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Bioengineering
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Machine Learning Technology in Biomedical Engineering—2nd Edition
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Machine Learning Technology in Biomedical Engineering—2nd Edition

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biomedical Engineering and Biomaterials".

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 11374

Special Issue Editors

Dr. Hongqing Yu

E-Mail Website
Guest Editor
School of Computing and Data Science Research Centre, University of Derby, Derby DE22 3AW, UK
Interests: data science; machine learning; knowledge discovery and representation; semantic technologies; deep machine learning; natural language processing
Special Issues, Collections and Topics in MDPI journals
Dr. Alaa AlZoubi

E-Mail Website
Guest Editor
College of Science and Engineering, University of Derby, Derby, UK
Interests: artificial intelligence; AI decision explainability; deep learning and computer vision
Prof. Dr. Yifan Zhao

E-Mail Website
Guest Editor
Faculty of Engineering and Applied Sciences, Cranfield University, Cranfield MK43 0AL, UK
Interests: machine learning; artificial intelligence; human factors; pattern recognition; digital twins; instrumentation, sensors and measurement science; systems engineering; through-life engineering services
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hongbo Du

E-Mail Website
Guest Editor
School of Computing, University of Buckingham, Buckingham, UK
Interests: big data processing; data mining; machine learning; image and time series analysis

Special Issue Information

Dear Colleagues,

This Special Issue titled "Machine Learning Technology in Biomedical Engineering—2nd Edition" aims to provide a platform for researchers to showcase their latest research and findings on the application of machine learning technology in the field of biomedical engineering. The use of machine learning technology in healthcare has been growing rapidly in recent years and has the potential to revolutionize many aspects of healthcare, including disease diagnosis, treatment, and personalized medicine.

This Special Issue will cover a wide range of topics related to the application of machine learning in biomedical engineering, including predictive modeling, image and signal processing, deep learning, drug discovery, biomarker discovery, and medical decision-making. Contributions from interdisciplinary teams combining expertise in machine learning and biomedical engineering are encouraged.

Importance:

The use of machine learning technology in biomedical engineering has significant potential to improve healthcare outcomes and make healthcare more efficient and accessible. By applying machine learning algorithms to large datasets of biomedical information, researchers and healthcare professionals can gain new insights into disease mechanisms, identify new biomarkers for disease, and develop more effective treatments. Machine learning algorithms can also be used to improve medical imaging analysis, automate medical diagnosis and decision-making, and optimize drug discovery processes.

This Special Issue is important because it provides a platform for researchers to share their latest findings and perspectives on the application of machine learning technology in biomedical engineering, and to encourage interdisciplinary collaboration between machine learning and biomedical engineering researchers. It is an exciting opportunity for researchers to contribute to the development of new technologies and methodologies that have the potential to significantly improve healthcare outcomes.

Dr. Hongqing Yu
Dr. Alaa AlZoubi
Prof. Dr. Yifan Zhao
Prof. Dr. Hongbo Du
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. Bioengineering 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 2700 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 engineering
  • big data
  • predictive modelling
  • image and signal processing
  • medical image analysis
  • deep learning
  • biomarker
  • personalized medicine
  • wearable devices and mobile health

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Further information on MDPI's Special Issue policies can be found here.

Related Special Issues

Published Papers (5 papers)

