Robust Single-Cell RNA-Seq Analysis Using Hyperdimensional Computing: Enhanced Clustering and Classification Methods

Background. Single-cell RNA sequencing (scRNA-seq) has transformed genomics by enabling the study of cellular heterogeneity. However, its high dimensionality, noise, and sparsity pose significant challenges for data analysis. Methods. We investigate the use of Hyperdimensional Computing (HDC), a brain-inspired computational framework recognized for its noise robustness and hardware efficiency, to tackle the challenges in scRNA-seq data analysis. We apply HDC to both supervised classification and unsupervised clustering tasks. Results. Our experiments demonstrate that HDC consistently outperforms established methods such as XGBoost, Seurat reference mapping, and scANVI in terms of noise tolerance and scalability. HDC achieves superior accuracy in classification tasks and maintains robust clustering performance across varying noise levels. Conclusions. These results highlight HDC as a promising framework for accurate and efficient single-cell data analysis. Its potential extends to other high-dimensional biological datasets including proteomics, epigenomics, and transcriptomics, with implications for advancing bioinformatics and personalized medicine.