Edge-exchangeable probabilistic network models generate edges as an i.i.d.~sequence from a discrete measure, providing a simple means for statistical inference of latent network properties. The measure is often constructed using the self-product of a realization from a Bayesian nonparametric (BNP) discrete prior; but unlike in standard BNP models, the self-product measure prior is not conjugate the likelihood, hindering the development of exact simulation and inference algorithms. Approximation via finite truncation of the discrete measure is a straightforward alternative, but incurs an unknown approximation error. In this paper, we develop methods for forward simulation and posterior inference in random self-product-measure models based on truncation, and provide theoretical guarantees on the quality of the results as a function of the truncation level. The techniques we present are general and extend to the broader class of discrete Bayesian nonparametric models.
Directed graphs occur throughout statistical modeling of networks, and exchangeability is a natural assumption when the ordering of vertices does not matter. There is a deep structural theory for exchangeable undirected graphs, which extends to the directed case via measurable objects known as digraphons. Using digraphons, we first show how to construct models for exchangeable directed graphs, including special cases such as tournaments, linear orderings, directed acyclic graphs, and partial orderings. We then show how to construct priors on digraphons via the infinite relational digraphon mod…
We construct an infinitely exchangeable process on the set $\cate$ of subsets of the power set of the natural numbers $\mathbb{N}$ via a Poisson point process with mean measure $Λ$ on the power set of $\mathbb{N}$. Each $E\in\cate$ has a least monotone cover in $\catf$, the collection of monotone subsets of $\cate$, and every monotone subset maps to an undirected graph $G\in\catg$, the space of undirected graphs with vertex set $\mathbb{N}$. We show a natural mapping $\cate\rightarrow\catf\rightarrow\catg$ which induces an infinitely exchangeable measure on the projective system $\catg^{\rest}…
We present a novel model architecture which leverages deep learning tools to perform exact Bayesian inference on sets of high dimensional, complex observations. Our model is provably exchangeable, meaning that the joint distribution over observations is invariant under permutation: this property lies at the heart of Bayesian inference. The model does not require variational approximations to train, and new samples can be generated conditional on previous samples, with cost linear in the size of the conditioning set. The advantages of our architecture are demonstrated on learning tasks that req…
Maximum entropy network ensembles have been very successful in modelling sparse network topologies and in solving challenging inference problems. However the sparse maximum entropy network models proposed so far have fixed number of nodes and are typically not exchangeable. Here we consider hierarchical models for exchangeable networks in the sparse limit, i.e. with the total number of links scaling linearly with the total number of nodes. The approach is grand canonical, i.e. the number of nodes of the network is not fixed a priori: it is finite but can be arbitrarily large. In this way the g…
Motivated by the problem of designing inference-friendly Bayesian nonparametric models in probabilistic programming languages, we introduce a general class of partially exchangeable random arrays which generalizes the notion of hierarchical exchangeability introduced in Austin and Panchenko (2014). We say that our partially exchangeable arrays are DAG-exchangeable since their partially exchangeable structure is governed by a collection of Directed Acyclic Graphs. More specifically, such a random array is indexed by $\mathbb{N}^{|V|}$ for some DAG $G=(V,E)$, and its exchangeability structure is…
We construct a novel class of stochastic blockmodels using Bayesian nonparametric mixtures. These model allows us to jointly estimate the structure of multiple networks and explicitly compare the community structures underlying them, while allowing us to capture realistic properties of the underlying networks. Inference is carried out using MCMC algorithms that incorporates sequentially allocated split-merge steps to improve mixing. The models are illustrated using a simulation study and a variety of real-life examples.
