,
help="char level embeddings")
parser.add_argument("--hl_dim",
type=int,
default=None,
help="hidden layer dim size")
parser.add_argument("--regularization",
type=int,
default=None,
help="hidden layer dim size")
parser.add_argument("--LR",
type=float,
default=1.0,
help="hidden layer dim size")
parser.add_argument("--save_every",
type=int,
default=1800,
help="save period")
parser.add_argument("--init_from",
type=str,
default=None,
help="model to init from")
args = parser.parse_args()
mode = args.mode
#out = args.name + "-" + datetime.now().strftime("%m%d-%H%M%S")
out = join('models', args.name)
char_th = 100
hl_dim = 140
if args.char_th is not None:
print(args.char_th)
char_th = int(args.char_th)
out += '--th' + str(char_th)
if args.hl_dim is not None:
print(args.hl_dim)
hl_dim = int(args.hl_dim)
out += '--hl' + str(hl_dim)
if args.init_from is None:
model = get_model(char_th, hl_dim, mode, WithIndicators())
else:
md = model_dir.ModelDir(args.init_from)
model = md.get_model()
extract = ExtractMultiParagraphsPerQuestion(MergeParagraphs(args.n_tokens),
ShallowOpenWebRanker(16),
model.preprocessor,
intern=True)
eval = [
LossEvaluator(),
MultiParagraphSpanEvaluator(8,
"triviaqa",
mode != "merge",
per_doc=False)
]
oversample = [1] * 4
if mode == "paragraph":
n_epochs = 120
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(ClusteredBatcher(
60, ContextLenBucketedKey(3), True),
oversample,
only_answers=True)
elif mode == "confidence" or mode == "sigmoid":
if mode == "sigmoid":
n_epochs = 640
else:
n_epochs = 160
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(
ClusteredBatcher(60, ContextLenBucketedKey(3), True), oversample)
else:
n_epochs = 80
test = RandomParagraphSetDatasetBuilder(
120, "merge" if mode == "merge" else "group", True, oversample)
train = StratifyParagraphSetsBuilder(30, mode == "merge", True,
oversample)
if args.n_epochs is not None:
n_epochs = args.n_epochs
out += '--' + str(n_epochs)
if args.LR != 1.0:
out += '--' + str(args.LR)
data = TriviaQaOpenDataset(args.source_dir)
async_encoding = 10
#async_encoding = 0
params = TrainParams(SerializableOptimizer("Adadelta",
dict(learning_rate=args.LR)),
num_epochs=n_epochs,
num_of_steps=250000,
ema=0.999,
max_checkpoints_to_keep=2,
async_encoding=async_encoding,
log_period=30,
eval_period=1800,
save_period=args.save_every,
eval_samples=dict(dev=None, train=6000),
regularization_weight=None)
data = PreprocessedData(data, extract, train, test, eval_on_verified=False)
data.preprocess(args.n_processes, 1000)
with open(__file__, "r") as f:
notes = f.read()
notes = "Mode: " + args.mode + "\n" + notes
if args.init_from is not None:
init_from = model_dir.ModelDir(args.init_from).get_best_weights()
if init_from is None:
init_from = model_dir.ModelDir(
args.init_from).get_latest_checkpoint()
else:
init_from = None
trainer.start_training(data,
model,
params,
eval,
model_dir.ModelDir(out),
notes,
initialize_from=init_from)
def main():
parser = argparse.ArgumentParser(description='Run the demo server')
parser.add_argument('model', help='Models to use')
parser.add_argument(
'-v',
'--voc',
help='vocab to use, only words from this file will be used')
parser.add_argument('-t',
'--tokens',
type=int,
default=400,
help='Number of tokens to use per paragraph')
parser.add_argument('--vec_dir', help='Location to find word vectors')
parser.add_argument('--n_paragraphs',
type=int,
default=12,
help="Number of paragraphs to run the model on")
parser.add_argument('--span_bound',
type=int,
default=8,
help="Max span size to return as an answer")
parser.add_argument(
'--tagme_api_key',
help="Key to use for TAGME (tagme.d4science.org/tagme)")
parser.add_argument('--bing_api_key', help="Key to use for bing searches")
parser.add_argument('--tagme_thresh', default=0.2, type=float)
