CovidBERT-Biomedical Relation Extraction for Covid-19

Abstract

Given the ongoing pandemic of Covid-19 which has had a devastating impact on society and the economy, and the explosive growth of biomedical literature, there has been a growing need to find suitable medical treatments and therapeutics in a short period of time. Developing new treatments and therapeutics can be expensive and a time consuming process. It can be practical to re-purpose existing approved drugs and put them in clinical trial. Hence we propose CovidBERT, a biomedical relationship extraction model based on BERT that extracts new relationships between various biomedical entities, namely gene-disease and chemical-disease relationships. We use the transformer architecture to train on Covid-19 related literature and fine-tune it using standard annotated datasets to show improvement in performance from baseline models. This research uses the transformer BERT model as its foundation and extracts relations from newly published biomedical papers.