  We explore the suitability of unsupervised representation learning methods on
biomedical text -- BioBERT, SciBERT, and BioSentVec -- for biomedical question
answering. To further improve unsupervised representations for biomedical QA,
we introduce a new pre-training task from unlabeled data designed to reason
about biomedical entities in the context. Our pre-training method consists of
corrupting a given context by randomly replacing some mention of a biomedical
entity with a random entity mention and then querying the model with the
correct entity mention in order to locate the corrupted part of the context.
This de-noising task enables the model to learn good representations from
abundant, unlabeled biomedical text that helps QA tasks and minimizes the
train-test mismatch between the pre-training task and the downstream QA tasks
by requiring the model to predict spans. Our experiments show that pre-training
BioBERT on the proposed pre-training task significantly boosts performance and
outperforms the previous best model from the 7th BioASQ Task 7b-Phase B
challenge.
