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Abstract Mixed-membership (MM) models such as latent Dirichlet allocation (LDA) have been applied to microbiome compositional data to identify latent subcommunities of microbial species. These subcommunities are informative for understanding the biological interplay of microbes and for predicting health outcomes. However, microbiome compositions typically display substantial cross-sample heterogeneities in subcommunity compositions—that is, the variability in the proportions of microbes in shared subcommunities across samples—which is not accounted for in prior analyses. As a result, LDA can produce inference, which is highly sensitive to the specification of the number of subcommunities and often divides a single subcommunity into multiple artificial ones. To address this limitation, we incorporate the logistic-tree normal (LTN) model into LDA to form a new MM model. This model allows cross-sample variation in the composition of each subcommunity around some “centroid” composition that defines the subcommunity. Incorporation of auxiliary Pólya-Gamma variables enables a computationally efficient collapsed blocked Gibbs sampler to carry out Bayesian inference under this model. By accounting for such heterogeneity, our new model restores the robustness of the inference in the specification of the number of subcommunities and allows meaningful subcommunities to be identified. 

Tree-based methods are popular nonparametric tools for capturing spatial heterogeneity and making predictions in multivariate problems. In unsupervised learning, trees and their ensembles have also been applied to a wide range of statistical inference tasks, such as multi-resolution sketching of distributional variations, localization of high-density regions, and design of efficient data compression schemes. In this paper, we study the spatial adaptation property of Bayesian tree-based methods in the unsupervised setting, with a focus on the density estimation problem. We characterize spatial heterogeneity of the underlying density function by using anisotropic Besov spaces, region-wise anisotropic Besov spaces, and two novel function classes as their extensions. For two types of commonly used prior distributions on trees under the context of unsupervised learning—the optional P{ó}lya tree (Wong and Ma, 2010) and the Dirichlet prior (Lu et al., 2013)—we calculate posterior concentration rates when the density function exhibits different types of heterogeneity. In specific, we show that the posterior concentration rate for trees is near minimax over the anisotropic Besov space. The rate is adaptive in the sense that to achieve such a rate we do not need any prior knowledge of the parameters of the Besov space. 

Tree-based methods are popular nonparametric tools for capturing spatial heterogeneity and making predictions in multivariate problems. In unsupervised learning, trees and their ensembles have also been applied to a wide range of statistical inference tasks, such as multi-resolution sketching of distributional variations, localization of high-density regions, and design of efficient data compression schemes. In this paper, we study the spatial adaptation property of Bayesian tree-based methods in the unsupervised setting, with a focus on the density estimation problem. We characterize spatial heterogeneity of the underlying density function by using anisotropic Besov spaces, region-wise anisotropic Besov spaces, and two novel function classes as their extensions. For two types of commonly used prior distributions on trees under the context of unsupervised learning—the optional P{ó}lya tree (Wong and Ma, 2010) and the Dirichlet prior (Lu et al., 2013)—we calculate posterior concentration rates when the density function exhibits different types of heterogeneity. In specific, we show that the posterior concentration rate for trees is near minimax over the anisotropic Besov space. The rate is adaptive in the sense that to achieve such a rate we do not need any prior knowledge of the parameters of the Besov space.