def gen_tf_record():
sequence_length = 300
data_loader = get_biobert_nli_data_loader(sequence_length)
todo = [("train", [data_loader.train_file]),
("dev", [data_loader.dev_file])]
batch_size = 32
dir_path = os.path.join(output_path,
"biobert_mnli_{}".format(sequence_length))
exist_or_mkdir(dir_path)
for name, files in todo[::-1]:
output_file = os.path.join(dir_path, name)
writer = RecordWriterWrap(output_file)
for file in files:
for e in data_loader.example_generator(file):
f = entry_to_feature_dict(e)
f["is_real_example"] = create_int_feature([1])
writer.write_feature(f)
if name == "dev":
while writer.total_written % batch_size != 0:
f["is_real_example"] = create_int_feature([0])
writer.write_feature(f)
writer.close()
print("Wrote %d total instances" % writer.total_written)
def convert_to_unpaired(source_path, output_path):
def feature_transformer(feature):
new_features_1 = collections.OrderedDict()
new_features_2 = collections.OrderedDict()
def put(feature_name):
return create_int_feature(take(feature[feature_name]))
new_features_1["input_ids"] = put("input_ids1")
new_features_1["input_mask"] = put("input_mask1")
new_features_1["segment_ids"] = put("segment_ids1")
new_features_1["label_ids"] = create_int_feature([1])
new_features_2["input_ids"] = put("input_ids2")
new_features_2["input_mask"] = put("input_mask2")
new_features_2["segment_ids"] = put("segment_ids2")
new_features_2["label_ids"] = create_int_feature([0])
return new_features_1, new_features_2
writer = RecordWriterWrap(output_path)
feature_itr = load_record_v2(source_path)
for feature in feature_itr:
new_features_1, new_features_2 = feature_transformer(feature)
writer.write_feature(new_features_1)
writer.write_feature(new_features_2)
writer.close()
def write_records(records: List[Record], max_seq_length, output_path):
tokenizer = get_tokenizer()
def encode(record: Record) -> OrderedDict:
tokens = ["[CLS]"] + record.claim_tokens + [
"[SEP]"
] + record.doc_tokens + ["[SEP]"]
segment_ids = [0] * (len(record.claim_tokens) + 2) \
+ [1] * (len(record.doc_tokens) + 1)
tokens = tokens[:max_seq_length]
segment_ids = segment_ids[:max_seq_length]
features = get_basic_input_feature(tokenizer, max_seq_length, tokens,
segment_ids)
labels = [0.] * (len(record.claim_tokens) + 2) + record.scores
labels += (max_seq_length - len(labels)) * [0.]
label_mask = [0] * (len(record.claim_tokens) + 2) + record.valid_mask
label_mask += (max_seq_length - len(label_mask)) * [0]
features['label_ids'] = create_float_feature(labels)
features['label_masks'] = create_int_feature(label_mask)
return features
writer = RecordWriterWrap(output_path)
features: List[OrderedDict] = lmap(encode, records)
foreach(writer.write_feature, features)
writer.close()
def write_records(records: List[Payload], max_seq_length, output_path):
tokenizer = get_tokenizer()
def tokenize_from_tokens(tokens: List[str]) -> List[str]:
output = []
for t in tokens:
ts = tokenizer.tokenize(t)
output.extend(ts)
return output
def encode(inst: Payload) -> OrderedDict:
tokens1: List[str] = tokenizer.tokenize(inst.candidate_text)
max_seg2_len = max_seq_length - 3 - len(tokens1)
tokens2 = tokenize_from_tokens(inst.passage)[:max_seg2_len]
tokens = ["[CLS]"] + tokens1 + ["[SEP]"] + tokens2 + ["[SEP]"]
segment_ids = [0] * (len(tokens1) + 2) \
+ [1] * (len(tokens2) + 1)
tokens = tokens[:max_seq_length]
segment_ids = segment_ids[:max_seq_length]
features = get_basic_input_feature(tokenizer, max_seq_length, tokens,
segment_ids)
features['label_ids'] = create_int_feature([inst.is_correct])
features['data_id'] = create_int_feature([inst.data_id])
return features
writer = RecordWriterWrap(output_path)
features: List[OrderedDict] = lmap(encode, records)
foreach(writer.write_feature, features)
writer.close()
def tf_record_gen(ranked_list: Dict[str, List[SimpleRankedListEntry]],
queries: Dict,
text_reader: Callable[[str], str],
