BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation.

ABSTRACT:

Motivation

Single cell RNA sequencing (scRNA-seq) technique enables the transcriptome profiling of hundreds to ten thousands of cells at the unprecedented individual level and provides new insights to study cell heterogeneity. However, its advantages are hampered by dropout events. To address this problem, we propose a Blockwise Accelerated Non-negative Matrix Factorization framework with Structural network constraints (BANMF-S) to impute those technical zeros.

Results

BANMF-S constructs a gene-gene similarity network to integrate prior information from the external PPI network by the Triadic Closure Principle and a cell-cell similarity network to capture the neighborhood structure and temporal information through a Minimum-Spanning Tree. By collaboratively employing these t

SUBMITTER: Zhao J 

PROVIDER: S-EPMC11379494 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature