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Pre-trained Language Models in Biomedical Domain: A Systematic Survey

Authors:

Jie FuAuthors Info & Claims

ACM Computing Surveys, Volume 56, Issue 3

Article No.: 55, Pages 1 - 52

https://doi.org/10.1145/3611651

Published: 05 October 2023 Publication History

Abstract

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing tasks. This also benefits the biomedical domain: researchers from informatics, medicine, and computer science communities propose various PLMs trained on biomedical datasets, e.g., biomedical text, electronic health records, protein, and DNA sequences for various biomedical tasks. However, the cross-discipline characteristics of biomedical PLMs hinder their spreading among communities; some existing works are isolated from each other without comprehensive comparison and discussions. It is nontrivial to make a survey that not only systematically reviews recent advances in biomedical PLMs and their applications but also standardizes terminology and benchmarks. This article summarizes the recent progress of pre-trained language models in the biomedical domain and their applications in downstream biomedical tasks. Particularly, we discuss the motivations of PLMs in the biomedical domain and introduce the key concepts of pre-trained language models. We then propose a taxonomy of existing biomedical PLMs that categorizes them from various perspectives systematically. Plus, their applications in biomedical downstream tasks are exhaustively discussed, respectively. Last, we illustrate various limitations and future trends, which aims to provide inspiration for the future research.

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Index Terms

Pre-trained Language Models in Biomedical Domain: A Systematic Survey
1. Computing methodologies
  1. Artificial intelligence
    1. Natural language processing
      1. Natural language generation
  2. Machine learning
    1. Machine learning approaches
      1. Bio-inspired approaches
      2. Neural networks

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cover image ACM Computing Surveys

ACM Computing Surveys Volume 56, Issue 3

March 2024

977 pages

EISSN:1557-7341

DOI:10.1145/3613568

Editor:
Albert Zomaya
University of Sydney, Australia

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Publication History

Published: 05 October 2023

Online AM: 01 August 2023

Accepted: 22 June 2023

Revised: 15 June 2023

Received: 28 October 2021

Published in CSUR Volume 56, Issue 3

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Chinese Key-Area Research and Development Program of Guangdong Province
Shenzhen Science and Technology Program
Guangdong Provincial Key Laboratory of Big Data Computing, The Chinese University of Hong Kong, Shenzhen, Shenzhen Key Research Project
Shenzhen Doctoral Startup Funding

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https://doi.org/10.4018/979-8-3693-6442-0.ch006
Матвеева ААнтонов Е(2024)МЕТОДИКА ФОРМИРОВАНИЯ БАЗЫ ДАННЫХ ХАРАКТЕРИСТИК СЛОЖНОГО ТЕХНОЛОГИЧЕСКОГО ОБЪЕКТА С ИСПОЛЬЗОВАНИЕМ БОЛЬШИХ ЯЗЫКОВЫХ МОДЕЛЕЙВестник НИЯУ МИФИ10.26583/vestnik.2024.5.713:5(351-357)Online publication date: 5-Nov-2024
https://doi.org/10.26583/vestnik.2024.5.7
Sprint GSchmitter-Edgecombe MCook D(2024)Building a Human Digital Twin (HDTwin) Using Large Language Models for Cognitive Diagnosis: Algorithm Development and ValidationJMIR Formative Research10.2196/638668(e63866)Online publication date: 23-Dec-2024
https://doi.org/10.2196/63866
Chang ESung S(2024)Use of SNOMED CT in Large Language Models: Scoping ReviewJMIR Medical Informatics10.2196/6292412(e62924)Online publication date: 7-Oct-2024
https://doi.org/10.2196/62924
Nunes MBone JFerreira JElvas L(2024)Health Care Language Models and Their Fine-Tuning for Information Extraction: Scoping ReviewJMIR Medical Informatics10.2196/6016412(e60164)Online publication date: 21-Oct-2024
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Matsui KUtsumi TAoki YMaruki TTakeshima MTakaesu Y(2024)Human-Comparable Sensitivity of Large Language Models in Identifying Eligible Studies Through Title and Abstract Screening: 3-Layer Strategy Using GPT-3.5 and GPT-4 for Systematic ReviewsJournal of Medical Internet Research10.2196/5275826(e52758)Online publication date: 16-Aug-2024
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Hao AYuan HHui SSu J(2024)Effective type label-based synergistic representation learning for biomedical event trigger detectionBMC Bioinformatics10.1186/s12859-024-05851-125:1Online publication date: 31-Jul-2024
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Chu ZWang ZZhang W(2024)Fairness in Large Language Models: A Taxonomic SurveyACM SIGKDD Explorations Newsletter10.1145/3682112.368211726:1(34-48)Online publication date: 25-Jul-2024
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Xie YLu JHo JNahab FHu XYang CHui Yang GWang HHan SHauff CZuccon GZhang Y(2024)PromptLink: Leveraging Large Language Models for Cross-Source Biomedical Concept LinkingProceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval10.1145/3626772.3657904(2589-2593)Online publication date: 11-Jul-2024
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August TLo KSmith NReinecke K(2024)Know Your Audience: The benefits and pitfalls of generating plain language summaries beyond the "general" audienceProceedings of the 2024 CHI Conference on Human Factors in Computing Systems10.1145/3613904.3642289(1-26)Online publication date: 11-May-2024
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