Dependency parsing of biomedical text with BERT

• Main Authors: Jenna Kanerva, Filip Ginter, Sampo Pyysalo
• Format: Article
• Language: English
• Published: BMC 2020-12-01
• Series: BMC Bioinformatics
• Subjects: Parsing; Deep learning; CRAFT
• Online Access: https://doi.org/10.1186/s12859-020-03905-8

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 fine-tune the UD-compatible Turku Neural Parser and UDify neural parsers to the task. We further evaluate the effect of transfer learning using a broad selection of BERT models, including several models pre-trained specifically for biomedical text processing. Results:  We find 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 find that initialization using a deep transfer learning model pre-trained on in-domain texts is key to maximizing the performance of the parsing methods.