MISC – missing imputation for single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) technology provides an effective way to study cell heterogeneity. However, due to the low capture efficiency and stochastic gene expression, scRNA-seq data often contains a high percentage of missing values. It has been showed that the missing rate can reach approximately 30% even after noise reduction. To accurately recover missing values in scRNA-seq data, we need to know where the missing data is; how much data is missing; and what are the values of these data.

To solve these three problems, researchers from the University of Arkansas Little Rock propose a novel model with a hybrid machine learning method, namely, missing imputation for single-cell RNA-seq (MISC). To solve the first problem, they transformed it to a binary classification problem on the RNA-seq expression matrix. Then, for the second problem, they searched for the intersection of the classification results, zero-inflated model and false negative model results. Finally, the researchers used the regression model to recover the data in the missing elements.

They compared the raw data without imputation, the mean-smooth neighbor cell trajectory, MISC on chronic myeloid leukemia data (CML), the primary somatosensory cortex and the hippocampal CA1 region of mouse brain cells. On the CML data, MISC discovered a trajectory branch from the CP-CML to the BC-CML, which provides direct evidence of evolution from CP to BC stem cells. On the mouse brain data, MISC clearly divides the pyramidal CA1 into different branches, and it is direct evidence of pyramidal CA1 in the subpopulations. In the meantime, with MISC, the oligodendrocyte cells became an independent group with an apparent boundary.

Flowchart of missing imputations on single-cell RNA-seq (MISC)

rna-seq

The workflow consists of data acquisition, problem modeling, machine learning and downstream validation. The machine learning approach includes binary classification, ensemble learning and regression

These results showed that the MISC model improved the cell type classification and could be instrumental to study cellular heterogeneity. Overall, MISC is a robust missing data imputation model for single-cell RNA-seq data.

Yang MQ, Weissman SM, Yang W, Zhang J, Canaann A, Guan R. (2018) MISC: missing imputation for single-cell RNA sequencing data. BMC Syst Biol 12(Suppl 7):114. [article]

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