Quantum annealing for enhanced feature selection in single-cell RNA sequencing data analysis

Feature selection is a machine learning technique for identifying relevant variables in classification and regression models. In single-cell RNA sequencing (scRNA-seq) data analysis, feature selection is used to identify relevant genes that are crucial for understanding cellular processes. Traditional feature selection methods often struggle with the complexity of scRNA-seq data and suffer from interpretation difficulties. Quantum annealing presents a promising alternative approach. In this study, we implement quantum annealing-empowered quadratic unconstrained binary optimization (QUBO) for feature selection in scRNA-seq data. Using data from a human cell differentiation system and an anticancer drug resistance study, we demonstrate that QUBO feature selection effectively identifies genes whose expression patterns reflect critical cell state transitions associated with differentiation and drug resistance development. Our findings indicate that quantum annealing-powered QUBO reveals complex gene expression patterns potentially missed by traditional methods, thereby enhancing scRNA-seq data analysis and interpretation.