Single-cell technologies are revolutionizing the entire field of biology. The
large volumes of data generated by single-cell technologies are
high-dimensional, sparse, heterogeneous, and have complicated dependency
structures, making analyses using conventional machine learning approaches
challenging and impractical. In tackling these challenges, deep learning often
demonstrates superior performance compared to traditional machine learning
methods. In this work, we give a comprehensive survey on deep learning in
single-cell analysis. We first introduce background on single-cell technologies
and their development, as well as fundamental concepts of deep learning
including the most popular deep architectures. We present an overview of the
single-cell analytic pipeline pursued in research applications while noting
divergences due to data sources or specific applications. We then review seven
popular tasks spanning through different stages of the single-cell analysis
pipeline, including multimodal integration, imputation, clustering, spatial
domain identification, cell-type deconvolution, cell segmentation, and
cell-type annotation. Under each task, we describe the most recent developments
in classical and deep learning methods and discuss their advantages and
disadvantages. Deep learning tools and benchmark datasets are also summarized
for each task. Finally, we discuss the future directions and the most recent
challenges. This survey will serve as a reference for biologists and computer
scientists, encouraging collaborations.Comment: 77 pages, 11 figures, 15 tables, deep learning, single-cell analysi