A Model Selection Approach to Hierarchical Shape Clustering with an Application to Cell Shapes
A Model Selection Approach to Hierarchical Shape Clustering with an Application to Cell Shapes
复制标题
分层形状聚类的模型选择方法及其在单元形状中的应用
DOI：
10.1101/2020.04.29.067892
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
M. Asgharian
中科院分区：
文献类型：
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作者：
M. Mirshahi;Vahid Partovi;M. Asgharian
形状是生物物种的一个重要表型，包含不同的环境和遗传信息。使用它们的形状信息对活细胞进行聚类可以为它们的功能和进化提供初步指导。层次聚类和树状图作为层次聚类的可视化工具，常被从业者用于分类和聚类。现有的层次形状聚类方法是基于距离的。这种方法往往缺乏适当的统计基础，无法对从业人员通常最感兴趣的重要参数（如聚类数）进行推断。我们从模型选择的角度来进行聚类，提出了一种基于形状球谐函数展开的线性模型的形状聚类方法。我们介绍了BIC型标准，称为CLUSBIC，并研究了该标准的一致性。特别注意的是，在研究模型选择标准和自然定义的模型选择文献中的概念，在指定的模型，重要的。当采用模型选择视角进行聚类时，这些概念不会自动扩展到形状聚类。为此，我们采取了一种新的方法，使用假设检验。我们应用我们提出的标准聚类一组真实的三维图像从HeLa细胞系。
Shape is an important phenotype of living species that contain different environmental and genetic information. Clustering living cells using their shape information can provide a preliminary guide to their functionality and evolution. Hierarchical clustering and dendrograms, as a visualization tool for hierarchical clustering, are commonly used by practitioners for classification and clustering. The existing hierarchical shape clustering methods are distance based. Such methods often lack a proper statistical foundation to allow for making inference on important parameters such as the number of clusters, often of prime interest to practitioners. We take a model selection perspective to clustering and propose a shape clustering method through linear models defined on Spherical Harmonics expansions of shapes. We introduce a BIC-type criterion, called CLUSBIC, and study consistency of the criterion. Special attention is paid to the notions of over- and under-specified models, important in studying model selection criteria and naturally defined in model selection literature. These notions do not automatically extend to shape clustering when a model selection perspective is adopted for clustering. To this end we take a novel approach using hypothesis testing. We apply our proposed criterion to cluster a set of real 3D images from HeLa cell line.
DOI：
10.1063/1.4748811
发表时间：
2012
期刊：
Physics of fluids (Woodbury, N.Y. : 1994)
影响因子：
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作者：
Lee,AM;Berny-Lang,MA;Liao,S;Kanso,E;Kuhn,P;McCarty,OJT;Newton,PK
通讯作者：
Newton,PK