parser.add_argument('--no_wiki',
action="store_true",
help="Dont use TAGME")
parser.add_argument('--n_web',
type=int,
default=10,
help='Number of web docs to fetch')
parser.add_argument('--blacklist_trivia_sites',
action="store_true",
help="Don't use trivia websites")
parser.add_argument('-c',
'--wiki_cache',
help="Cache wiki articles in this directory")
parser.add_argument('--n_dl_threads',
type=int,
default=5,
help="Number of threads to download documents with")
parser.add_argument('--request_timeout', type=int, default=60)
parser.add_argument('--download_timeout', type=int, default=25)
parser.add_argument('--workers',
type=int,
default=1,
help="Number of server workers")
parser.add_argument('--debug',
default=None,
choices=["random_model", "dummy_qa"])
args = parser.parse_args()
span_bound = args.span_bound
if args.tagme_api_key is not None:
tagme_api_key = args.tagme_api_key
else:
tagme_api_key = environ.get("TAGME_API_KEY")
if args.bing_api_key is not None:
bing_api_key = args.bing_api_key
else:
bing_api_key = environ.get("BING_API_KEY")
if bing_api_key is None and args.n_web > 0:
raise ValueError("If n_web > 0 you must give a BING_API_KEY")
if args.debug is None:
model = ModelDir(args.model)
else:
model = RandomPredictor(5, WithIndicators())
if args.vec_dir is not None:
loader = LoadFromPath(args.vec_dir)
else:
loader = ResourceLoader()
if args.debug == "dummy_qa":
qa = DummyQa()
else:
qa = QaSystem(
args.wiki_cache,
MergeParagraphs(args.tokens),
ShallowOpenWebRanker(args.n_paragraphs),
args.voc,
model,
loader,
bing_api_key,
tagme_api_key=tagme_api_key,
n_dl_threads=args.n_dl_threads,
blacklist_trivia_sites=args.blacklist_trivia_sites,
download_timeout=args.download_timeout,
span_bound=span_bound,
tagme_threshold=None if args.no_wiki else args.tagme_thresh,
n_web_docs=args.n_web)
logging.propagate = False
formatter = logging.Formatter("%(asctime)s: %(levelname)s: %(message)s")
handler = logging.StreamHandler()
handler.setFormatter(formatter)
logging.root.addHandler(handler)
logging.root.setLevel(logging.DEBUG)
app = Sanic()
app.config.REQUEST_TIMEOUT = args.request_timeout
@app.route("/answer")
async def answer(request):
try:
question = request.args["question"][0]
if question == "":
return response.json({'message': 'No question given'},
status=400)
spans, paras = await qa.answer_question(question)
answers = select_answers(paras, spans, span_bound, 10)
return json([x.to_json() for x in answers])
except Exception as e:
log.info("Error: " + str(e))
raise ServerError("Server Error", status_code=500)
@app.route('/answer-from', methods=['POST'])
async def answer_from(request):
try:
args = ujson.loads(request.body.decode("utf-8"))
question = args.get("question")
if question is None or question == "":
return response.json({'message': 'No question given'},
status=400)
doc = args["document"]
if len(doc) > 500000:
raise ServerError("Document too large", status_code=400)
spans, paras = qa.answer_with_doc(question, doc)
answers = select_answers(paras, spans, span_bound, 10)
return json([x.to_json() for x in answers])
except Exception as e:
log.info("Error: " + str(e))
raise ServerError("Server Error", status_code=500)
app.static('/', './docqa//server/static/index.html')
app.static('/about.html', './docqa//service/static/about.html')
app.run(host="0.0.0.0", port=8000, workers=args.workers, debug=False)
def main(Data: pd.DataFrame, nlp, model_dir, model):
#parser = argparse.ArgumentParser(description="Run an ELMo model on user input")
#parser.add_argument("model", help="Model directory")
#parser.add_argument("question", help="Question to answer")
#parser.add_argument("documents", help="List of text documents to answer the question with", nargs='+')
#args = parser.parse_args()
#print("Preprocessing...")
# Load the model
#model_dir = ModelDir(MODEL_DIR)
#model = model_dir.get_model()
print(model)
if not isinstance(model, ParagraphQuestionModel):
raise ValueError(
"This script is built to work for ParagraphQuestionModel models only"
)
#print(model)
# Read the documents
documents = []
documents.append(Data.at[0, 'Filetext'])
"""import pyodbc
conn = pyodbc.connect("Driver={ODBC Driver 13 for SQL Server};"
"Server=192.168.100.15;"
"Database=PharmaAce;"
"UID=sa;"
"PWD=admin@123;"
"Trusted_Connection=no;")
cursor=conn.cursor()
#(23211,28690,33214,25638,25837,26454,28693,26137,31428,32087)
for doc in cursor.execute("select cast(filetext as varchar(max)) as filetext from kpl_tmp"):
documents.append(doc[0])
#doc="D:\Document QnA\document-qa-master\Data\Drug_Delivery_Surveying_Global_Competitive_Landscape_BMI.txt"
if not isfile(doc):
raise ValueError(doc + " does not exist")
with open(doc, "r") as f:
documents.append(f.read())
"""
#print("Loaded %d documents" % len(documents))
#temp=documents[0].split()
# Split documents into lists of paragraphs
#documents=[" ".join(temp[i:(i+400)]) for i in range(1,len(temp),400)]
documents = [re.split("\s*\n\s*", doc) for doc in documents]
# Tokenize the input, the models expects data to be tokenized using `NltkAndPunctTokenizer`
# Note the model expects case-sensitive input
tokenizer = NltkAndPunctTokenizer()
question = tokenizer.tokenize_paragraph_flat(
Data.at[0, 'Question']) # List of words
# Now list of document->paragraph->sentence->word
documents = [[tokenizer.tokenize_paragraph(p) for p in doc]
for doc in documents]
# Now group the document into paragraphs, this returns `ExtractedParagraph` objects
# that additionally remember the start/end token of the paragraph within the source document
splitter = MergeParagraphs(400)
#splitter = PreserveParagraphs() # Uncomment to use the natural paragraph grouping
documents = [splitter.split(doc) for doc in documents]
#print(str(len(documents))+" kpl") #kpl
# Now select the top paragraphs using a `ParagraphFilter`
print(len(documents)) #kpl
if len(documents) == 1:
# Use TF-IDF to select top paragraphs from the document
selector = TopTfIdf(NltkPlusStopWords(True), n_to_select=5)
context = selector.prune(question, documents[0])
else:
# Use a linear classifier to select top paragraphs among all the documents
selector = ShallowOpenWebRanker(n_to_select=10)
context = selector.prune(question, flatten_iterable(documents))
#print("Select %d paragraph" % len(context))
if model.preprocessor is not None:
# Models are allowed to define an additional pre-processing step
# This will turn the `ExtractedParagraph` objects back into simple lists of tokens
context = [
model.preprocessor.encode_text(question, x) for x in context
]
else:
# Otherwise just use flattened text
context = [flatten_iterable(x.text) for x in context]
print("Setting up model")
# Tell the model the batch size (can be None) and vocab to expect, This will load the
# needed word vectors and fix the batch size to use when building the graph / encoding the input
voc = set(question)
for txt in context:
voc.update(txt)
model.set_input_spec(nlp,
ParagraphAndQuestionSpec(batch_size=len(context)),
voc)
# Now we build the actual tensorflow graph, `best_span` and `conf` are
# tensors holding the predicted span (inclusive) and confidence scores for each
# element in the input batch, confidence scores being the pre-softmax logit for the span
#print("Build tf graph") #kpl
print("after set input spec")
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# We need to use sess.as_default when working with the cuNND stuff, since we need an active
