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- Title
Reconstruction of Single-Cell Trajectories Using Stochastic Tree Search.
- Authors
Zhai, Jingyi; Ji, Hongkai; Jiang, Hui
- Abstract
The recent advancement in single-cell RNA sequencing technologies enables the understanding of dynamic cellular processes at the single-cell level. Using trajectory inference methods, pseudotimes can be estimated based on reconstructed single-cell trajectories which can be further used to gain biological knowledge. Existing methods for modeling cell trajectories, such as minimal spanning tree or k-nearest neighbor graph, often lead to locally optimal solutions. In this paper, we propose a penalized likelihood-based framework and introduce a stochastic tree search (STS) algorithm aiming at the global solution in a large and non-convex tree space. Both simulated and real data experiments show that our approach is more accurate and robust than other existing methods in terms of cell ordering and pseudotime estimation.
- Subjects
MULTICASTING (Computer networks); SPANNING trees; RNA sequencing; K-nearest neighbor classification
- Publication
Genes, 2023, Vol 14, Issue 2, p318
- ISSN
2073-4425
- Publication type
Article
- DOI
10.3390/genes14020318