The beta-negative binomial process (BNBP), an integer-valued stochastic process, is employed to partition a count vector into a latent random count matrix. As the marginal probability distribution of the BNBP that governs the exchangeable random partitions of grouped data has not yet been developed, current inference for the BNBP has to truncate the number of atoms of the beta process. This paper introduces an exchangeable partition probability function to explicitly describe how the BNBP clusters the data points of each group into a random number of exchangeable partitions, which are shared a…
University of Technology Sydney（悉尼科技大学）；University of New South Wales（新南威尔士大学）；Fudan University（复旦大学）
Modelling exchangeable relational data can be described by \textit{graphon theory}. Most Bayesian methods for modelling exchangeable relational data can be attributed to this framework by exploiting different forms of graphons. However, the graphons adopted by existing Bayesian methods are either piecewise-constant functions, which are insufficiently flexible for accurate modelling of the relational data, or are complicated continuous functions, which incur heavy computational costs for inference. In this work, we introduce a smoothing procedure to piecewise-constant graphons to form {\em smoo…
Dependent nonparametric processes extend distributions over measures, such as the Dirichlet process and the beta process, to give distributions over collections of measures, typically indexed by values in some covariate space. Such models are appropriate priors when exchangeability assumptions do not hold, and instead we want our model to vary fluidly with some set of covariates. Since the concept of dependent nonparametric processes was formalized by MacEachern [1], there have been a number of models proposed and used in the statistics and machine learning literatures. Many of these models ex…
We consider a discrete latent variable model for two-way data arrays, which allows one to simultaneously produce clusters along one of the data dimensions (e.g. exchangeable observational units or features) and contiguous groups, or segments, along the other (e.g. consecutively ordered times or locations). The model relies on a hidden Markov structure but, given its complexity, cannot be estimated by full maximum likelihood. We therefore introduce composite likelihood methodology based on considering different subsets of the data. The proposed approach is illustrated by simulation, and with an…
We consider inference for high-dimensional separately and jointly exchangeable arrays where the dimensions may be much larger than the sample sizes. For both exchangeable arrays, we first derive high-dimensional central limit theorems over the rectangles and subsequently develop novel multiplier bootstraps with theoretical guarantees. These theoretical results rely on new technical tools such as Hoeffding-type decomposition and maximal inequalities for the degenerate components in the Hoeffiding-type decomposition for the exchangeable arrays. We exhibit applications of our methods to uniform c…
We show that lower-dimensional marginal densities of dependent zero-mean normal distributions truncated to the positive orthant exhibit a mass-shifting phenomenon. Despite the truncated multivariate normal density having a mode at the origin, the marginal density assigns increasingly small mass near the origin as the dimension increases. The phenomenon accentuates with stronger correlation between the random variables. A precise quantification characterizing the role of the dimension as well as the dependence is provided. This surprising behavior has serious implications towards Bayesian const…
University of Tübingen（蒂宾根大学）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
Simulation-based inference (SBI) solves statistical inverse problems by repeatedly running a stochastic simulator and inferring posterior distributions from model-simulations. To improve simulation efficiency, several inference methods take a sequential approach and iteratively adapt the proposal distributions from which model simulations are generated. However, many of these sequential methods are difficult to use in practice, both because the resulting optimisation problems can be challenging and efficient diagnostic tools are lacking. To overcome these issues, we present Truncated Sequentia…
The proposal and study of dependent prior processes has been a major research focus in the recent Bayesian nonparametric literature. In this paper, we introduce a flexible class of dependent nonparametric priors, investigate their properties and derive a suitable sampling scheme which allows their concrete implementation. The proposed class is obtained by normalizing dependent completely random measures, where the dependence arises by virtue of a suitable construction of the Poisson random measures underlying the completely random measures. We first provide general distributional results for t…
In Bayesian nonparametric inference, random discrete probability measures are commonly used as priors within hierarchical mixture models for density estimation and for inference on the clustering of the data. Recently, it has been shown that they can also be exploited in species sampling problems: indeed they are natural tools for modeling the random proportions of species within a population thus allowing for inference on various quantities of statistical interest. For applications that involve large samples, the exact evaluation of the corresponding estimators becomes impracticable and, ther…