# session to figure out the # of parameters needed for each layer. The cpu-compatible models don't need this.
with sess.as_default():
# 8 means to limit the span to size 8 or less
best_spans, conf = model.get_prediction().get_best_span(8)
# Loads the saved weights
model_dir.restore_checkpoint(sess)
print("after loading weights")
# Now the model is ready to run
# The model takes input in the form of `ContextAndQuestion` objects, for example:
data = [
ParagraphAndQuestion(x, question, None, "user-question%d" % i)
for i, x in enumerate(context)
]
#print("Starting run")
# The model is run in two steps, first it "encodes" a batch of paragraph/context pairs
# into numpy arrays, then we use `sess` to run the actual model get the predictions
encoded = model.encode(
data, is_train=True) # batch of `ContextAndQuestion` -> feed_dict
best_spans, conf = sess.run([best_spans, conf],
feed_dict=encoded) # feed_dict -> predictions
best_para = np.argmax(
conf
) # We get output for each paragraph, select the most-confident one to print
#print("Best Paragraph: " + str(best_para))
#print("Best span: " + str(best_spans[best_para]))
#print("Answer text: " + " ".join(context[best_para][best_spans[best_para][0]:best_spans[best_para][1]+1]))
#print("Confidence: " + str(conf[best_para]))
return " ".join(
context[best_para][best_spans[best_para][0]:best_spans[best_para][1] +
1])
#if __name__ == "__main__":
# main()
def getAnswer(self):
#parser = argparse.ArgumentParser(description="Run an ELMo model on user input")
#parser.add_argument("model", help="Model directory")
#parser.add_argument("question", help="Question to answer")
#parser.add_argument("documents", help="List of text documents to answer the question with", nargs='+')
#args = parser.parse_args()
#print("Preprocessing...")
# Load the model
model_dir = ModelDir(MODEL_DIR)
model = model_dir.get_model()
if not isinstance(model, ParagraphQuestionModel):
raise ValueError(
"This script is built to work for ParagraphQuestionModel models only"
)
conn = pyodbc.connect(DB_CONN)
cursor = conn.cursor()
#(23211,28690,33214,25638,25837,26454,28693,26137,31428,32087)
query="select cast(filetext as varchar(max)) as filetext, name, type from dbo.UserworkspaceData where objectmasterid= "+\
str(self.ObjectMasterId)+\
" order by id asc"
#query="select cast(filetext as varchar(max)) as filetext from kpl_tmp"
documents = []
document = ""
name = ""
filetype = 0
for doc in cursor.execute(query):
document = document + doc[0]
name = doc[1]
filetype = doc[2]
#open("E:/kpl.txt","w+").write(document)
documents.append(document)
#documents.replace("\n\n","\n")
#r.sub("",documents)
#documents=" ".join(documents.split())
#open("E:\kpl_test.txt","w+").write(document)
#doc="D:\Document QnA\document-qa-master\Data\Drug_Delivery_Surveying_Global_Competitive_Landscape_BMI.txt"
# =============================================================================
# if not isfile(doc):
# raise ValueError(doc + " does not exist")
# with open(doc, "r") as f:
# documents.append(f.read())
# =============================================================================
#print("Loaded %d documents" % len(documents))
#temp=documents[0].split()
# Split documents into lists of paragraphs
#documents=[" ".join(temp[i:(i+400)]) for i in range(1,len(temp),400)]
documents = [re.split("\s*\n\s*", doc) for doc in documents]
# Tokenize the input, the models expects data to be tokenized using `NltkAndPunctTokenizer`
# Note the model expects case-sensitive input
tokenizer = NltkAndPunctTokenizer()
question = tokenizer.tokenize_paragraph_flat(
self.Question) # List of words
# Now list of document->paragraph->sentence->word
documents = [[tokenizer.tokenize_paragraph(p) for p in doc]
for doc in documents]
# Now group the document into paragraphs, this returns `ExtractedParagraph` objects
# that additionally remember the start/end token of the paragraph within the source document
splitter = MergeParagraphs(400)
