Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis

Abstract: Feature selection is vital for identifying relevant variables in classification and regression models, especially in single-cell RNA sequencing (scRNA-seq) data analysis. Traditional methods like LASSO often struggle with the nonlinearities and multicollinearities in scRNA-seq data due to complex gene expression and extensive gene interactions. Quantum annealing, a form of quantum computing, offers a promising solution. In this study, we apply quantum annealing-empowered quadratic unconstrained binary optimization (QUBO) for feature selection in scRNA-seq data. Using data from a human cell differentiation system, we show that QUBO identifies genes with nonlinear expression patterns related to differentiation time, many of which play roles in the differentiation process. In contrast, LASSO tends to select genes with more linear expression changes. Our findings suggest that the QUBO method, powered by quantum annealing, can reveal complex gene expression patterns that traditional methods might overlook, enhancing scRNA-seq data analysis and interpretation.