Machine learning approaches for cancer prognosis and diagnosis via non-coding RNA: a comprehensive review.

Abstract

Non-coding RNAs (ncRNAs), once considered genomic dark matter, are now established as key regulators of gene expression with widespread roles in cellular homeostasis and disease. In cancer, ncRNA expression is frequently and systematically dysregulated, and many of these molecules circulate in stable, protected form within biofluids, offering a compelling basis for non-invasive or minimally invasive diagnostic strategies. However, their clinical translation remains substantially hindered to date due to biological complexity, technical noise, and high dimensionality inherent to ncRNA expression datasets. In this context, machine learning (ML) has emerged as a powerful analytical tool to address these challenges, enabling the identification of subtle, reproducible ncRNA signatures predictive of diverse malignancies. This review critically evaluates ML-driven frameworks for cancer diagnosis and prognosis across four ncRNA subclasses, namely miRNAs, lncRNAs, circRNAs, and piRNAs, while also acknowledging the biophysical and thermodynamic models that reinforce ncRNA bioinformatics. Despite substantial methodological progress in ML-based cancer diagnosis and prognosis, key challenges persist, including tumor biological heterogeneity, limited multicenter validation, and the lack of widely adopted standardized protocols for preprocessing, normalization, and reporting workflows. Furthermore, many current ML models lack interpretability in biological or clinical context, constraining their translational utility. By synthesizing recent advances and identifying unresolved barriers, this review charts a roadmap for developing a robust, clinically actionable ncRNA biomarker platform for cancer detection. With global cancer incidence projected to exceed 35 million annual cases by 2050, validated ncRNA-ML-driven frameworks hold potential to revolutionize early-stage detection and personalized therapeutic strategies, thereby reducing the escalating socio-economic burden of cancer worldwide.