{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/self-supervised-intermediate-fine-tuning-of","title":"Self-Supervised Intermediate Fine-Tuning of Biomedical Language Models for Interpreting Patient Case Descriptions","arxiv_id":null,"date":"2022-10-01","proceeding":"COLING 2022 10","authors":["Israa Alghanmi","Luis Espinosa-Anke","Steven Schockaert"],"abstract":"Interpreting patient case descriptions has emerged as a challenging problem for biomedical NLP, where the aim is typically to predict diagnoses, to recommended treatments, or to answer questions about cases more generally. Previous work has found that biomedical language models often lack the knowledge that is needed for such tasks. In this paper, we aim to improve their performance through a self-supervised intermediate fine-tuning strategy based on PubMed abstracts. Our solution builds on the observation that many of these abstracts are case reports, and thus essentially patient case descriptions. As a general strategy, we propose to fine-tune biomedical language models on the task of predicting masked medical concepts from such abstracts. We find that the success of this strategy crucially depends on the selection of the medical concepts to be masked. By ensuring that these concepts are sufficiently salient, we can substantially boost the performance of biomedical language models, achieving state-of-the-art results on two benchmarks.","url_abs":"https://aclanthology.org/2022.coling-1.123","url_pdf":"https://aclanthology.org/2022.coling-1.123.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"self-supervised-intermediate-fine-tuning-of","repo_url":"https://github.com/israa-alghanmi/intermediate-ft-biomedical-lms","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}