#splitter = PreserveParagraphs() # Uncomment to use the natural paragraph grouping
documents = [splitter.split(doc) for doc in documents]
#print(str(len(documents))+" kpl") #kpl
# Now select the top paragraphs using a `ParagraphFilter`
if len(documents) == 1:
# Use TF-IDF to select top paragraphs from the document
selector = TopTfIdf(NltkPlusStopWords(True), n_to_select=5)
context = selector.prune(question, documents[0])
else:
# Use a linear classifier to select top paragraphs among all the documents
selector = ShallowOpenWebRanker(n_to_select=10)
context = selector.prune(question, flatten_iterable(documents))
#print("Select %d paragraph" % len(context))
if model.preprocessor is not None:
# Models are allowed to define an additional pre-processing step
# This will turn the `ExtractedParagraph` objects back into simple lists of tokens
context = [
model.preprocessor.encode_text(question, x) for x in context
]
else:
# Otherwise just use flattened text
context = [flatten_iterable(x.text) for x in context]
#x=open("E:\context.txt","a+")
#[x.write(" ".join(cont)) for cont in context]
#x.write("\n.......................................................\n")
#print("Setting up model")
# Tell the model the batch size (can be None) and vocab to expect, This will load the
# needed word vectors and fix the batch size to use when building the graph / encoding the input
voc = set(question)
for txt in context:
voc.update(txt)
model.set_input_spec(self.nlp,
ParagraphAndQuestionSpec(batch_size=len(context)),
voc)
# Now we build the actual tensorflow graph, `best_span` and `conf` are
# tensors holding the predicted span (inclusive) and confidence scores for each
# element in the input batch, confidence scores being the pre-softmax logit for the span
#print("Build tf graph") #kpl
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# We need to use sess.as_default when working with the cuNND stuff, since we need an active
# session to figure out the # of parameters needed for each layer. The cpu-compatible models don't need this.
with sess.as_default():
# 8 means to limit the span to size 8 or less
best_spans, conf = model.get_prediction().get_best_span(8)
# Loads the saved weights
model_dir.restore_checkpoint(sess)
# Now the model is ready to run
# The model takes input in the form of `ContextAndQuestion` objects, for example:
data = [
ParagraphAndQuestion(x, question, None, "user-question%d" % i)
for i, x in enumerate(context)
]
#print("Starting run")
# The model is run in two steps, first it "encodes" a batch of paragraph/context pairs
# into numpy arrays, then we use `sess` to run the actual model get the predictions
encoded = model.encode(
data, is_train=True) # batch of `ContextAndQuestion` -> feed_dict
best_spans, conf = sess.run(
[best_spans, conf], feed_dict=encoded) # feed_dict -> predictions
best_para = np.argmax(
conf
) # We get output for each paragraph, select the most-confident one to print
#print("Best Paragraph: " + str(best_para))
#print("Best span: " + str(best_spans[best_para]))
#print("Answer text: " + " ".join(context[best_para][best_spans[best_para][0]:best_spans[best_para][1]+1]))
#print("Confidence: " + str(conf[best_para]))
Answer = " ".join(context[best_para]
[best_spans[best_para][0]:best_spans[best_para][1] +
1])
print("Confidence: " + str(conf[best_para]))
print("Best Paragraph: " + str(best_para))
print("Best span: " + str(best_spans[best_para]))
print("Answer text: " + Answer)
print(" ".join(context[best_para]))
context[best_para][best_spans[best_para][
0]] = r"<em>" + context[best_para][best_spans[best_para][0]]
context[best_para][best_spans[best_para][1]] = context[best_para][
best_spans[best_para][1]] + r"</em>"
start = 0
end = len(context[best_para])
positions = [
x for x, n in enumerate(context[best_para]
[0:best_spans[best_para][0]]) if n == "."
