Fine-tuning coreference resolution for different styles of clinical narratives

Liao, Yuxiang, Liu, Hantao ORCID: https://orcid.org/0000-0003-4544-3481 and Spasić, Irena ORCID: https://orcid.org/0000-0002-8132-3885 2024. Fine-tuning coreference resolution for different styles of clinical narratives. Journal of Biomedical Informatics 149 , 104578. 10.1016/j.jbi.2023.104578

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Abstract

Objective: Coreference resolution (CR) is a natural language processing (NLP) task that is concerned with finding all expressions within a single document that refer to the same entity. This makes it crucial in supporting downstream NLP tasks such as summarization, question answering and information extraction. Despite great progress in CR, our experiments have highlighted a substandard performance of the existing open-source CR tools in the clinical domain. We set out to explore some practical solutions to fine-tune their performance on clinical data. Methods: We first explored the possibility of automatically producing silver standards following the success of such an approach in other clinical NLP tasks. We designed an ensemble approach that leverages multiple models to automatically annotate co-referring mentions. Subsequently, we looked into other ways of incorporating human feedback to improve the performance of an existing neural network approach. We proposed a semi-automatic annotation process to facilitate the manual annotation process. We also compared the effectiveness of active learning relative to random sampling in an effort to further reduce the cost of manual annotation. Results: Our experiments demonstrated that the silver standard approach was ineffective in fine-tuning the CR models. Our results indicated that active learning should also be applied with caution. The semi-automatic annotation approach combined with continued training was found to be well suited for the rapid transfer of CR models under low-resource conditions. The ensemble approach demonstrated a potential to further improve accuracy by leveraging multiple fine-tuned models. Conclusion: Overall, we have effectively transferred a general CR model to a clinical domain. Our findings based on extensive experimentation have been summarized into practical suggestions for rapid transferring of CR models across different styles of clinical narratives. Keywords: natural language processing, coreference resolution, transfer learning, active learning, ensemble algorithm

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Computer Science & Informatics
Subjects:	Q Science > QA Mathematics > QA76 Computer software
Publisher:	Elsevier
ISSN:	1532-0464
Funders:	China Scholarship Council-Cardiff University Scholarship
Date of First Compliant Deposit:	22 January 2024
Date of Acceptance:	12 December 2023
Last Modified:	22 Jan 2024 11:46
URI:	https://orca.cardiff.ac.uk/id/eprint/164860

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