CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data

Abstract

A key challenge in analyzing single-cell RNA sequencing data is the large number of false zeros, known as "dropout zeros", which are caused by technical limitations such as shallow sequencing depth or inefficient mRNA capture. To address this challenge, we propose a novel imputation model called CPARI, which combines cell partitioning with our designed absolute and relative imputation methods. Initially, CPARI employs a new approach to select highly variable genes and constructs an average consensus matrix using C-mean fuzzy clustering-based blockchain technology to obtain results at different resolutions. Hierarchical clustering is then applied to further refine these blocks, resulting in well-defined cellular partitions. Subsequently, CPARI identifies dropout events and determines the imputation positions of these identified zeros. An autoencoder is trained within each cellular block to learn gene features and reconstruct data. Our uniquely defined absolute imputation technique is first applied to the identified positions, followed by our relative imputation technique to address remaining dropout zeros, ensuring that both global consistency and local variation are maintained. Through comprehensive analyses conducted on simulated and real scRNA-seq datasets, including quantitative assessment, differential expression analysis, cell clustering, cell trajectory inference, robustness evaluation, and large-scale data imputation, CPARI demonstrates superior performance compared to 12 other art-of-state imputation models. Additionally, ablation experiments further confirm the significance and necessity of both the cell partitioning and relative imputation components of CPARI. Notably, CPARI as a new denoising approach could distinguish between real biological zeros and dropout zeros and minimize false positives, and maximize the accuracy of imputation.

Keywords: absolute imputation; average consensus matrix; cell partitioning; relative imputation; single-cell RNA-seq.