When complexity does not pay: Benchmarking deep learning and ensemble methods for biomarker discovery

Abstract

Abstract The integration of multi-omics data holds great promise for identifying robust and clinically relevant biomarkers, yet the increasing complexity of computational methods raises questions about their practical utility. In this study, we present a comprehensive benchmarking framework that evaluates 27 feature selection strategies and 11 predictive models across three real-world disease cohorts: Alzheimer’s disease, progressive supranuclear palsy, and breast cancer. We compare traditional machine learning, ensemble-based methods, and state-of-the-art deep learning models in terms of predictive performance, stability, and biological interpretability. Our results reveal that ensemble feature selection consistently improves robustness and accuracy, particularly for compact biomarker panels. Surprisingly, deep learning models did not outperform simpler classifiers such as logistic regression (L.Regression), support vector machines, or multilayer perceptrons, which often achieved comparable or superior results with lower computational cost and greater interpretability. Triple-omics yielded the highest validation, followed by dual-omics and then single-omics (Triple gt; Dual gt; Single). Biological validation against five independent databases confirmed the clinical relevance of the identified biomarkers, including both well-established and novel candidates. To support reproducibility and community adoption, we provide a web-based tool for applying our benchmarking pipeline. Our findings advocate for a pragmatic approach to biomarker discovery—prioritizing methodological transparency, reproducibility, and biological insight over algorithmic complexity.