  Biomedical text mining is becoming increasingly important as the number of
biomedical documents rapidly grows. With the progress in natural language
processing (NLP), extracting valuable information from biomedical literature
has gained popularity among researchers, and deep learning has boosted the
development of effective biomedical text mining models. However, directly
applying the advancements in NLP to biomedical text mining often yields
unsatisfactory results due to a word distribution shift from general domain
corpora to biomedical corpora. In this article, we investigate how the recently
introduced pre-trained language model BERT can be adapted for biomedical
corpora. We introduce BioBERT (Bidirectional Encoder Representations from
Transformers for Biomedical Text Mining), which is a domain-specific language
representation model pre-trained on large-scale biomedical corpora. With almost
the same architecture across tasks, BioBERT largely outperforms BERT and
previous state-of-the-art models in a variety of biomedical text mining tasks
when pre-trained on biomedical corpora. While BERT obtains performance
comparable to that of previous state-of-the-art models, BioBERT significantly
outperforms them on the following three representative biomedical text mining
tasks: biomedical named entity recognition (0.62% F1 score improvement),
biomedical relation extraction (2.80% F1 score improvement) and biomedical
question answering (12.24% MRR improvement). Our analysis results show that
pre-training BERT on biomedical corpora helps it to understand complex
biomedical texts. We make the pre-trained weights of BioBERT freely available
at https://github.com/naver/biobert-pretrained, and the source code for
fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.
