Biomedical Informatics

ISSN: 3005-3862 (Print)

ISSN: 3005-3854 (Online)

CODEN: BIABAB

About This Journal
Special Issues
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Single-Cell Multi-Omics
Special Issue Editor:   Wing Kin Sung, Puwen Tan
Submission Deadline:  31 December 2026
Computational Methods and Models for Precision Medicine
Special Issue Editor:   Rosalba Giugno, Simone Avesani, Manuel Tognon, Eva Viesi
Submission Deadline:  31 August 2026
Latest Articles
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The application of artificial intelligence-driven generative design and bioinformatics modeling in tissue engineering scaffolds
Hao Deng,Zheng Qin,Mingru Kong
Review21 Aug 2026OPEN ACCESS

The architecture of a tissue-engineering scaffold affects how cells attach, migrate, and remodel newly formed tissue. At present, many scaffolds are still developed through repeated adjustment of a few structural variables, making it difficult to balance porosity with mechanical strength or degradation with the pace of tissue formation. Generative artificial intelligence may help shift scaffold development toward a target-driven process. Given a desired biological or mechanical outcome, a model could identify structures that are likely to achieve it. This possibility depends on training data that connect scaffold features with biological responses. In this review, we consider the use of generative methods together with bioinformatics for scaffold design. We describe potentially useful data sources, including micro-computed tomography (CT) images, mechanical measurements, single-cell RNA sequencing, and degradation data. We also examine generative adversarial networks, variational autoencoders, diffusion models, and evolutionary algorithms. Rather than treating these approaches as interchangeable, we discuss the design tasks for which their strengths differ. Examples from cardiac, bone, cartilage, and related applications show how tissue context shapes data requirements and model selection. We close by considering data comparability, validation across length scales, and the practical challenges of clinical use. These issues will determine whether generative tools can support more tailored scaffold design.

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LC-JEPA: a logic-constrained self-supervised framework for trustworthy ECG arrhythmia analysis
Bailing Zhang,Genlang Chen,Yuan Miao
Article16 Apr 2026OPEN ACCESS

The trustworthiness of medical AI systems is often undermined by their potential to violate established clinical principles, a critical issue in self-supervised learning (SSL) frameworks where explicit domain knowledge is typically disregarded. To address this trust deficit, we propose the Logic-Constrained Joint Embedding Predictive Architecture (LC-JEPA). LC-JEPA is a novel framework that bridges neural and symbolic learning by seamlessly integrating predefined medical rules into the SSL process via differentiable logic programming. It utilizes a dedicated Differentiable Constraint Satisfaction Layer (D-CSL) to formally encode clinical constraints, enabling end-to-end joint optimization of both predictive accuracy and logical consistency. We introduce the Constraint Satisfaction Rate (CSR) as a specialized metric to quantify adherence to medical knowledge. Comprehensive evaluation on the MIT-BIH Arrhythmia Database demonstrates that LC-JEPA achieves high accuracy (97.5%) while significantly improving domain adherence (CSR of 93.9%), substantially outperforming unconstrained baselines (e.g., Vanilla JEPA’s 86.4% CSR). Extensive sensitivity analysis confirms that the logic constraint is essential: removing it causes accuracy to drop from 97.5% to 32.1%, while the specific constraint weight λ ∈ [0.1,2.0] has minimal impact on performance. By successfully uniting representation learning with symbolic reasoning, LC-JEPA provides a robust and generalizable solution for building safer, more reliable, and clinically deployable trustworthy AI systems for ECG arrhythmia analysis.

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Interpretable blood glucose prediction for type 1 diabetes using neural-symbolic Fourier operators and clinical rules
Bailing Zhang
Article22 Dec 2025OPEN ACCESS

Accurate and interpretable blood glucose prediction is critical for optimizing insulin therapy and preventing adverse events in type 1 diabetes (T1D) management. However, existing deep learning models often lack transparency, limiting their clinical adoption. We introduce a novel neural-symbolic framework that integrates Fourier neural operators (FNOs) with clinical rules to predict 30-minute-ahead blood glucose levels with high accuracy and interpretability. FNOs capture periodic glucose patterns, such as circadian rhythms and meal responses, while differentiable clinical rules encode medical knowledge, providing actionable insights like hypoglycemia risk alerts. Evaluated on the OhioT1DM dataset, our model achieves a mean absolute error (MAE) of 10.2 mg/dL, meeting ISO 15197:2013 standards, and 99.8% Clarke Error Grid A+B coverage, ensuring clinical safety. Leave-one-subject-out cross-validation across 12 subjects demonstrates robust generalization (MAE = 8.85 ± 1.33 mg/dL), addressing concerns about sample size limitations. The model exhibits strong robustness to continuous glucose monitoring (CGM) measurement noise (maintaining ISO compliance at 10% noise) and missing data (5.4% performance degradation at 40% data loss). By generating interpretable outputs, such as trend analyses and risk warnings, our framework supports clinical decision-making, enhances patient trust, and facilitates personalized diabetes care. This work advances medical informatics by combining data-driven and knowledge-driven methods, offering a scalable solution for real-time glucose monitoring and insulin dosing in T1D.

