Year: 2024
Author: Tiejun Li, Yizhuo Wang, Guoguo Yang, Peijie Zhou
CSIAM Transactions on Applied Mathematics, Vol. 5 (2024), Iss. 1 : pp. 182–220
Abstract
In the previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1–55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition dynamical processes underlying snapshot data. The current paper is devoted to the algorithmic study of some key components in RNA velocity workflow. Four important points are addressed in this paper: (1) We construct a rational time-scale fixation method which can determine the global gene-shared latent time for cells. (2) We present an uncertainty quantification strategy for the inferred parameters obtained through the EM algorithm. (3) We establish the optimal criterion for the choice of velocity kernel bandwidth with respect to the sample size in the downstream analysis and discuss its implications. (4) We propose a temporal distance estimation approach between two cell clusters along the cellular development path. Some illustrative numerical tests are also carried out to verify our analysis. These results are intended to provide tools and insights in further development of RNA velocity type methods in the future.
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Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/10.4208/csiam-am.SO-2023-0026
CSIAM Transactions on Applied Mathematics, Vol. 5 (2024), Iss. 1 : pp. 182–220
Published online: 2024-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 39
Keywords: Time-scale fixation uncertainty quantification optimal kernel bandwidth temporal distance estimation.