CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data.

ABSTRACT: Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and have many arbitrary parameter choices. Methods that can model scRNA-seq data as non-discrete "gene expression programs" (GEPs) can better preserve the data's structure, but currently, they are often not scalable, not consistent across repeated runs, and lack an established method for choosing key parameters. Here, we developed a GPU-based unsupervised learning approach, "consensus and scalable inference of gene expression programs" (CSI-GEP). We show that CSI-GEP can recover ground truth GEPs in real and simulated atlas-scale scRNA-seq datasets, s

SUBMITTER: Liu X 

PROVIDER: S-EPMC11770216 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature