From Biostatistics to Machine Learning: Modern Approaches in Bioengineering for Modeling and Understanding Biological Complexity

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biosignal Processing".

Deadline for manuscript submissions: 1 December 2025 | Viewed by 661

Special Issue Editors


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Guest Editor
Division of Biostatistics, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
Interests: biostatistics; statistical genetics; bioinformatics; omics data analysis; proteomics; metabolomics; machine learning; integrative analysis; medical data analysis; computational biology
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Division of Biostatistics, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
Interests: biostatistics; clinical trial; controlled clinical trial; data accuracy; data interpretation, statistical; high dimensional data analysis; historical data for clinical trials; machine learning; missing data; right-censored data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Biostatistics and machine learning have become increasingly vital as researchers aim to decode and manipulate complex biological systems. This Special Issue seeks to highlight innovative statistical methods and machine learning tools that advance our understanding of biological processes and enhance the design, modeling, and optimization of bioengineering applications.

We welcome original research, methodological papers, and review articles that showcase how cutting-edge statistical and machine learning approaches contribute to solving challenges in bioengineering.

Scope and Topics of Interest (include but are not limited to):

  • Statistical modeling of multi-omics and high-dimensional biological data;
  • Bayesian methods in synthetic biology and bioengineering;
  • Machine learning and AI-driven tools in bioengineering;
  • Experimental design and optimization for bioprocessing;
  • Spatial and temporal modeling in tissue engineering;
  • Causal inference in biological networks;
  • Uncertainty quantification in biological system modeling;
  • Integration of statistics with mechanistic modeling;
  • Predictive modeling for biomanufacturing and drug delivery systems.
  • Applications of statistical genomics in bioengineering contexts.

Dr. Chien-Wei (Masaki) Lin
Prof. Dr. Kwang Woo Ahn
Guest Editors

Manuscript Submission Information

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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

  • statistics
  • machine learning
  • AI
  • computational tools
  • prediction and classification

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Published Papers (1 paper)

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Research

17 pages, 5062 KiB  
Article
DropDAE: Denosing Autoencoder with Contrastive Learning for Addressing Dropout Events in scRNA-seq Data
by Wanlin Juan, Kwang Woo Ahn, Yi-Guang Chen and Chien-Wei Lin
Bioengineering 2025, 12(8), 829; https://doi.org/10.3390/bioengineering12080829 - 31 Jul 2025
Viewed by 432
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized molecular biology and genomics by enabling the profiling of individual cell types, providing insights into cellular heterogeneity. Deep learning methods have become popular in single cell analysis for tasks such as dimension reduction, cell clustering, and data [...] Read more.
Single-cell RNA sequencing (scRNA-seq) has revolutionized molecular biology and genomics by enabling the profiling of individual cell types, providing insights into cellular heterogeneity. Deep learning methods have become popular in single cell analysis for tasks such as dimension reduction, cell clustering, and data imputation. In this work, we introduce DropDAE, a denoising autoencoder (DAE) model enhanced with contrastive learning, to specifically address the dropout events in scRNA-seq data, where certain genes show very low or even zero expression levels due to technical limitations. DropDAE uses the architecture of a denoising autoencoder to recover the underlying data patterns while leveraging contrastive learning to enhance group separation. Our extensive evaluations across multiple simulation settings based on synthetic data and a real-world dataset demonstrate that DropDAE not only reconstructs data effectively but also further improves clustering performance, outperforming existing methods in terms of accuracy and robustness. Full article
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