Dependency parsing of biomedical text with BERT

Abstract Background: : Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading formalism for dependency parsing. While a number of recent tasks centering on UD have substantially advanced the state of the art in multilingual parsing, there has been only little study of parsing texts from specialized domains such as biomedicine. Methods: : We explore the application of state-of-the-art neural dependency parsing methods to biomedical text using the recently introduced CRAFT-SA shared task dataset. The CRAFT-SA task broadly follows the UD representation and recent UD task conventions, allowing us to fne-tune the UD-compatible Turku Neural Parser and UDify neural parsers to the task. We further evaluate the efect of transfer learning using a broad selection of BERT models, including several models pre-trained specifcally for biomedical text processing. Results: : We fnd that recently introduced neural parsing technology is capable of generating highly accurate analyses of biomedical text, substantially improving on the best performance reported in the original CRAFT-SA shared task. We also fnd that initialization using a deep transfer learning model pre-trained on in-domain texts is key to maximizing the performance of the parsing methods. Keywords: Parsing, Deep learning, CRAFT