output_path,
max_seq_length: int,
data_info_save_name,
):
writer = RecordWriterWrap(output_path)
tokenizer = get_tokenizer()
dummy_label = 0
data_id_idx = 0
data_id_info = {}
for query_id_str in ranked_list:
query_rep = queries[query_id_str]
query_str = query_rep['query']
for ranked_entry in ranked_list[query_id_str]:
data_id = data_id_idx
data_id_idx += 1
data_id_info[data_id] = (query_id_str, ranked_entry.doc_id)
text = text_reader(ranked_entry.doc_id)
tokens, segment_ids = encode_query_and_text(tokenizer, query_str, text, max_seq_length)
features = get_basic_input_feature(tokenizer,
max_seq_length,
tokens,
segment_ids)
features['label_ids'] = create_int_feature([dummy_label])
features['data_id'] = create_int_feature([data_id])
writer.write_feature(features)
save_to_pickle(data_id_info, data_info_save_name)
writer.close()
def work(self, job_id):
qid_to_max_seg_idx: Dict[str, Dict[str, int]] = self.best_seg_collector.get_best_seg_info_2d(job_id)
qids = self.query_group[job_id]
output_path = os.path.join(self.out_dir, str(job_id))
writer = RecordWriterWrap(output_path)
for qid in qids:
sr_per_qid = self.seg_resource_loader.load_for_qid(qid)
doc_ids = list(qid_to_max_seg_idx[qid].keys())
max_seg_idx_d = qid_to_max_seg_idx[qid]
pos_doc, neg_doc = self.pool_pos_neg_doc(doc_ids, sr_per_qid)
def get_max_seg(sr_per_doc: SRPerQueryDoc) -> SegmentRepresentation:
max_seg_idx = max_seg_idx_d[sr_per_doc.doc_id]
try:
seg = sr_per_doc.segs[max_seg_idx]
except IndexError:
print('qid={} doc_id={}'.format(qid, sr_per_doc.doc_id))
print("max_seg_idx={} but len(segs)={}".format(max_seg_idx, len(sr_per_doc.segs)))
raise
return seg
pos_seg = get_max_seg(pos_doc)
neg_seg = get_max_seg(neg_doc)
feature = encode_sr_pair(pos_seg,
neg_seg,
self.max_seq_length,
)
writer.write_feature(feature)
writer.close()
def work(self, job_id):
qid_to_max_seg_idx: Dict[Tuple[str, str], int] = self.best_seg_collector.get_best_seg_info(job_id)
qids = self.query_group[job_id]
output_path = os.path.join(self.out_dir, str(job_id))
writer = RecordWriterWrap(output_path)
for qid in qids:
sr_per_qid = self.seg_resource_loader.load_for_qid(qid)
for sr_per_doc in sr_per_qid.sr_per_query_doc:
if len(sr_per_doc.segs) == 1:
continue
qdid = qid, sr_per_doc.doc_id
max_seg_idx = qid_to_max_seg_idx[qdid]
label_id = sr_per_doc.label
try:
seg = sr_per_doc.segs[max_seg_idx]
feature = encode_sr(seg,
self.max_seq_length,
label_id,
)
writer.write_feature(feature)
except IndexError:
print('qid={} doc_id={}'.format(qid, sr_per_doc.doc_id))
print("max_seg_idx={} but len(segs)={}".format(max_seg_idx, len(sr_per_doc.segs)))
raise
writer.close()
def augment_topic_ids(records, topic_id, save_path):
writer = RecordWriterWrap(save_path)
for feature in records:
first_inst = feature_to_ordered_dict(feature)
first_inst["topic_ids"] = create_int_feature([topic_id])
writer.write_feature(first_inst)
writer.close()
def tfrecord_convertor(source_path: FilePath, output_path: FilePath,
feature_transformer):
writer = RecordWriterWrap(output_path)
feature_itr = load_record_v2(source_path)
for feature in feature_itr:
new_features = feature_transformer(feature)
writer.write_feature(new_features)
writer.close()
def encode2(itr_lm, itr_nli, out_path):
writer = RecordWriterWrap(out_path)
for nli_entry in itr_nli:
lm_entry = itr_lm.__next__()
new_features = combine_feature(lm_entry, nli_entry)
writer.write_feature(new_features)
print("Wrote {} items".format(writer.total_written))
writer.close()
def do_filtering(file_path, out_path, condition_fn, debug_call_back=None):
writer = RecordWriterWrap(out_path)
for item in load_record(file_path):
features = feature_to_ordered_dict(item)
if condition_fn(features):
if debug_call_back is not None:
debug_call_back(features)
writer.write_feature(features)
writer.close()
def baseline_bert_gen_unbal_resplit(outpath, split):
tokenizer = get_tokenizer()
