A Review of Recent Work in Transfer Learning and Domain Adaptation for Natural Language Processing of Electronic Health Records

Abstract

OBJECTIVES: We survey recent work in biomedical NLP on building more adaptable or generalizable models, with a focus on work dealing with electronic health record (EHR) texts, to better understand recent trends in this area and identify opportunities for future research. METHODS: We searched PubMed, the Institute of Electrical and Electronics Engineers (IEEE), the Association for Computational Linguistics (ACL) anthology, the Association for the Advancement of Artificial Intelligence (AAAI) proceedings, and Google Scholar for the years 2018-2020. We reviewed abstracts to identify the most relevant and impactful work, and manually extracted data points from each of these papers to characterize the types of methods and tasks that were studied, in which clinical domains, and current state-of-the-art results. RESULTS: The ubiquity of pre-trained transformers in clinical NLP research has contributed to an increase in domain adaptation and generalization-focused work that uses these models as the key component. Most recently, work has started to train biomedical transformers and to extend the fine-tuning process with additional domain adaptation techniques. We also highlight recent research in cross-lingual adaptation, as a special case of adaptation. CONCLUSIONS: While pre-trained transformer models have led to some large performance improvements, general domain pre-training does not always transfer adequately to the clinical domain due to its highly specialized language. There is also much work to be done in showing that the gains obtained by pre-trained transformers are beneficial in real world use cases. The amount of work in domain adaptation and transfer learning is limited by dataset availability and creating datasets for new domains is challenging. The growing body of research in languages other than English is encouraging, and more collaboration between researchers across the language divide would likely accelerate progress in non-English clinical NLP. IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.