BioMedInformatics

BioMedInformatics is an international, peer-reviewed, open access journal that covers all areas of biomedical informatics, computational biology, and medicine. Established in 2021, the journal is now five years old and reflects the evolution of the field through its consistent thematic focus on Artificial Intelligence (AI)-driven diagnosis and prediction, with a particular emphasis on translational clinical decision support and biomedical signal and imaging analysis. Despite the predominance of AI-related topics, classical bioinformatics remains a major focus, with a particular emphasis on the discovery of biomarkers and the development of data resources. This editorial summarises this evolution, which accurately reflects the field as a whole.

Background/Objectives: Software is now core infrastructure in biomedical science, yet fragmented workflows across subfields hinder reproducibility and delay the translation of data into actionable decisions. There is a critical need for a cross-disciplinary synthesis to bridge these silos and establish a unified framework for software maturity. This narrative review addresses this gap by synthesizing representative software ecosystems across three major pillars: bioinformatics, molecular modeling/simulations, and epidemiology/public health. Methods: A narrative review of articles indexed in PubMed/NCBI, Web of Science, and Scopus between 2000 and 2025 was conducted. Domain-specific terms related to bioinformatics, molecular modeling, docking, molecular dynamics, epidemiology, public health, and workflow management were combined with software- and algorithm-focused keywords. Studies describing, validating, or applying documented tools with biomedical relevance were included. Results: Across domains, mature data standards and reference resources (e.g., FASTQ, BAM/CRAM, VCF, mzML), widely adopted platforms (e.g., BLAST+ (v2.16.0, NCBI, Bethesda, MD, USA), Bioconductor (v3.20, Bioconductor Foundation, Seattle, WA, USA), AutoDock Vina (v1.2.5, Scripps Research, La Jolla, CA, USA), GROMACS (v2024.3, GROMACS Team, Stockholm, Sweden), Epi Info (v7.2.6, CDC, Atlanta, GA, USA), QGIS (v3.40, QGIS.org, Gossau, Switzerland), and increasing use of workflow engines were identified. Software pipelines routinely transform molecular and surveillance data into interpretable features supporting hypothesis generation. Conclusions: Integrated, standards-based, and validated software pipelines can shorten the path from measurement to decision in biomedicine and public health. Future progress depends on reproducibility practices, benchmarking, user-centered design, portable implementations, and responsible deployment of machine learning.

Background: Depression is a common mental disorder, and early and objective diagnosis of depression is challenging. New advances in deep learning show promise for processing audio and video content when screening for depression. Nevertheless, the majority of current methods rely on raw video processing or multimodal pipelines, which are computationally costly and challenging to understand and create privacy issues, restricting their use in actual clinical settings. Methods: Based solely on spatiotemporal 3D face landmark representations, we describe a unique, totally visual, and lightweight deep learning approach to overcome these constraints. In this paper we introduce, for the first time, a pure visual deep learning framework, based on spatiotemporal 3D facial landmarks extracted from clinical interview videos contained in the DAIC-WOZ and Extended DAIC-WOZ (E-DAIC) datasets. Our method does not use raw video or any type of semi-automated multimodal fusion. Whereas raw video streaming can be computationally expensive and is not well suited to investigating specific variables, we first take a temporal series of 3D landmarks, convert them to pseudo-images (224 × 224 × 3), and then use them within a CNN-LSTM framework. Importantly, CNN-LSTM provides the ability to analyze the spatial configuration and temporal dimensions of facial behavior. Results: The experimental results indicate macro-average F1 scores of 0.74 on DAIC-WOZ and 0.762 on E-DAIC, demonstrating robust performance under heavy class imbalances, with a variability of ±0.03 across folds. Conclusion: These results indicate that landmark-based spatiotemporal modeling represents the future of lightweight, interpretable, and scalable automatic depression detection. Second, our results suggest exciting opportunities for completely embedding ADI systems within the framework of real-world MHA.