data: List[PerspectiveCandidate] = load_data_point_50_train_val(split)
max_seq_length = 512
writer = RecordWriterWrap(outpath)
for entry in data:
writer.write_feature(enc_to_feature(tokenizer, max_seq_length, entry))
writer.close()
def write_pairwise_record(tokenizer, max_seq_length, insts, out_path):
writer = RecordWriterWrap(out_path)
for inst in insts:
(tokens, segment_ids), (tokens2, segment_ids2) = inst
features = combine_features(tokens, segment_ids, tokens2, segment_ids2,
tokenizer, max_seq_length)
writer.write_feature(features)
writer.close()
def work(self, job_id):
tfrecord_path = os.path.join(self.input_dir, str(job_id))
features = load_record(tfrecord_path)
save_path = os.path.join(self.out_dir, str(job_id))
writer = RecordWriterWrap(save_path)
for f in rel_filter(features, self.relevance_scores,
self.cpid_to_label):
writer.write_feature(f)
writer.close()
def work(self, job_id):
tfrecord_path = os.path.join(self.input_dir, str(job_id))
features = load_record(tfrecord_path)
save_path = os.path.join(self.out_dir, str(job_id))
writer = RecordWriterWrap(save_path)
for f in collect_passages(features, self.relevance_scores,
self.cpid_to_label, self.num_max_para,
self.window_size):
writer.write_feature(f)
writer.close()
def work(self, job_id):
features: List[ParagraphClaimPersFeature] = pickle.load(
open(os.path.join(self.input_dir, str(job_id)), "rb"))
writer = RecordWriterWrap(os.path.join(self.out_dir, str(job_id)))
for f in features:
f2: ParagraphFeature = to_paragraph_feature(f)
encoded_list: List[OrderedDict] = format_paragraph_features(
self.tokenizer, self.max_seq_length, f2)
foreach(writer.write_feature, encoded_list)
writer.close()
def write(self, insts: List[Instance], out_path):
writer = RecordWriterWrap(out_path)
for inst in insts:
feature = get_basic_input_feature(self.tokenizer,
self.max_seq_length, inst.tokens,
inst.seg_ids)
feature["data_id"] = create_int_feature([int(inst.data_id)])
feature["label_ids"] = create_int_feature([int(inst.label)])
writer.write_feature(feature)
writer.close()
def do(data_id):
working_dir = os.environ["TF_WORKING_DIR"]
tokenzier = get_tokenizer()
name1 = os.path.join(working_dir, "bert_loss", "{}.pickle".format(data_id))
name2 = os.path.join(working_dir, "bfn_loss", "{}.pickle".format(data_id))
tf_logging.debug("Loading " + name1)
output1 = PredictionOutput(name1)
tf_logging.debug("Loading " + name2)
output2 = PredictionOutput(name2)
assert len(output1.input_ids) == len(output2.input_ids)
out_path = os.path.join(working_dir,
"loss_pred_train_data/{}".format(data_id))
record_writer = RecordWriterWrap(out_path)
n_inst = len(output1.input_ids)
sep_id = tokenzier.vocab["[SEP]"]
tf_logging.debug("Iterating")
ticker = TimeEstimator(n_inst, "", 1000)
for i in range(n_inst):
if i % 1000 == 0:
assert_input_equal(output1.input_ids[i], output2.input_ids[i])
try:
features = get_segment_and_mask(output1.input_ids[i], sep_id)
except:
try:
sep_indice = get_sep_considering_masking(
output1.input_ids[i], sep_id, output1.masked_lm_ids[i],
output1.masked_lm_positions[i])
features = get_segment_and_mask_inner(output1.input_ids[i],
sep_indice)
except:
tokens = tokenzier.convert_ids_to_tokens(output1.input_ids[i])
print(tokenization.pretty_tokens(tokens))
print(output1.masked_lm_ids[i])
print(output1.masked_lm_positions[i])
raise
features["next_sentence_labels"] = create_int_feature([0])
features["masked_lm_positions"] = create_int_feature(
output1.masked_lm_positions[i])
features["masked_lm_ids"] = create_int_feature(
output1.masked_lm_ids[i])
features["masked_lm_weights"] = create_float_feature(
output1.masked_lm_weights[i])
features["loss_base"] = create_float_feature(
output1.masked_lm_example_loss[i])
features["loss_target"] = create_float_feature(
output2.masked_lm_example_loss[i])
record_writer.write_feature(features)
ticker.tick()
record_writer.close()
