论文标题
多元群集点过程以量化和探索多实体配置:应用于生物膜图像数据
Multivariate cluster point process to quantify and explore multi-entity configurations: Application to biofilm image data
论文作者
论文摘要
在许多领域都遇到了相似或不同对象的簇。经常使用的方法将每个群集的中心对象视为潜在的对象。但是,通常一种或多种类型的对象聚集在另一种类型的对象周围。这种布置在细胞的生物医学图像中很常见,在该图像中,附近的细胞类型可能相互作用。量化空间关系可以阐明生物学机制。即使中央对象(父母)与外围物体(后代)不同,即使中央对象(父母)不同,也可以有效地应用父母。我们提出了新型的多元群集点过程(MCPP),以量化多对象(例如多细胞)布置。与常用的方法不同,MCPP在集群中利用了中央父对象的位置。它说明了可能多层的多元聚类。模型公式需要指定哪种对象类型作为群集中心以及驻留于周围的中心。如果此类信息未知,则可以通过通过偏差信息标准(DIC)比较不同模型的拟合来探索对象类型的相对作用。在模拟数据中,我们比较了一系列模型的DIC; MCPP正确识别了模拟关系。它还比经典单变量Neyman-Scott过程模型产生了更准确和精确的参数估计。我们还使用MCPP来量化所提出的配置并在人牙斑块生物膜图像数据中探索新的配置。 MCPP模型量化了链球菌周围链球菌和卟啉菌的同时聚类,并围绕链球菌周围的巴斯德拉氏科进行了聚类,并成功地捕获了所有分类单元的假设结构。进一步的探索表明,五杆菌和瘦菌(Leptrichia)之间存在聚类,这是一种以前未报告的关系。
Clusters of similar or dissimilar objects are encountered in many fields. Frequently used approaches treat the central object of each cluster as latent. Yet, often objects of one or more types cluster around objects of another type. Such arrangements are common in biomedical images of cells, in which nearby cell types likely interact. Quantifying spatial relationships may elucidate biological mechanisms. Parent-offspring statistical frameworks can be usefully applied even when central objects (parents) differ from peripheral ones (offspring). We propose the novel multivariate cluster point process (MCPP) to quantify multi-object (e.g., multi-cellular) arrangements. Unlike commonly used approaches, the MCPP exploits locations of the central parent object in clusters. It accounts for possibly multilayered, multivariate clustering. The model formulation requires specification of which object types function as cluster centers and which reside peripherally. If such information is unknown, the relative roles of object types may be explored by comparing fit of different models via the deviance information criterion (DIC). In simulated data, we compared DIC of a series of models; the MCPP correctly identified simulated relationships. It also produced more accurate and precise parameter estimates than the classical univariate Neyman-Scott process model. We also used the MCPP to quantify proposed configurations and explore new ones in human dental plaque biofilm image data. MCPP models quantified simultaneous clustering of Streptococcus and Porphyromonas around Corynebacterium and of Pasteurellaceae around Streptococcus and successfully captured hypothesized structures for all taxa. Further exploration suggested the presence of clustering between Fusobacterium and Leptotrichia, a previously unreported relationship.