Triple and quadruple optimization for feature selection in cancer biomarker discovery

The proliferation of omics data has advanced cancer biomarker discovery but often falls short in external validation, mainly due to a narrow focus on prediction accuracy that neglects clinical utility and validation feasibility. We introduce three- and four-objective optimization strategies based on genetic algorithms to identify clinically actionable biomarkers in omics studies, addressing classification tasks aimed at distinguishing hard-to-differentiate cancer subtypes beyond histological analysis alone. Our hypothesis is that by optimizing more than one characteristic of cancer biomarkers, we may identify biomarkers that will enhance their success in external validation. Our objectives are to: (i) assess the biomarker panel’s accuracy using a machine learning (ML) framework; (ii) ensure the biomarkers exhibit significant fold-changes across subtypes, thereby boosting the success rate of PCR or immunohistochemistry validations; (iii) select a concise set of biomarkers to simplify the validation process and reduce clinical costs; and (iv) identify biomarkers crucial for predicting overall survival, which plays a significant role in determining the prognostic value of cancer subtypes. We implemented and applied triple and quadruple optimization algorithms to renal carcinoma gene expression data from TCGA. The study targets kidney cancer subtypes that are difficult to distinguish through histopathology methods. Selected RNA-seq biomarkers were assessed against the gold standard method, which relies solely on clinical information, and in external microarray-based validation datasets. Notably, these biomarkers achieved over 0.8 of accuracy in external validations and added significant value to survival predictions, outperforming the use of clinical data alone with a superior c-index. The provided tool also helps explore the trade-off between objectives, offering multiple solutions for clinical evaluation before proceeding to costly validation or clinical trials.