Application of Deep Learning on Single-Cell RNA-sequencing Data Analysis: A Review

Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states and phenotypes, and has helped elucidate biological processes, such as those occurring during development of complex organisms and improved our understanding of disease states, such as cancer, diabetes, and COVID, among others. Deep learning, a recent advance of artificial intelligence that has been used to address many problems involving large datasets, has also emerged as a promising tool for scRNA-seq data analysis, as it has a capacity to extract informative, compact features from noisy, heterogeneous, and high-dimensional scRNA-seq data to improve downstream analysis. The present review aims at surveying recently developed deep learning techniques in scRNA-seq data analysis, identifying key steps within the scRNA-seq data analysis pipeline that have been advanced by deep learning, and explaining the benefits of deep learning over more conventional analysis tools. Finally, we summarize the challenges in current deep learning approaches faced within scRNA-seq data and discuss potential directions for improvements in deep algorithms for scRNA-seq data analysis.

Block Model Guided Unsupervised Feature Selection

Feature selection is a core area of data mining with a recent innovation of graph-driven unsupervised feature selection for linked data. In this setting we have a dataset $\mathbf{Y}$ consisting of $n$ instances each with $m$ features and a corresponding $n$ node graph (whose adjacency matrix is $\mathbf{A}$) with an edge indicating that the two instances are similar. Existing efforts for unsupervised feature selection on attributed networks have explored either directly regenerating the links by solving for $f$ such that $f(\mathbf{y}_i,\mathbf{y}_j) \approx \mathbf{A}_{i,j}$ or finding community structure in $\mathbf{A}$ and using the features in $\mathbf{Y}$ to predict these communities. However, graph-driven unsupervised feature selection remains an understudied area with respect to exploring more complex guidance. Here we take the novel approach of first building a block model on the graph and then using the block model for feature selection. That is, we discover $\mathbf{F}\mathbf{M}\mathbf{F}^T \approx \mathbf{A}$ and then find a subset of features $\mathcal{S}$ that induces another graph to preserve both $\mathbf{F}$ and $\mathbf{M}$. We call our approach Block Model Guided Unsupervised Feature Selection (BMGUFS). Experimental results show that our method outperforms the state of the art on several real-world public datasets in finding high-quality features for clustering.