Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network

Loading...
Thumbnail Image
File version

Accepted Manuscript (AM)

Author(s)
Zeng, Y
Zhou, X
Rao, J
Lu, Y
Yang, Y
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
2020
Size
File type(s)
Location
License
Abstract

Recent advances in single-cell RNA sequencing (scRNA-seq) technologies provide a great opportunity to study gene expression at cellular resolution, and the scRNA-seq data has been routinely conducted to unfold cell heterogeneity and diversity. A critical step for the scRNA-seq analyses is to cluster the same type of cells, and many methods have been developed for cell clustering. However, existing clustering methods are limited to extract the representations from expression data of individual cells, while ignoring the high-order structural relations between cells. Here, we proposed a new method (GraphSCC) to cluster cells based on scRNA-seq data by accounting structural relations between cells through a graph convolutional network. The representation learned from the graph convolutional network, together with another representation output from a denoising autoencoder network, are optimized by a dual self-supervised module for better cell clustering. Extensive experiments indicate that GraphSCC model outperforms state-of-the-art methods in various evaluation metrics on both simulated and real datasets.

Journal Title
Conference Title

Proceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020

Book Title
Edition
Volume
Issue
Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement

© 2020 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Item Access Status
Note
Access the data
Related item(s)
Subject

Biological sciences

Persistent link to this record
Citation

Zeng, Y; Zhou, X; Rao, J; Lu, Y; Yang, Y, Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network, Proceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020, 2020, pp. 519-522