Biomedical Natural Language Processing and Text Mining

A special issue of Information (ISSN 2078-2489). This special issue belongs to the section "Biomedical Information and Health".

Deadline for manuscript submissions: 15 September 2024 | Viewed by 2391

Special Issue Editors

Associate Professor, School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
Interests: biomedical text mining; natural language processing; deep learning
Special Issues, Collections and Topics in MDPI journals

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Guest Editor

Special Issue Information

Dear Colleagues,

With the rapid development of biomedical research, a large quantity of biomedical text data is available in the biomedical domain. These biomedical texts, such as biomedical literature, clinical notes and medical guidelines, have become an important biomedical domain resource and provide a rich source of knowledge for biomedical research. However, the large size of the body of biomedical text and its rapid growth (e.g., >3000 articles are published in biomedical journals every day) make document search and information access a demanding task. 

In recent years, biomedical natural language processing (NLP) or text mining with the goal of developing text mining, NLP, and machine learning techniques for various biomedical applications has received considerable attention and has seen great progress. For example, LitCOVID (https://www.ncbi.nlm.nih.gov/research/coronavirus/), a curated literature hub for tracking up-to-date scientific information about COVID-19, automatically collects the COVID-19 articles and further categorizes them according to research topic. Despite this success, many challenges remain to be solved in the field. 

This Special Issue aims to bring together NLP researchers and experts in the biomedical field to advance the current state of the art and share insights and challenges. The goal is to develop computational methods and software tools for analyzing and better understanding unstructured biomedical text data towards accelerated knowledge discovery and improving health.

Topics of interest include, but are not limited to, the following: 

  • Biomedical text classification;
  • Biomedical information retrieval;
  • Biomedical named entity recognition and normalization (linking);
  • Biomedical relation and event extractions;
  • Biomedical literature-based discovery;
  • Biomedical text summarization;
  • Biomedical question answering;
  • Pre-trained language models for biomedical NLP;
  • Biomedical machine translation;
  • BioNLP applications;
  • BioNLP resources and evaluation. 

Dr. Ling Luo
Prof. Dr. Diego Reforgiato Recupero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Information is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomedical text classification
  • biomedical information retrieval
  • biomedical named entity recognition and normalization (linking)
  • biomedical relation and event extractions
  • biomedical literature-based discovery
  • biomedical text summarization
  • biomedical question answering
  • pre-trained language models for biomedical NLP
  • biomedical machine translation
  • BioNLP applications
  • BioNLP resources and evaluation.

Published Papers (1 paper)

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Research

29 pages, 4460 KiB  
Article
Performance of 4 Pre-Trained Sentence Transformer Models in the Semantic Query of a Systematic Review Dataset on Peri-Implantitis
by Carlo Galli, Nikolaos Donos and Elena Calciolari
Information 2024, 15(2), 68; https://doi.org/10.3390/info15020068 - 23 Jan 2024
Viewed by 1743
Abstract
Systematic reviews are cumbersome yet essential to the epistemic process of medical science. Finding significant reports, however, is a daunting task because the sheer volume of published literature makes the manual screening of databases time-consuming. The use of Artificial Intelligence could make literature [...] Read more.
Systematic reviews are cumbersome yet essential to the epistemic process of medical science. Finding significant reports, however, is a daunting task because the sheer volume of published literature makes the manual screening of databases time-consuming. The use of Artificial Intelligence could make literature processing faster and more efficient. Sentence transformers are groundbreaking algorithms that can generate rich semantic representations of text documents and allow for semantic queries. In the present report, we compared four freely available sentence transformer pre-trained models (all-MiniLM-L6-v2, all-MiniLM-L12-v2, all-mpnet-base-v2, and All-distilroberta-v1) on a convenience sample of 6110 articles from a published systematic review. The authors of this review manually screened the dataset and identified 24 target articles that addressed the Focused Questions (FQ) of the review. We applied the four sentence transformers to the dataset and, using the FQ as a query, performed a semantic similarity search on the dataset. The models identified similarities between the FQ and the target articles to a varying degree, and, sorting the dataset by semantic similarities using the best-performing model (all-mpnet-base-v2), the target articles could be found in the top 700 papers out of the 6110 dataset. Our data indicate that the choice of an appropriate pre-trained model could remarkably reduce the number of articles to screen and the time to completion for systematic reviews. Full article
(This article belongs to the Special Issue Biomedical Natural Language Processing and Text Mining)
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