Automatic Extraction of Disease Risk Factors from Medical Publications

Maxim Rubchinsky, Ella Rabinovich, Adi Shraibman, Netanel Golan, Tali Sahar, Dorit Shweiki

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We present a novel approach to automating the identification of risk factors for diseases from medical literature, leveraging pre-trained models in the bio-medical domain, while tuning them for the specific task. Faced with the challenges of the diverse and unstructured nature of medical articles, our study introduces a multi-step system to first identify relevant articles, then classify them based on the presence of risk factor discussions and, finally, extract specific risk factor information for a disease through a question-answering model. Our contributions include the development of a comprehensive pipeline for the automated extraction of risk factors and the compilation of several datasets, which can serve as valuable resources for further research in this area. These datasets encompass a wide range of diseases, as well as their associated risk factors, meticulously identified and validated through a fine-grained evaluation scheme. We conducted both automatic and thorough manual evaluation, demonstrating encouraging results. We also highlight the importance of improving models and expanding dataset comprehensiveness to keep pace with the rapidly evolving field of medical research..

Original languageEnglish
Title of host publicationBioNLP 2024 - 23rd Meeting of the ACL Special Interest Group on Biomedical Natural Language Processing, Proceedings of the Workshop and Shared Tasks
EditorsDina Demner-Fushman, Sophia Ananiadou, Makoto Miwa, Kirk Roberts, Junichi Tsujii
PublisherAssociation for Computational Linguistics (ACL)
Pages474-485
Number of pages12
ISBN (Electronic)9798891761308
StatePublished - 2024
Externally publishedYes
Event23rd Meeting of the ACL Special Interest Group on Biomedical Natural Language Processing, BioNLP 2024 - Bangkok, Thailand
Duration: 16 Aug 2024 → …

Publication series

NameBioNLP 2024 - 23rd Meeting of the ACL Special Interest Group on Biomedical Natural Language Processing, Proceedings of the Workshop and Shared Tasks

Conference

Conference23rd Meeting of the ACL Special Interest Group on Biomedical Natural Language Processing, BioNLP 2024
Country/TerritoryThailand
CityBangkok
Period16/08/24 → …

Bibliographical note

Publisher Copyright:
©2024 Association for Computational Linguistics.

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Language and Linguistics
  • Computer Science Applications
  • Information Systems
  • Software

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