Natural Language Processing in Biomedicine:
A Practical Guide


(Springer Nature, expected publication in early 2024)




This first edition of "A Practical Guide to Natural Language Processing", edited by Hua Xu and Dina Demner-Fushman, will be published by Springer Nature in their Cognitive Informatics in Health and Medicine book series. Natural Language Processing (NLP), a major component of artificial intelligence (AI), automates computer understanding of the meaning of a text in a document. The end-goal of NLP is to approach human understanding of language. NLP is an interdisciplinary domain that combines computer science and computational linguistics. In the clinical and biomedical domain, it also requires domain knowledge. This first edition focuses on the application of NLP primarily in healthcare. The book includes three sections. The first section begins with an introduction to NLP, related linguistic information, and machine learning and deep learning algorithms. The second section focuses on the traditional biomedical NLP tasks and methods such as named entity recognition and relation extraction, as well as the recent advancements due to large language models. The third section discusses various systems and their applications in biomedical, clinical, social media, and other biomedical texts. The book is recommended to both beginners and experts in the field of NLP and AI.

Natural Language Processing in Biomedicine: A Practical Guide


Editors:

Hua Xu, PhD, Yale University, New Haven, CT

Dina Demner-Fushman, MD, PhD, Computational Health Research Branch, National Institutes of Health, Bethesda, MD

Table of Contents


Front Matter

Dedication

Foreword by Lucila Ohno-Machado

Preface by Hua Xu and Dina Demner-Fushman

Table of Contents and Contributors

I. Introduction and Basic Knowledge

  1. Introduction

Dina Demner-Fushman and Hua Xu

  1. Overview of Linguistic Information

Dina Demner-Fushman and Carol Friedman

  1. Machine Learning and Deep Learning Algorithms

Steven Berthard

II. Biomedical NLP Tasks and Methods

  1. Named Entity Recognition

Murthy V Devarakonda, Kalpana Raja, and Hua Xu

  1. Relational Extraction

Murthy V Devarakonda, Kalpana Raja, and Hua Xu

  1. Medical Concept Normalization

Hua Xu, Dina Demner-Fushman, Na Hong, and Kalpana Raja

  1. Text Classification

Trevor Cohen, Serguei Pakhomov, Amandalynne Paullada, and Meliha Yetisgen

  1. Information Retrieval

Kirk Roberts

  1. Question Answering

Dina Demner-Fushman

  1. Large Language Modesl and Biomedical Text Generation

Yonghui Wu

III. Systems and Applications

  1. Development of Clinical NLP Systems

Hua Xu, Dina Demner-Fushman

  1. NLP Applications: Clinical Documents

Yanshan Wang

  1. NLP Applications: Biomedical Literature

Rui Zhang, Andrej Kastrin, Dimitar Hristovski, Marcelo Fiszman, and Halil Kilicoglu

  1. NLP Applications: Social Media

Abeed Sarker

  1. NLP Applications: Other Biomedical Texts

Kirk Roberts, Hua Xu, and Dina Demner-Fushman

Subject Index