期刊
NATURE COMPUTATIONAL SCIENCE
卷 1, 期 7, 页码 491-501出版社
SPRINGERNATURE
DOI: 10.1038/s43588-021-00099-8
关键词
-
类别
资金
- National Natural Science Foundation of China [31900862, 61872216, 81630103]
- Turing AI Institute of Nanjing
DeepSEM is a deep generative model that can jointly infer gene regulatory networks (GRNs) and biologically meaningful representation of single-cell RNA sequencing (scRNA-seq) data. By developing a neural network version of the structural equation model (SEM), DeepSEM outperforms existing methods on various single-cell computational tasks and the predicted gene regulations can be validated by epigenetic data.
Gene regulatory networks (GRNs) encode the complex molecular interactions that govern cell identity. Here we propose DeepSEM, a deep generative model that can jointly infer GRNs and biologically meaningful representation of single-cell RNA sequencing (scRNA-seq) data. In particular, we developed a neural network version of the structural equation model (SEM) to explicitly model the regulatory relationships among genes. Benchmark results show that DeepSEM achieves comparable or better performance on a variety of single-cell computational tasks, such as GRN inference, scRNA-seq data visualization, clustering and simulation, compared with the state-of-the-art methods. In addition, the gene regulations predicted by DeepSEM on cell-type marker genes in the mouse cortex can be validated by epigenetic data, which further demonstrates the accuracy and efficiency of our method. DeepSEM can provide a useful and powerful tool to analyze scRNA-seq data and infer a GRN.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据