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Natural Language Processing in Biomedicine

A Practical Guide

  • Textbook
  • © 2024

Overview

Editors:
  1. Hua Xu

    1. Yale University, New Haven, USA

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  2. Dina Demner Fushman

    1. United States National Library of Medicine, Bethesda, USA

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  • Uses a coherent design of chapters covering NLP methods, systems and applications, with useful examples and cases
  • Contains pedagogical features such as learning objectives, glossaries, references, key readings and example questions
  • Features schematics and illustrations to explain key points

Part of the book series: Cognitive Informatics in Biomedicine and Healthcare (CIBH)

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About this book

This textbook covers broad topics within the application of natural language processing (NLP) in biomedicine, and provides in-depth review of the NLP solutions that reveal information embedded in biomedical text. The need for biomedical NLP research and development has grown rapidly in the past two decades as an important field in cognitive informatics.
 
Natural Language Processing in Biomedicine: A Practical Guide introduces the history of the biomedical NLP field and takes the reader through the basic aspects of NLP including different levels of linguistic information and widely used machine learning and deep learning algorithms. The book details common biomedical NLP tasks, such as named entity recognition, concept normalization, relation extraction, text classification, information retrieval, and question answering. The book illustrates the tasks with real-life use cases and introduces real-world datasets, novel machine learning and deep learning algorithms, and large language models. Relevant resources for corpora and medical terminologies are also introduced. The final chapters are devoted to discussing applications of biomedical NLP in healthcare and life sciences. This textbook therefore represents essential reading for students in biomedical informatics programs, as well as for professionals who are conducting research or building biomedical NLP systems.

Keywords

Table of contents (15 chapters)

  1. Front Matter

    Pages i-xvi
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  2. Introduction and Basic Knowledge

    1. Front Matter

      Pages 1-1
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    2. Introduction to Natural Language Processing of Clinical Text

      • Dina Demner Fushman, Hua Xu
      Pages 3-11

    3. Overview of Linguistic Information

      • Dina Demner Fushman, Carol Friedman
      Pages 13-42

    4. Machine Learning and Deep Learning Algorithms

      • Steven Bethard
      Pages 43-76

  3. Biomedical NLP Tasks and Methods

    1. Front Matter

      Pages 77-77
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    2. Named Entity Recognition

      • Murthy V. Devarakonda, Kalpana Raja, Hua Xu
      Pages 79-99

    3. Relation Extraction

      • Murthy V. Devarakonda, Kalpana Raja, Hua Xu
      Pages 101-135

    4. Medical Concept Normalization

      • Hua Xu, Dina Demner Fushman, Na Hong, Kalpana Raja
      Pages 137-164

    5. Text Classification

      • Trevor Cohen, Serguei Pakhomov, Amandalynne Paullada, Meliha Yetisgen
      Pages 165-194

    6. Information Retrieval

      • Kirk Roberts
      Pages 195-230

    7. Question Answering

      • Dina Demner Fushman
      Pages 231-263

    8. Large Language Model and Text Generation

      • Yonghui Wu
      Pages 265-297

  4. Systems and Applications

    1. Front Matter

      Pages 299-299
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    2. Development of Clinical NLP Systems

      • Hua Xu, Dina Demner Fushman
      Pages 301-324

    3. NLP Applications—Clinical Documents

      • Yanshan Wang
      Pages 325-349

    4. NLP Applications—Biomedical Literature

      • Rui Zhang, Andrej Kastrin, Dimitar Hristovski, Marcelo Fiszman, Halil Kilicoglu
      Pages 351-395

    5. NLP Applications—Social Media

      • Abeed Sarker
      Pages 397-427

    6. NLP Applications—Other Biomedical Texts

      • Kirk Roberts, Hua Xu, Dina Demner Fushman
      Pages 429-444
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Editors and Affiliations

  • Yale University, New Haven, USA

    Hua Xu

  • United States National Library of Medicine, Bethesda, USA

    Dina Demner Fushman

About the editors

Dr. Hua Xu is Robert T. McCluskey Professor and Vice Chair for Research and Development within the Section of Biomedical Informatics and Data Science at Yale School of Medicine.  He received his Ph.D. in Biomedical Informatics from Columbia University. His primary research interests include biomedical natural language processing (NLP) and data mining, as well as their applications in secondary use of electronic health records data for clinical and translational research. His research is funded by multiple agencies (i.e., NLM, NCI, NIGMS, NIA, AHA, and NSF). NLP methods and tools developed in his lab have been top ranked in various biomedical NLP shared tasks and widely used to support diverse biomedical applications. He previously chaired the American Medical Informatics Association (AMIA) NLP Working Group and currently leads the Observational Health Data Sciences and Informatics (OHDSI) NLP Working Group. His contributions have been recognized with fellowships from both theAmerican College of Medical Informatics (ACMI) and the International Academy of Health Sciences Informatics (IAHSI).


Dr. Dina Demner-Fushmsn is an Investigator at the National Library of Medicine, NIH. Dr. Demner-Fushman leads research in the areas of Information Extraction for Clinical Decision Support, EMR Database Research and Development, and Image and Text Indexing for Clinical Decision Support and Education. The outgrowths of these projects are the evidence-based decision support system, InfoBot, used at the NIH Clinical Center from 2009 to 2020, an image retrieval engine, Open-i, launched in 2012, and an automatic question answering service CHiQA launched in 2018. Dr. Demner-Fushman authored more than 300 articles, book chapters and books in the fields of information retrieval, natural language processing, and biomedical and clinical informatics.  Dr. Demner-Fushman is a Fellow of the American College of Medical Informatics (ACMI), an Associate Editor of the Journal of the American Medical Informatics Association, a member of Nature’s Scientific Data Editorial Board, past chair of the AMIA NLP SIG, and a founding member and chair of the Association for Computational Linguistics (ACL) Special Interest Group on biomedical natural language processing.

Bibliographic Information

  • Book Title: Natural Language Processing in Biomedicine

  • Book Subtitle: A Practical Guide

  • Editors: Hua Xu, Dina Demner Fushman

  • Series Title: Cognitive Informatics in Biomedicine and Healthcare

  • DOI: https://doi.org/10.1007/978-3-031-55865-8

  • Publisher: Springer Cham

  • eBook Packages: Medicine, Medicine (R0)

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2024

  • Hardcover ISBN: 978-3-031-55864-1Published: 09 June 2024

  • Softcover ISBN: 978-3-031-55867-2Due: 10 July 2024

  • eBook ISBN: 978-3-031-55865-8Published: 08 June 2024

  • Series ISSN: 2662-7280

  • Series E-ISSN: 2662-7299

  • Edition Number: 1

  • Number of Pages: XVI, 444

  • Number of Illustrations: 33 b/w illustrations, 42 illustrations in colour

  • Topics: Health Informatics, Cognitive Psychology

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