def augment_topic_ids(records, save_path):
writer = RecordWriterWrap(save_path)
for feature in records:
first_inst = feature_to_ordered_dict(feature)
input_ids = first_inst["input_ids"].int64_list.value
token_ids = input_ids[1]
topic = token_ids_to_topic[token_ids]
topic_id = data_generator.argmining.ukp_header.all_topics.index(topic)
first_inst["topic_ids"] = create_int_feature([topic_id])
writer.write_feature(first_inst)
writer.close()
def _write_instances(self, insts, output_file):
writer = RecordWriterWrap(output_file)
for instance in insts:
word_tokens, def_tokens, segment_ids = instance
word_tokens_ids = self.tokenizer.convert_tokens_to_ids(word_tokens)
features = get_basic_input_feature(self.tokenizer, self.max_seq_length, def_tokens, segment_ids)
while len(word_tokens_ids) < self.max_word_tokens:
word_tokens_ids.append(0)
features["word"] = create_int_feature(word_tokens_ids)
writer.write_feature(features)
writer.close()
tf_logging.info("Wrote %d total instances", writer.total_written)
def work(job_id):
outfile = os.path.join(working_dir, "BLC_data", "{}".format(job_id))
if os.path.exists(outfile):
return "Skip"
tf_logging.debug("Loading data")
data = load(job_id)
tf_logging.debug("Done")
if data is None:
return "No Input"
writer = RecordWriterWrap(outfile)
batch_size, seq_length = data[0]['input_ids'].shape
keys = list(data[0].keys())
vectors = flatten_batches(data)
basic_keys = "input_ids", "input_mask", "segment_ids"
any_key = keys[0]
data_len = len(vectors[any_key])
num_predictions = len(vectors["grouped_positions"][0][0])
for i in range(data_len):
mask_valid = [0] * seq_length
loss1_arr = [0] * seq_length
loss2_arr = [0] * seq_length
positions = vectors["grouped_positions"][i]
num_trials = len(positions)
for t_i in range(num_trials):
for p_i in range(num_predictions):
loc = vectors["grouped_positions"][i][t_i][p_i]
loss1 = vectors["grouped_loss1"][i][t_i][p_i]
loss2 = vectors["grouped_loss2"][i][t_i][p_i]
loss1_arr[loc] = loss1
loss2_arr[loc] = loss2
assert mask_valid[loc] == 0
mask_valid[loc] = 1
features = collections.OrderedDict()
for key in basic_keys:
features[key] = create_int_feature(vectors[key][i])
features["loss_valid"] = create_int_feature(mask_valid)
features["loss1"] = create_float_feature(loss1_arr)
features["loss2"] = create_float_feature(loss2_arr)
features["next_sentence_labels"] = create_int_feature([0])
writer.write_feature(features)
#if i < 20:
# log_print_feature(features)
writer.close()
return "Done"
def write_instances(self, new_inst_list, outfile):
writer = RecordWriterWrap(outfile)
example_numbers = []
for (inst_index, instance) in enumerate(new_inst_list):
tokens, segment_ids = instance
features = get_basic_input_feature(self.tokenizer,
self.target_seq_length, tokens,
segment_ids)
features["use_context"] = create_int_feature([1])
writer.write_feature(features)
writer.close()
tf_logging.info("Wrote %d total instances", writer.total_written)
return example_numbers
def write(self, insts, out_path):
writer = RecordWriterWrap(out_path)
f = open(out_path + ".info", "wb")
doc_id_list = []
for inst in insts:
tokens, segment_ids, doc_id = inst
feature = get_basic_input_feature(self.tokenizer,
self.max_seq_length, tokens,
segment_ids)
doc_id_list.append(doc_id)
writer.write_feature(feature)
pickle.dump(doc_id_list, f)
writer.close()
def write_instances(self, new_inst_list, outfile):
writer = RecordWriterWrap(outfile)
example_numbers = []
feature_formatter = MLMFeaturizer(self.tokenizer, self.max_seq_length,
self.max_predictions_per_seq)
for (inst_index, instance) in enumerate(new_inst_list):
features = feature_formatter.instance_to_features(instance)
writer.write_feature(features)
if inst_index < 20:
log_print_inst(instance, features)
writer.close()
tf_logging.info("Wrote %d total instances", writer.total_written)
return example_numbers
def write_instances(self, new_inst_list, outfile):
