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Machine Learning in Biomedical Sciences

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: 20 November 2025 | Viewed by 1254

Special Issue Editors


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Guest Editor
Dipartimento di Economia, Management e Metodi Quantitativi, Università degli Studi di Milano, 20122 Milan, Italy
Interests: machine learning; deep learning; artificial intelligence; explainable AI; pattern recognition; signal processing

Special Issue Information

Dear Colleagues,

Machine learning (ML) has emerged as a transformative tool in the biomedical sciences, offering unprecedented opportunities for analyzing complex biological data and enhancing patient care. The integration of ML with biomedical research has led to significant advancements in diagnostics, personalized medicine, drug discovery, and understanding of complex diseases. As we navigate through vast datasets, ranging from genomic sequences to clinical records, machine learning provides powerful techniques to uncover patterns, make predictions, and inform decision making.

The convergence of biomedical data with advanced ML techniques such as deep learning, natural language processing, and computer vision is revolutionizing how we approach medical research and healthcare delivery. This integration allows for more accurate diagnostic tools, predictive models for disease progression, and the development of innovative therapeutic strategies. Furthermore, ML algorithms are becoming essential in handling the ever-growing data from medical imaging, electronic health records, and high-throughput omic technologies.

This Special Issue on "Machine Learning in Biomedical Sciences" aims to collect the latest research and developments in this rapidly evolving field. We invite contributions that explore the application of machine learning methods to various aspects of biomedical sciences, including diagnostic systems, predictive analytics, personalized treatment plans, and biomedical data analysis. This Special Issue seeks to provide a platform for researchers and practitioners to discuss the challenges, innovations, and future directions of ML in the biomedical domain.

Recommended topics include the following:

  • Machine learning in medical imaging and diagnostics;
  • Predictive models for disease progression and patient outcomes;
  • Deep learning applications in genomics and proteomics;
  • Natural language processing (NLP) in clinical text analysis;
  • Integration of ML with electronic health records (EHRs) for personalized medicine;
  • Drug discovery and development using machine learning;
  • ML methods for analyzing high-throughput biological data;
  • Reinforcement learning in treatment planning and decision support;
  • Explainable AI in healthcare and biomedical research;
  • Ethical considerations and biases in ML applications in biomedicine;
  • Case studies on successful ML implementations in healthcare systems;
  • Real-time data analysis and decision making in medical settings;
  • Future trends and challenges in ML applications in biomedical sciences.

We encourage submissions from researchers, clinicians, and data scientists working at the intersection of machine learning and biomedical sciences. This Special Issue aims to provide insights into how ML is shaping the future of biomedicine and improving patient outcomes.

Dr. Matteo Bodini
Dr. Giovanni Cugliari
Dr. Andrea Loddo
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. Applied Sciences is an international peer-reviewed open access semimonthly 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 2400 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

  • machine learning
  • biomedical sciences
  • medical imaging
  • predictive analytics
  • genomics
  • personalized medicine
  • natural language processing (NLP)
  • electronic health records (EHRs)
  • drug discovery
  • explainable AI

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Published Papers (2 papers)

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Research

12 pages, 489 KiB  
Article
Generative Artificial Intelligence and Risk Appetite in Medical Decisions in Rheumatoid Arthritis
by Florian Berghea, Dan Andras and Elena Camelia Berghea
Appl. Sci. 2025, 15(10), 5700; https://doi.org/10.3390/app15105700 - 20 May 2025
Viewed by 385
Abstract
With Generative AI (GenAI) entering medicine, understanding its decision-making under uncertainty is important. It is well known that human subjective risk appetite influences medical decisions. This study investigated whether the risk appetite of GenAI can be evaluated and if established human risk assessment [...] Read more.
With Generative AI (GenAI) entering medicine, understanding its decision-making under uncertainty is important. It is well known that human subjective risk appetite influences medical decisions. This study investigated whether the risk appetite of GenAI can be evaluated and if established human risk assessment tools are applicable for this purpose in a medical context. Five GenAI systems (ChatGPT 4.5, Gemini 2.0, Qwen 2.5 MAX, DeepSeek-V3, and Perplexity) were evaluated using Rheumatoid Arthritis (RA) clinical scenarios. We employed two methods adapted from human risk assessment: the General Risk Propensity Scale (GRiPS) and the Time Trade-Off (TTO) technique. Queries involving RA cases with varying prognoses and hypothetical treatment choices were posed repeatedly to assess risk profiles and response consistency. All GenAIs consistently identified the same RA cases for the best and worst prognoses. However, the two risk assessment methodologies yielded varied results. The adapted GRiPS showed significant differences in general risk propensity among GenAIs (ChatGPT being the least risk-averse and Qwen/DeepSeek the most), though these differences diminished in specific prognostic contexts. Conversely, the TTO method indicated a strong general risk aversion (unwillingness to trade lifespan for pain relief) across systems yet revealed Perplexity as significantly more risk-tolerant than Gemini. The variability in risk profiles obtained using the GRiPS versus the TTO for the same AI systems raises questions about tool applicability. This discrepancy suggests that these human-centric instruments may not adequately or consistently capture the nuances of risk processing in Artificial Intelligence. The findings imply that current tools might be insufficient, highlighting the need for methodologies specifically tailored for evaluating AI decision-making under medical uncertainty. Full article
(This article belongs to the Special Issue Machine Learning in Biomedical Sciences)
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29 pages, 73880 KiB  
Article
Boundary-Aware Transformer for Optic Cup and Disc Segmentation in Fundus Images
by Soohyun Wang, Byoungkug Kim and Doo-Seop Eom
Appl. Sci. 2025, 15(9), 5165; https://doi.org/10.3390/app15095165 - 6 May 2025
Viewed by 256
Abstract
Segmentation of the Optic Disc (OD) and Optic Cup (OC) boundaries in fundus images is a critical step for early glaucoma diagnosis, but accurate segmentation is challenging due to low boundary contrast and significant anatomical variability. To address these challenges, this study proposes [...] Read more.
Segmentation of the Optic Disc (OD) and Optic Cup (OC) boundaries in fundus images is a critical step for early glaucoma diagnosis, but accurate segmentation is challenging due to low boundary contrast and significant anatomical variability. To address these challenges, this study proposes a novel segmentation framework that integrates structure-preserving data augmentation, Boundary-aware Transformer Attention (BAT), and Geometry-aware Loss. We enhance data diversity while preserving vascular and tissue structures through truncated Gaussian-based sampling and colormap transformations. BAT strengthens boundary recognition by globally learning the inclusion relationship between the OD and OC within the skip connection paths of U-Net. Additionally, Geometry-aware Loss, which combines the normalized Hausdorff Distance with the Dice Loss, reduces fine-grained boundary errors and improves boundary precision. The proposed model outperforms existing state-of-the-art models across five public datasets—DRIONS-DB, Drishti-GS, REFUGE, G1020, and ORIGA—and achieves Dice scores of 0.9127 on Drishti-GS and 0.9014 on REFUGE for OC segmentation. For joint segmentation of the OD and OC, it attains high Dice scores of 0.9892 on REFUGE, 0.9782 on G1020, and 0.9879 on ORIGA. Ablation studies validate the independent contributions of each component and demonstrate their synergistic effect when combined. Furthermore, the proposed model more accurately captures the relative size and spatial alignment of the OD and OC and produces smooth and consistent boundary predictions in clinically significant regions such as the region of interest (ROI). These results support the clinical applicability of the proposed method in medical image analysis tasks requiring precise, boundary-focused segmentation. Full article
(This article belongs to the Special Issue Machine Learning in Biomedical Sciences)
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