论文标题
通过高斯工艺对空间分子分析数据的贝叶斯建模
Bayesian Modeling of Spatial Molecular Profiling Data via Gaussian Process
论文作者
论文摘要
组织内基因表达(mRNA和蛋白质)的位置,时机和丰度定义了细胞功能的分子机制。空间分子分析中的最新技术突破,包括基于成像的技术和基于测序的技术,已使单个细胞的全面分子表征能够保留其空间和形态的环境。这种新的生物信息学场景要求采用有效且可靠的计算方法来识别具有空间模式的基因。我们代表了一种新型的贝叶斯分层模型,用于分析具有几个独特特征的空间转录组学数据。它通过部署零充气的负二项式模型来对零充气和过度分散的计数进行建模,从而大大提高模型稳定性和鲁棒性。此外,贝叶斯推理框架使我们能够以从头开始的参数估计借用强度。结果,提出的模型在模拟研究和两个实际数据应用中都表现出对现有方法的准确性和鲁棒性的竞争性能。相关的R/C ++源代码可在https://github.com/minzhe/boost-gp上获得。
The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based technologies and sequencing-based technologies, have enabled the comprehensive molecular characterization of single cells while preserving their spatial and morphological contexts. This new bioinformatics scenario calls for effective and robust computational methods to identify genes with spatial patterns. We represent a novel Bayesian hierarchical model to analyze spatial transcriptomics data, with several unique characteristics. It models the zero-inflated and over-dispersed counts by deploying a zero-inflated negative binomial model that greatly increases model stability and robustness. Besides, the Bayesian inference framework allows us to borrow strength in parameter estimation in a de novo fashion. As a result, the proposed model shows competitive performances in accuracy and robustness over existing methods in both simulation studies and two real data applications. The related R/C++ source code is available at https://github.com/Minzhe/BOOST-GP.