scBiGNN: Bilevel Graph Representation Learning for Cell Type
Classification from Single-cell RNA Sequencing Data
- URL: http://arxiv.org/abs/2312.10310v1
- Date: Sat, 16 Dec 2023 03:54:26 GMT
- Title: scBiGNN: Bilevel Graph Representation Learning for Cell Type
Classification from Single-cell RNA Sequencing Data
- Authors: Rui Yang, Wenrui Dai, Chenglin Li, Junni Zou, Dapeng Wu, Hongkai Xiong
- Abstract summary: Graph neural networks (GNNs) have been widely used for automatic cell type classification.
scBiGNN comprises two GNN modules to identify cell types.
scBiGNN outperforms a variety of existing methods for cell type classification from scRNA-seq data.
- Score: 62.87454293046843
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput
gene expression data to study the cellular heterogeneity and dynamics of
complex organisms. Graph neural networks (GNNs) have been widely used for
automatic cell type classification, which is a fundamental problem to solve in
scRNA-seq analysis. However, existing methods do not sufficiently exploit both
gene-gene and cell-cell relationships, and thus the true potential of GNNs is
not realized. In this work, we propose a bilevel graph representation learning
method, named scBiGNN, to simultaneously mine the relationships at both gene
and cell levels for more accurate single-cell classification. Specifically,
scBiGNN comprises two GNN modules to identify cell types. A gene-level GNN is
established to adaptively learn gene-gene interactions and cell representations
via the self-attention mechanism, and a cell-level GNN builds on the cell-cell
graph that is constructed from the cell representations generated by the
gene-level GNN. To tackle the scalability issue for processing a large number
of cells, scBiGNN adopts an Expectation Maximization (EM) framework in which
the two modules are alternately trained via the E-step and M-step to learn from
each other. Through this interaction, the gene- and cell-level structural
information is integrated to gradually enhance the classification performance
of both GNN modules. Experiments on benchmark datasets demonstrate that our
scBiGNN outperforms a variety of existing methods for cell type classification
from scRNA-seq data.
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