Visualization and Analysis of Single Cell RNA-Seq Data by Maximizing Correntropy Based Non-Negative Low Rank Representation

The exploration of single cell RNA-sequencing (scRNA-seq) technology generates a new perspective to analyze biological problems. One of the major applications of scRNA-seq data is to discover subtypes of cells by cell clustering. Nevertheless, it is challengeable for traditional methods to handle scRNA-seq data with high level of technical noise and notorious dropouts. To better analyze single cell data, a novel scRNA-seq data analysis model called Maximum correntropy criterion based Non-negative and Low Rank Representation (MccNLRR) is introduced. Specifically, the maximum correntropy criterion, as an effective loss function, is more robust to the high noise and large outliers existed in the data. Moreover, the low rank representation is proven to be a powerful tool for capturing the global and local structures of data. Therefore, some important information, such as the similarity of cells in the subspace, is also extracted by it. Then, an iterative algorithm on the basis of the half-quadratic optimization and alternating direction method is developed to settle the complex optimization problem. Before the experiment, we also analyze the convergence and robustness of MccNLRR. At last, the results of cell clustering, visualization analysis, and gene markers selection on scRNA-seq data reveal that MccNLRR method can distinguish cell subtypes accurately and robustly.

Automated summary

The MccNLRR method, based on the maximum correntropy criterion, offers robustness in handling high technical noise and dropouts in scRNA-seq data. By combining an effective loss function with low rank representation, it accurately and robustly distinguishes cell subtypes while capturing global and local structures of the data.