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Research

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16 pages, 1847 KiB  
Article
Machine Learning Approach for Predicting Hypertension Based on Body Composition in South Korean Adults
by Jeong-Woo Seo, Sanghun Lee and Mi Hong Yim
Bioengineering 2024, 11(9), 921; https://doi.org/10.3390/bioengineering11090921 - 14 Sep 2024
Viewed by 1170
Abstract
(1) Background: Various machine learning techniques were used to predict hypertension in Korean adults aged 20 and above, using a range of body composition indicators. Muscle and fat components of body composition are closely related to hypertension. The aim was to identify which [...] Read more.
(1) Background: Various machine learning techniques were used to predict hypertension in Korean adults aged 20 and above, using a range of body composition indicators. Muscle and fat components of body composition are closely related to hypertension. The aim was to identify which body composition indicators are significant predictors of hypertension for each gender; (2) Methods: A model was developed to classify hypertension using six different machine learning techniques, utilizing age, BMI, and body composition indicators such as body fat mass, lean mass, and body water of 2906 Korean men and women; (3) Results: The elastic-net technique demonstrated the highest classification accuracy. In the hypertension prediction model, the most important variables for men were age, skeletal muscle mass (SMM), and body fat mass (BFM), in that order. For women, the significant variables were age and BFM. However, there was no difference between soft lean mass and SMM; (4) Conclusions: Hypertension affects not only BFM but also SMM in men, whereas in women, BFM has a stronger effect than SMM. Full article
(This article belongs to the Special Issue Machine Learning Technology in Biomedical Engineering—2nd Edition)
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23 pages, 5017 KiB  
Article
Explainable DCNN Decision Framework for Breast Lesion Classification from Ultrasound Images Based on Cancer Characteristics
by Alaa AlZoubi, Ali Eskandari, Harry Yu and Hongbo Du
Bioengineering 2024, 11(5), 453; https://doi.org/10.3390/bioengineering11050453 - 2 May 2024
Cited by 2 | Viewed by 1531
Abstract
In recent years, deep convolutional neural networks (DCNNs) have shown promising performance in medical image analysis, including breast lesion classification in 2D ultrasound (US) images. Despite the outstanding performance of DCNN solutions, explaining their decisions remains an open investigation. Yet, the explainability of [...] Read more.
In recent years, deep convolutional neural networks (DCNNs) have shown promising performance in medical image analysis, including breast lesion classification in 2D ultrasound (US) images. Despite the outstanding performance of DCNN solutions, explaining their decisions remains an open investigation. Yet, the explainability of DCNN models has become essential for healthcare systems to accept and trust the models. This paper presents a novel framework for explaining DCNN classification decisions of lesions in ultrasound images using the saliency maps linking the DCNN decisions to known cancer characteristics in the medical domain. The proposed framework consists of three main phases. First, DCNN models for classification in ultrasound images are built. Next, selected methods for visualization are applied to obtain saliency maps on the input images of the DCNN models. In the final phase, the visualization outputs and domain-known cancer characteristics are mapped. The paper then demonstrates the use of the framework for breast lesion classification from ultrasound images. We first follow the transfer learning approach and build two DCNN models. We then analyze the visualization outputs of the trained DCNN models using the EGrad-CAM and Ablation-CAM methods. We map the DCNN model decisions of benign and malignant lesions through the visualization outputs to the characteristics such as echogenicity, calcification, shape, and margin. A retrospective dataset of 1298 US images collected from different hospitals is used to evaluate the effectiveness of the framework. The test results show that these characteristics contribute differently to the benign and malignant lesions’ decisions. Our study provides the foundation for other researchers to explain the DCNN classification decisions of other cancer types. Full article
(This article belongs to the Special Issue Machine Learning Technology in Biomedical Engineering—2nd Edition)
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20 pages, 5357 KiB  
Article
Synergizing Deep Learning-Enabled Preprocessing and Human–AI Integration for Efficient Automatic Ground Truth Generation
by Christopher Collazo, Ian Vargas, Brendon Cara, Carla J. Weinheimer, Ryan P. Grabau, Dmitry Goldgof, Lawrence Hall, Samuel A. Wickline and Hua Pan
Bioengineering 2024, 11(5), 434; https://doi.org/10.3390/bioengineering11050434 - 28 Apr 2024
Viewed by 1406
Abstract
The progress of incorporating deep learning in the field of medical image interpretation has been greatly hindered due to the tremendous cost and time associated with generating ground truth for supervised machine learning, alongside concerns about the inconsistent quality of images acquired. Active [...] Read more.
The progress of incorporating deep learning in the field of medical image interpretation has been greatly hindered due to the tremendous cost and time associated with generating ground truth for supervised machine learning, alongside concerns about the inconsistent quality of images acquired. Active learning offers a potential solution to these problems of expanding dataset ground truth by algorithmically choosing the most informative samples for ground truth labeling. Still, this effort incurs the costs of human labeling, which needs minimization. Furthermore, automatic labeling approaches employing active learning often exhibit overfitting tendencies while selecting samples closely aligned with the training set distribution and excluding out-of-distribution samples, which could potentially improve the model’s effectiveness. We propose that the majority of out-of-distribution instances can be attributed to inconsistent cross images. Since the FDA approved the first whole-slide image system for medical diagnosis in 2017, whole-slide images have provided enriched critical information to advance the field of automated histopathology. Here, we exemplify the benefits of a novel deep learning strategy that utilizes high-resolution whole-slide microscopic images. We quantitatively assess and visually highlight the inconsistencies within the whole-slide image dataset employed in this study. Accordingly, we introduce a deep learning-based preprocessing algorithm designed to normalize unknown samples to the training set distribution, effectively mitigating the overfitting issue. Consequently, our approach significantly increases the amount of automatic region-of-interest ground truth labeling on high-resolution whole-slide images using active deep learning. We accept 92% of the automatic labels generated for our unlabeled data cohort, expanding the labeled dataset by 845%. Additionally, we demonstrate expert time savings of 96% relative to manual expert ground-truth labeling. Full article
(This article belongs to the Special Issue Machine Learning Technology in Biomedical Engineering—2nd Edition)
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25 pages, 4657 KiB  
Article
AutoEpiCollect, a Novel Machine Learning-Based GUI Software for Vaccine Design: Application to Pan-Cancer Vaccine Design Targeting PIK3CA Neoantigens
by Madhav Samudrala, Sindhusri Dhaveji, Kush Savsani and Sivanesan Dakshanamurthy
Bioengineering 2024, 11(4), 322; https://doi.org/10.3390/bioengineering11040322 - 27 Mar 2024
Viewed by 2241
Abstract
Previous epitope-based cancer vaccines have focused on analyzing a limited number of mutated epitopes and clinical variables preliminarily to experimental trials. As a result, relatively few positive clinical outcomes have been observed in epitope-based cancer vaccines. Further efforts are required to diversify the [...] Read more.
Previous epitope-based cancer vaccines have focused on analyzing a limited number of mutated epitopes and clinical variables preliminarily to experimental trials. As a result, relatively few positive clinical outcomes have been observed in epitope-based cancer vaccines. Further efforts are required to diversify the selection of mutated epitopes tailored to cancers with different genetic signatures. To address this, we developed the first version of AutoEpiCollect, a user-friendly GUI software, capable of generating safe and immunogenic epitopes from missense mutations in any oncogene of interest. This software incorporates a novel, machine learning-driven epitope ranking method, leveraging a probabilistic logistic regression model that is trained on experimental T-cell assay data. Users can freely download AutoEpiCollectGUI with its user guide for installing and running the software on GitHub. We used AutoEpiCollect to design a pan-cancer vaccine targeting missense mutations found in the proto-oncogene PIK3CA, which encodes the p110ɑ catalytic subunit of the PI3K kinase protein. We selected PIK3CA as our gene target due to its widespread prevalence as an oncokinase across various cancer types and its lack of presence as a gene target in clinical trials. After entering 49 distinct point mutations into AutoEpiCollect, we acquired 361 MHC Class I epitope/HLA pairs and 219 MHC Class II epitope/HLA pairs. From the 49 input point mutations, we identified MHC Class I epitopes targeting 34 of these mutations and MHC Class II epitopes targeting 11 mutations. Furthermore, to assess the potential impact of our pan-cancer vaccine, we employed PCOptim and PCOptim-CD to streamline our epitope list and attain optimized vaccine population coverage. We achieved a world population coverage of 98.09% for MHC Class I data and 81.81% for MHC Class II data. We used three of our predicted immunogenic epitopes to further construct 3D models of peptide-HLA and peptide-HLA-TCR complexes to analyze the epitope binding potential and TCR interactions. Future studies could aim to validate AutoEpiCollect’s vaccine design in murine models affected by PIK3CA-mutated or other mutated tumor cells located in various tissue types. AutoEpiCollect streamlines the preclinical vaccine development process, saving time for thorough testing of vaccinations in experimental trials. Full article
(This article belongs to the Special Issue Machine Learning Technology in Biomedical Engineering—2nd Edition)
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Review

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33 pages, 3011 KiB  
Review
Building an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundation Models
by Baradwaj Simha Sankar, Destiny Gilliland, Jack Rincon, Henning Hermjakob, Yu Yan, Irsyad Adam, Gwyneth Lemaster, Dean Wang, Karol Watson, Alex Bui, Wei Wang and Peipei Ping
Bioengineering 2024, 11(10), 984; https://doi.org/10.3390/bioengineering11100984 - 29 Sep 2024
Cited by 2 | Viewed by 3353
Abstract
Foundation Models (FMs) are gaining increasing attention in the biomedical artificial intelligence (AI) ecosystem due to their ability to represent and contextualize multimodal biomedical data. These capabilities make FMs a valuable tool for a variety of tasks, including biomedical reasoning, hypothesis generation, and [...] Read more.
Foundation Models (FMs) are gaining increasing attention in the biomedical artificial intelligence (AI) ecosystem due to their ability to represent and contextualize multimodal biomedical data. These capabilities make FMs a valuable tool for a variety of tasks, including biomedical reasoning, hypothesis generation, and interpreting complex imaging data. In this review paper, we address the unique challenges associated with establishing an ethical and trustworthy biomedical AI ecosystem, with a particular focus on the development of FMs and their downstream applications. We explore strategies that can be implemented throughout the biomedical AI pipeline to effectively tackle these challenges, ensuring that these FMs are translated responsibly into clinical and translational settings. Additionally, we emphasize the importance of key stewardship and co-design principles that not only ensure robust regulation but also guarantee that the interests of all stakeholders—especially those involved in or affected by these clinical and translational applications—are adequately represented. We aim to empower the biomedical AI community to harness these models responsibly and effectively. As we navigate this exciting frontier, our collective commitment to ethical stewardship, co-design, and responsible translation will be instrumental in ensuring that the evolution of FMs truly enhances patient care and medical decision-making, ultimately leading to a more equitable and trustworthy biomedical AI ecosystem. Full article
(This article belongs to the Special Issue Machine Learning Technology in Biomedical Engineering—2nd Edition)
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