]
if len(positions) >= 2: start = positions[len(positions) - 2] + 1
positions = [
x
for x, n in enumerate(context[best_para][best_spans[best_para][1] +
1:]) if n == "."
]
if len(positions) > 1:
end = best_spans[best_para][1] + 1 + positions[1]
d = dict()
if conf[best_para] > 10:
d["answer"] = Answer
else:
d["answer"] = ""
d["name"] = name
d["filetype"] = filetype
d["paragraph"] = re.sub(r' (?=\W)', '',
" ".join(context[best_para][start:end]))
d["ObjectMasterId"] = self.ObjectMasterId
return d
#if __name__ == "__main__":
# main()
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"corpus",
choices=["en", "fr", "de", "ru", "pt", "zh", "pl", "uk", "ta"])
parser.add_argument(
'mode',
choices=["confidence", "merge", "shared-norm", "sigmoid", "paragraph"])
# Note I haven't tested modes other than `shared-norm` on this corpus, so
# some things might need adjusting
parser.add_argument("-t",
"--n_tokens",
default=400,
type=int,
help="Paragraph size")
args = parser.parse_args()
mode = args.mode
corpus = args.corpus
model = get_model(100, 140, mode, WithIndicators())
extract = ExtractMultiParagraphsPerQuestion(MergeParagraphs(args.n_tokens),
ShallowOpenWebRanker(16),
model.preprocessor,
intern=True)
oversample = [
1
] * 2 # Sample the top two answer-containing paragraphs twice
if mode == "paragraph":
n_epochs = 120
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(ClusteredBatcher(
60, ContextLenBucketedKey(3), True),
oversample,
only_answers=True)
elif mode == "confidence" or mode == "sigmoid":
if mode == "sigmoid":
n_epochs = 640
else:
n_epochs = 160
test = RandomParagraphSetDatasetBuilder(120, "flatten", True,
oversample)
train = StratifyParagraphsBuilder(
ClusteredBatcher(60, ContextLenBucketedKey(3), True), oversample)
else:
n_epochs = 80
test = RandomParagraphSetDatasetBuilder(
120, "merge" if mode == "merge" else "group", True, oversample)
train = StratifyParagraphSetsBuilder(30, mode == "merge", True,
oversample)
data = XQADataset(corpus)
data = PreprocessedData(data, extract, train, test, eval_on_verified=False)
data.preprocess(1, 1000)
# dump preprocessed dev data for bert
data.cache_preprocess("dev_data_%s.pkl" % args.corpus)
parser.add_argument('--input_file',
required=True,
help="input file, e.g. train_data.pkl")
parser.add_argument('--output_train_file',
required=True,
help="output train file, e.g. train_output.json")
parser.add_argument('--num_epoch',
required=True,
type=int,
help="num_epoch, e.g. 10")
args = parser.parse_args()
mode = "shared-norm"
model = get_model(100, 140, mode, WithIndicators())
extract = ExtractMultiParagraphsPerQuestion(MergeParagraphs(400),
ShallowOpenWebRanker(16),
model.preprocessor,
intern=True)
oversample = [1] * 2
train = StratifyParagraphSetsBuilder(30, mode == "merge", True, oversample)
test = RandomParagraphSetDatasetBuilder(
120, "merge" if mode == "merge" else "group", True, oversample)
data = PreprocessedData(None, extract, train, test, eval_on_verified=False)
data.load_preprocess(args.input_file)
outputs = []
training_data = data.get_train()
for i in range(args.num_epoch):
for batch in training_data.get_epoch():