Machine Learning Models for Cancer Research: A Narrative Review of Bulk RNA-Seq Applications

Integrating the advantages of machine learning with the rapidly accumulating high-throughput sequencing data facilitates our capacity for biological discovery and the advancement of molecular medicine. In recent years, bulk RNA-seq technology has established itself as a cost-effective and widely used method for obtaining complete transcriptome profiles of test samples, enabling the identification of key cancer-associated expression patterns. Various machine learning algorithms, in turn, enable the development of informative diagnostic and prognostic models, ensuring the efficient processing of high-dimensional RNA-Seq data. The convergence of these methods shows great promise for oncology. In this narrative review, we describe bulk RNA-Seq-based ML models in oncology as a complete workflow from data preprocessing to model validation. We provide practical recommendations for algorithm selection and study design, and discuss bulk RNA-Seq deconvolution as a cost-effective alternative to single-cell RNA-Seq for analyzing tumor cellular composition. These insights offer a practical guide for developing reproducible diagnostic and prognostic models with translational potential. © 2025 by the authors.