Datasets:
Tasks:
Text Generation
Sub-tasks:
language-modeling
Languages:
English
Multilinguality:
monolingual
Size Categories:
n>1M
Language Creators:
expert-generated
Annotations Creators:
machine-generated
License:
# coding=utf-8 | |
# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor. | |
# | |
# Licensed under the Apache License, Version 2.0 (the "License"); | |
# you may not use this file except in compliance with the License. | |
# You may obtain a copy of the License at | |
# | |
# http://www.apache.org/licenses/LICENSE-2.0 | |
# | |
# Unless required by applicable law or agreed to in writing, software | |
# distributed under the License is distributed on an "AS IS" BASIS, | |
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
# See the License for the specific language governing permissions and | |
# limitations under the License. | |
# template from : https://github.com/huggingface/datasets/blob/master/templates/new_dataset_script.py | |
"""Loading script for the biolang dataset for language modeling in biology.""" | |
from __future__ import absolute_import, division, print_function | |
import json | |
from pathlib import Path | |
import datasets | |
import shutil | |
_CITATION = """\ | |
@Unpublished{ | |
huggingface: dataset, | |
title = {biolang}, | |
authors={Thomas Lemberger, EMBO}, | |
year={2021} | |
} | |
""" | |
_DESCRIPTION = """\ | |
This dataset is based on abstracts from the open access section of EuropePubMed Central to train language models in the domain of biology. | |
""" | |
_HOMEPAGE = "https://europepmc.org/downloads/openaccess" | |
_LICENSE = "CC BY 4.0" | |
_URLs = { | |
"biolang": "https://huggingface.co/datasets/EMBO/biolang/resolve/main/oapmc_abstracts_figs.zip", | |
} | |
class BioLang(datasets.GeneratorBasedBuilder): | |
"""BioLang: a dataset to train language models in biology.""" | |
VERSION = datasets.Version("0.0.1") | |
BUILDER_CONFIGS = [ | |
datasets.BuilderConfig(name="MLM", version="0.0.1", description="Dataset for general masked language model."), | |
datasets.BuilderConfig(name="DET", version="0.0.1", description="Dataset for part-of-speech (determinant) masked language model."), | |
datasets.BuilderConfig(name="VERB", version="0.0.1", description="Dataset for part-of-speech (verbs) masked language model."), | |
datasets.BuilderConfig(name="SMALL", version="0.0.1", description="Dataset for part-of-speech (determinants, conjunctions, prepositions, pronouns) masked language model."), | |
] | |
DEFAULT_CONFIG_NAME = "MLM" # It's not mandatory to have a default configuration. Just use one if it make sense. | |
def _info(self): | |
if self.config.name == "MLM": | |
features = datasets.Features( | |
{ | |
"input_ids": datasets.Sequence(feature=datasets.Value("int32")), | |
"special_tokens_mask": datasets.Sequence(feature=datasets.Value("int8")), | |
} | |
) | |
elif self.config.name in ["DET", "VERB", "SMALL"]: | |
features = datasets.Features({ | |
"input_ids": datasets.Sequence(feature=datasets.Value("int32")), | |
"tag_mask": datasets.Sequence(feature=datasets.Value("int8")), | |
}) | |
return datasets.DatasetInfo( | |
description=_DESCRIPTION, | |
features=features, # Here we define them above because they are different between the two configurations | |
supervised_keys=('input_ids', 'pos_mask'), | |
homepage=_HOMEPAGE, | |
license=_LICENSE, | |
citation=_CITATION, | |
) | |
def _split_generators(self, dl_manager): | |
"""Returns SplitGenerators.""" | |
if self.config.data_dir: | |
data_dir = self.config.data_dir | |
else: | |
url = _URLs["biolang"] | |
data_dir = dl_manager.download_and_extract(url) | |
data_dir += "/oapmc_abstracts_figs" | |
return [ | |
datasets.SplitGenerator( | |
name=datasets.Split.TRAIN, | |
gen_kwargs={ | |
"filepath": data_dir + "/train.jsonl", | |
"split": "train", | |
}, | |
), | |
datasets.SplitGenerator( | |
name=datasets.Split.TEST, | |
gen_kwargs={ | |
"filepath": data_dir + "/test.jsonl", | |
"split": "test" | |
}, | |
), | |
datasets.SplitGenerator( | |
name=datasets.Split.VALIDATION, | |
gen_kwargs={ | |
"filepath": data_dir + "/eval.jsonl", | |
"split": "eval", | |
}, | |
), | |
] | |
def _generate_examples(self, filepath, split): | |
""" Yields examples. """ | |
with open(filepath, encoding="utf-8") as f: | |
for id_, row in enumerate(f): | |
data = json.loads(row) | |
if self.config.name == "MLM": | |
yield id_, { | |
"input_ids": data["input_ids"], | |
"special_tokens_mask": data['special_tokens_mask'] | |
} | |
elif self.config.name == "DET": | |
pos_mask = [0] * len(data['input_ids']) | |
for idx, label in enumerate(data['label_ids']): | |
if label == 'DET': | |
pos_mask[idx] = 1 | |
yield id_, { | |
"input_ids": data['input_ids'], | |
"tag_mask": pos_mask, | |
} | |
elif self.config.name == "VERB": | |
pos_mask = [0] * len(data['input_ids']) | |
for idx, label in enumerate(data['label_ids']): | |
if label == 'VERB': | |
pos_mask[idx] = 1 | |
yield id_, { | |
"input_ids": data['input_ids'], | |
"tag_mask": pos_mask, | |
} | |
elif self.config.name == "SMALL": | |
pos_mask = [0] * len(data['input_ids']) | |
for idx, label in enumerate(data['label_ids']): | |
if label in ['DET', 'CCONJ', 'SCONJ', 'ADP', 'PRON']: | |
pos_mask[idx] = 1 | |
yield id_, { | |
"input_ids": data['input_ids'], | |
"tag_mask": pos_mask, | |
} | |