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在细胞动态的最佳运输中,除Sinkhorn分歧

Jayshawn Cooper¹, Christina Young¹, Pilhwa Lee¹

¹Department of Mathematics, Morgan State University, 1700 E. Cold Spring Lane, Baltimore, 21251, MD, USA.

bioRxiv : the preprint server for biology

|January 27, 2025

概括

辛克霍恩分歧在单细胞RNA-seq分析中改善了细胞命运轨迹预测,特别是在密集的时间点. 它的好处随着时间的稀疏而减少,使其应用取决于上下文.

科学领域:

计算生物学计算生物学
单细胞基因组学单细胞基因组学
发展生物学发展生物学

背景情况:

单细胞RNA测序 (scRNA-seq) 对于理解细胞的分化和重编程等过程至关重要.
最佳运输 (OT) 模拟了细胞动态,但来自热带调节的算法偏差需要缓解.

研究的目的:

评估Sinkhorn差异在去偏差OT中的有效性,用于scRNA-seq数据分析.
确定时间采样密度对Sinkhorn分歧在预测细胞命运轨迹方面的表现的影响.

主要方法:

使用最佳运输算法来制定细胞动态.
应用Sinkhorn分歧来纠正OT中的调节偏差.
从小鼠胚胎纤维细胞重编程和表皮形态发生的scRNA-seq数据分析,时间点密度不同.

主要成果:

在重编程具有密集时间点的模型中,Sinkhorn分歧改善了细胞命运轨迹预测.
通过辛克霍恩分歧平衡的强热规律化,有利于具有较少时间点 (9 个时间点) 的细胞表型.
辛克霍恩分歧的优势随着时间点 (5 个时间点) 的进一步缩短和人口规模的扩大而减少,并且对表皮形态发生并不重要.

结论:

在scRNA-seq中,Sinkhorn分歧对于准确的细胞系预测的实用性取决于数据的时间稀疏性.
具体上下文的应用是关键:对密集的时间序列数据来说,Sinkhorn分歧是有益的,但对稀疏的数据来说不那么有益.

关键词:

沉声喇分歧的分歧算法偏差是一种算法偏差.热规范化热规范化血统的确定血统的确定最佳的运输最佳的运输.一个单细胞分析.

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