writer = RecordWriterWrap(outfile)
example_numbers = []
for (inst_index, instance) in enumerate(new_inst_list):
features = get_basic_input_feature(self.tokenizer,
self.max_seq_length,
instance.tokens,
instance.segment_ids)
writer.write_feature(features)
if inst_index < 20:
log_print_inst(instance, features)
writer.close()
return example_numbers
def write(self, insts, out_path):
writer = RecordWriterWrap(out_path)
def tokens_to_int_feature(tokens):
return create_int_feature(
self.tokenizer.convert_tokens_to_ids(tokens))
for inst in insts:
query_tokens, content_tokens, label = inst
feature = collections.OrderedDict()
feature['query'] = tokens_to_int_feature(
query_tokens[:self.max_query_len])
feature['content'] = tokens_to_int_feature(
content_tokens[:self.max_seq_length])
feature['label_ids'] = create_int_feature([label])
writer.write_feature(feature)
writer.close()
def write_instances(self, instances, outfile):
writer = RecordWriterWrap(outfile)
example_numbers = []
get_basic_input_features_fn = partial(get_basic_input_feature,
self.tokenizer,
self.max_seq_length)
for (inst_index, instance) in enumerate(instances):
features = get_basic_input_features_fn(instance.tokens,
instance.segment_ids)
features["use_context"] = create_int_feature([1])
writer.write_feature(features)
if inst_index < 20:
log_print_inst(instance, features)
writer.close()
tf_logging.info("Wrote %d total instances", writer.total_written)
return example_numbers
def gen_mismatched():
sequence_length = 300
data_loader = get_modified_nli_data_loader(sequence_length)
dir_path = os.path.join(output_path,
"nli_tfrecord_cls_{}".format(sequence_length))
name = "dev_mis"
output_file = os.path.join(dir_path, name)
batch_size = 32
writer = RecordWriterWrap(output_file)
for e in data_loader.example_generator(data_loader.dev_file2):
f = entry_to_feature_dict(e)
f["is_real_example"] = create_int_feature([1])
writer.write_feature(f)
while writer.total_written % batch_size != 0:
f["is_real_example"] = create_int_feature([0])
writer.write_feature(f)
writer.close()
print("Wrote %d total instances" % writer.total_written)
def gen_with_aux_emb(outpath, aux_embedding_d, split, dims):
tokenizer = get_tokenizer()
data: List[PerspectiveCandidate] = load_data_point(split)
max_seq_length = 512
zero_vector = [0.] * dims
not_found = set()
def get_aux_embedding_fn(cid):
cid = int(cid)
if cid in aux_embedding_d:
return aux_embedding_d[cid]
else:
if cid not in not_found:
not_found.add(cid)
print("Aux embedding not found", cid)
return {}
def enc_to_feature(pc: PerspectiveCandidate) -> OrderedDict:
emb_model = get_aux_embedding_fn(pc.cid)
seg1 = tokenizer.tokenize(pc.claim_text)
seg2 = tokenizer.tokenize(pc.p_text)
input_tokens = ["[CLS]"] + seg1 + ["[SEP]"] + seg2 + ["[SEP]"]
aux_emb = get_word_embedding(emb_model, input_tokens, dims)
aux_emb += (max_seq_length - len(aux_emb)) * [zero_vector]
aux_emb = np.array(aux_emb)
flat_aux_emb = np.reshape(aux_emb, [-1])
segment_ids = [0] * (len(seg1) + 2) + [1] * (len(seg2) + 1)
feature = get_basic_input_feature(tokenizer, max_seq_length,
input_tokens, segment_ids)
feature["label_ids"] = create_int_feature([int(pc.label)])
feature["aux_emb"] = create_float_feature(flat_aux_emb)
return feature
writer = RecordWriterWrap(outpath)
for entry in data:
writer.write_feature(enc_to_feature(entry))
writer.close()
def write_instances(self, new_inst_list, outfile):
writer = RecordWriterWrap(outfile)
example_numbers = []
for (inst_index, instance) in enumerate(new_inst_list):
features = get_basic_input_feature(self.tokenizer,
self.max_seq_length,
instance.tokens,
instance.segment_ids)
features["next_sentence_labels"] = btd.create_int_feature([0])
writer.write_feature(features)
if inst_index < 20:
log_print_inst(instance, features)
writer.close()
tf_logging.info("Wrote %d total instances", writer.total_written)
return example_numbers