The Application of Large Language Models in Clinical Practice

A special issue of BioMedInformatics (ISSN 2673-7426). This special issue belongs to the section "Clinical Informatics".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 1835

Special Issue Editor


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Guest Editor
Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
Interests: using natural language processing; information retrieval; user modeling; artificial intelligence to create intelligent natural language dialog systems and extract information from biomedical text
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Special Issue Information

Dear Colleagues,

Large language models (LLMs) now make it possible to accelerate advances in medical practice by making it easier to deploy advanced natural language processing methods for a wide range of challenges. LLMs can help find connections between large and disparate sources of information, including patient data, medical literature, and other underutilized sources of information, such as national census data. LLMs can also allow clinicians to access summary information drawn from disparate clinical notes, including progress notes, consultation notes, discharge summaries, referral notes, and SOAP notes.

This Special Issue aims to bring together researchers and practitioners working in the areas of natural language processing and clinical applications of deep learning and their assessment. We welcome original research articles that report on novel and significant findings in the following areas:

  • Medical, nursing, and community health worker supporting applications of large language models.
  • Diagnostics, e.g., methods for identifying diseases, recommending treatments, or predicting patient risks and outcomes.
  • Streamlining clinical workflows.
  • Summarization and de-identification of clinical notes.
  • Ethical considerations and mitigation strategies for addressing bias when using LLM.

We welcome original and unpublished research articles that report on innovative and significant research findings related to the application of large language models in clinical practice. We only accept full-length research articles for this Special Issue, and we encourage authors to follow the standard research paper format and provide a clear and concise description of their research findings.

This Special Issue aims to present cutting-edge research in the field of large language model applications in clinical practice. We welcome high-quality research papers that report on novel and significant research findings that contribute to improved patient outcomes or our understanding of them. We look forward to receiving your submissions and making this Special Issue a success.

Prof. Dr. Susan McRoy
Guest Editor

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Keywords

  • applications of large language models
  • user studies or evaluations
  • clinical decision support
  • diagnostics
  • summarization
  • de-identification
  • ethical considerations and mitigation strategies when using LLM

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Published Papers (1 paper)

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19 pages, 2587 KB  
Article
Assessment of ChatGPT in Recommending Immunohistochemistry Panels for Salivary Gland Tumors
by Maria Cuevas-Nunez, Cosimo Galletti, Luca Fiorillo, Aida Meto, Wilmer Rodrigo Díaz-Castañeda, Shokoufeh Shahrabi Farahani, Guido Fadda, Valeria Zuccalà, Victor Gil Manich, Javier Bara-Casaus and Maria-Teresa Fernández-Figueras
BioMedInformatics 2025, 5(4), 66; https://doi.org/10.3390/biomedinformatics5040066 - 26 Nov 2025
Cited by 1 | Viewed by 1344
Abstract
Background: Salivary gland tumors pose a diagnostic challenge due to their histological heterogeneity and overlapping features. While immunohistochemistry (IHC) is critical for accurate classification, selecting appropriate markers can be subjective and influenced by resource availability. Artificial intelligence (AI), particularly large language models (LLMs), [...] Read more.
Background: Salivary gland tumors pose a diagnostic challenge due to their histological heterogeneity and overlapping features. While immunohistochemistry (IHC) is critical for accurate classification, selecting appropriate markers can be subjective and influenced by resource availability. Artificial intelligence (AI), particularly large language models (LLMs), may support diagnostic decisions by recommending IHC panels. This study evaluated the performance of ChatGPT-4, a free and widely accessible general-purpose LLM, in recommending IHC markers for salivary gland tumors. Methods: ChatGPT-4 was prompted to generate IHC recommendations for 21 types of salivary gland tumors. A consensus of expert pathologists established reference panels. Each tumor type was queried using a standardized prompt designed to elicit IHC marker recommendations (“What IHC markers are recommended to confirm a diagnosis of [tumor type]?”). Outputs were assessed using a structured scoring rubric measuring accuracy, completeness, and relevance. Agreement was measured using Cohen’s Kappa, and diagnostic performance was evaluated via sensitivity, specificity, and F1-scores. Repeated-measures ANOVA and Bland–Altman analysis assessed consistency across three prompts. Results were compared to a rule-based system aligned with expert protocols. Results: ChatGPT-4 demonstrated moderate overall agreement with the pathologist panel (κ = 0.53). Agreement was higher for benign tumors (κ = 0.67) than for malignant ones (κ = 0.40), with pleomorphic adenoma showing the strongest concordance (κ = 0.74). Sensitivity values across tumor types ranged from 0.25 to 0.96, with benign tumors showing higher sensitivity (>0.80) and lower specificity (<0.50) observed in complex malignancies. The overall F1-score was 0.84 for benign and 0.63 for malignant tumors. Repeated prompts produced moderate variability without significant differences (p > 0.05). Compared with the rule-based system, ChatGPT included more incorrect and missed markers, indicating lower diagnostic precision. Conclusions: ChatGPT-4 shows promise as a low-cost tool for IHC panel selection but currently lacks the precision and consistency required for clinical application. Further refinement is needed before integration into diagnostic workflows. Full article
(This article belongs to the Special Issue The Application of Large Language Models in Clinical Practice)
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