Single cell clustering using ZINB model and variational graph attention autoencoder

Ge Zhang; Xuye Kou; Yitong Chen; Zhou Zhang

doi:10.1117/12.3036853

13 July 2024 Single cell clustering using ZINB model and variational graph attention autoencoder

Ge Zhang, Xuye Kou, Yitong Chen, Zhou Zhang

Proceedings Volume 13208, Third International Conference on Biomedical and Intelligent Systems (IC-BIS 2024); 1320805 (2024) https://doi.org/10.1117/12.3036853
Event: 3rd International Conference on Biomedical and Intelligent Systems (IC-BIS 2024), 2024, Nanchang, China

Abstract

Single-cell RNA sequencing allows to discovery of new cell subtypes based on transcriptomic information. Clustering analysis is an effective approach for exploring single-cell heterogeneity. Nevertheless, current single-cell clustering methodologies are challenged by the high-dimensional, sparse, and dropouts on the one hand, and on the other hand, they neglect the thorough exploration of potential relationships between cells and noise removal. To tackle these challenges, this study introduces a novel self-optimized single-cell clustering algorithm named scZVEA, which combines ZeroInflated Negative Binomial (ZINB) model and variational graph attention autoencoder. The scZVEA framework comprises three key modules. Firstly, a Deep Count Autoencoder (DCA) is designed to model data distribution and eliminate noise. Then, a variational graph attention autoencoder to extract latent features from the data. Lastly, the self-optimized clustering module enables the two previously independent clustering and feature modules to mutually benefit each other by iteratively updating cluster centers to further enhance clustering performance. Experimental findings based on six authentic scRNAseq datasets illustrate that the proposed clustering algorithm significantly enhances clustering accuracy when compared to alternative methods.

(2024) Published by SPIE. Downloading of the abstract is permitted for personal use only.

Citation Download Citation

Ge Zhang, Xuye Kou, Yitong Chen, and Zhou Zhang "Single cell clustering using ZINB model and variational graph attention autoencoder", Proc. SPIE 13208, Third International Conference on Biomedical and Intelligent Systems (IC-BIS 2024), 1320805 (13 July 2024); https://doi.org/10.1117/12.3036853

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KEYWORDS

Matrices

Data modeling

Denoising

Tissues

Ablation

Network architectures

Dimension reduction

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