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Development and validation of a machine learning model elucidating risk factors in severe COVID-19
Claire Y. Zhao,Xiang(Jay) Ji,Shunjie Guan,Sima S. Toussi,Jennifer Hammond,Subha Madhavan
Article20 Jan 2025OPEN ACCESS
Objectives: COVID-19 remains a significant healthcare burden. Leveraging the combined power of clinical trial data and big data from the real world, this study elucidated baseline factors predictive of subsequent outcomes relating to severe COVID-19 disease (SD) and the effect of nirmatrelvir/ritonavir (Tx), a protease inhibitor, on disease progression. Methods: We retrospectively analyzed data from the Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients (EPIC-HR) clinical trial (NCT04960202) to discern observational associations between baseline factors and subsequent SD outcome. Baseline factors, including demographics, clinical laboratory results, symptoms, medical history, vital signs, and electrocardiogram features, were studied using machine learning (ML) for their importance in predicting hospitalization or death through Day 28, with Tx effects analyzed statistically. Generalizability of results was evaluated using real-world data (RWD) Optum Electronic Health Records. Results: Modeling indicated Tx was the greatest predictor of whether a patient progressed to SD. The most important baseline factors associated with increased risk of SD were elevated baseline (1) viral load (VL; > ~4 log10 copies/mL), (2) hsCRP (> ~1 mg/dL), (3) ferritin (> ~280 ug/L), (4) haptoglobin (> ~210 mg/dL), and (5) increased age (> ~48 years). Tx reduced VL and abnormally high hsCRP and haptoglobin to greater extents than placebo at the measured time points. RWD validation supported findings on increased risk with elevated hsCRP and ferritin and increased age (no data were available on VL and haptoglobin). Conclusion: ML analysis identified critical baseline factors immediately before or at the beginning of COVID-19 infection predictive of progression to SD in adults that are common to a heterogeneous population. This study provides insights on multivariate signatures of COVID-19 disease progression and Tx effects, which may aid future studies and inform treatment decision making.
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Distinct nuclear and cytoplasmic transcriptomic signatures reveal-transcription alone is insufficient to determine glucose-induced transcriptomic dynamics
Atefeh Bagheri,Jinsil Kim,Peng Jiang
Article07 Aug 2025OPEN ACCESS

Glucose profoundly influences cellular transcriptomes, but whether these changes are primarily driven by transcription remains unclear. Traditional bulk RNA sequencing, which interrogates total mRNA from whole cells, obscures distinct dynamics of nuclear and cytoplasmic transcriptomes. Nuclear RNA levels primarily reflect transcriptional activity but are also influenced by nuclear export, whereas cytoplasmic RNA abundances result from transcription, nuclear export, RNA stability (i.e., RNA half-life), and active RNA degradation mechanisms. In this study, we systematically investigate glucose-induced transcriptomic responses in a subcellular location-and cell type-specific manner using three cell lines: FHC (normal colonic epithelial cells), MCF10A (normal breast epithelial cells), and MCF7 (metastatic breast cancer cells). Our findings reveal that, although nuclear and cytoplasmic mRNA levels show strong global correlations, glucose-induced changes in mRNA abundance exhibit minimal concordance between the nucleus and cytoplasm. Additionally, glucose-induced changes in exon inclusion levels often diverge between the nucleus and cytoplasm, underscoring the importance of post-transcriptional processes in shaping the cytoplasmic transcriptome response to glucose level changes. Glucose-induced differentially expressed genes (DEGs) and differentially spliced exons (ΔPSI) are enriched in distinct pathways exhibiting unique enrichment patterns depending on the subcellular location and cell line. These findings underscore the complexity of glucose-induced transcriptomic regulation, demonstrating that transcription alone is insufficient to explain the observed dynamics.

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Micro-expression detection in ASD movies: a YOLOv8-SMART approach
Yutong Gu,Hanni Li,Jiarong Liu,Chenxi Liu,Yuxuan Li,Chen Li,Ning Xu
Technique Report25 Feb 2025OPEN ACCESS
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder in which individuals often face social difficulties as well as language and communication challenges. Micro-expressions are extremely brief changes in facial expression. Moreover, the micro-expressions exhibited by individuals with ASD frequently represent an accurate reflection of their internal feelings. Therefore, using the Cinemetrics method to extract micro-expressions from ASD patients in movies and targeting them for detection can help doctors make early diagnosis of ASD patients. In this paper, we establish a dataset of micro-expressions of ASD patients in movies, use the improved YOLOv8-SMART algorithm for target detection, and compare it with other target detection algorithms without improvement. The comparison results prove that our algorithm effectively improves the recognition of micro-expressions, which provides reference value for future practical applications in the task of micro-expression recognition in ASD patients.
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