Harvard University（哈佛大学）；Universita di Pavia（帕维亚大学）；University of Kent（肯特大学）；MD Anderson Cancer Center（MD安德森癌症中心）
Many popular Bayesian nonparametric priors can be characterized in terms of exchangeable species sampling sequences. However, in some applications, exchangeability may not be appropriate. We introduce a {novel and probabilistically coherent family of non-exchangeable species sampling sequences characterized by a tractable predictive probability function with weights driven by a sequence of independent Beta random variables. We compare their theoretical clustering properties with those of the Dirichlet Process and the two parameters Poisson-Dirichlet process. The proposed construction provides …
University of Amsterdam（阿姆斯特丹大学）；University of Liège（列日大学）
Parametric stochastic simulators are ubiquitous in science, often featuring high-dimensional input parameters and/or an intractable likelihood. Performing Bayesian parameter inference in this context can be challenging. We present a neural simulation-based inference algorithm which simultaneously offers simulation efficiency and fast empirical posterior testability, which is unique among modern algorithms. Our approach is simulation efficient by simultaneously estimating low-dimensional marginal posteriors instead of the joint posterior and by proposing simulations targeted to an observation o…
Bayesian Inference for Left-Truncated Log-Logistic Distributions for Time-to-event Data Analysis
NCIAS, Arizona State University（国家癌症研究所亚利桑那州立大学分校）；Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University（生物统计中心，生物医学信息学系，俄亥俄州立大学）；Department of Electrical and Computer Engineering, The University of Texas at Austin（电气与计算机工程系，德克萨斯大学奥斯汀分校）；Department of Mathematics, The University of Hawaii at Mānoa（数学系，夏威夷大学毛伊分校）
Finite mixtures are a flexible modeling tool for irregularly shaped densities and samples from heterogeneous populations. When modeling with mixtures using an exchangeable prior on the component features, the component labels are arbitrary and are indistinguishable in posterior analysis. This makes it impossible to attribute any meaningful interpretation to the marginal posterior distributions of the component features. We propose a model in which a small number of observations are assumed to arise from some of the labeled component densities. The resulting model is not exchangeable, allowing …
We investigate Bayesian non-parametric inference of the $Λ$-measure of $Λ$-coalescent processes with recurrent mutation, parametrised by probability measures on the unit interval. We give verifiable criteria on the prior for posterior consistency when observations form a time series, and prove that any non-trivial prior is inconsistent when all observations are contemporaneous. We then show that the likelihood given a data set of size $n \in \mathbb{N}$ is constant across $Λ$-measures whose leading $n - 2$ moments agree, and focus on inferring truncated sequences of moments. We provide a large…
Completely random measures (CRMs) and their normalizations are a rich source of Bayesian nonparametric priors. Examples include the beta, gamma, and Dirichlet processes. In this paper we detail two major classes of sequential CRM representations---series representations and superposition representations---within which we organize both novel and existing sequential representations that can be used for simulation and posterior inference. These two classes and their constituent representations subsume existing ones that have previously been developed in an ad hoc manner for specific processes. Si…
Basic principles of statistical inference are commonly violated in network data analysis. Under the current approach, it is often impossible to identify a model that accommodates known empirical behaviors, possesses crucial inferential properties, and accurately models the data generating process. In the absence of one or more of these properties, sensible inference from network data cannot be assured. Our proposed framework decomposes every network model into a (relatively) exchangeable data generating process} and a sampling mechanism that relates observed data to the population network. Thi…
We consider the problem of drawing samples from posterior distributions formed under a Dirichlet prior and a truncated multinomial likelihood, by which we mean a Multinomial likelihood function where we condition on one or more counts being zero a priori. Sampling this posterior distribution is of interest in inference algorithms for hierarchical Bayesian models based on the Dirichlet distribution or the Dirichlet process, particularly Gibbs sampling algorithms for the Hierarchical Dirichlet Process Hidden Semi-Markov Model. We provide a data augmentation sampling algorithm that is easy to imp…
Many exact Markov chain Monte Carlo algorithms have been developed for posterior inference in Bayesian nonparametric models which involve infinite-dimensional priors. However, these methods are not generic and special methodology must be developed for different classes of prior or different models. Alternatively, the infinite-dimensional prior can be truncated and standard Markov chain Monte Carlo methods used for inference. However, the error in approximating the infinite-dimensional posterior can be hard to control for many models. This paper describes an adaptive truncation method which all…
Modeled along the truncated approach in Panigrahi (2016), selection-adjusted inference in a Bayesian regime is based on a selective posterior. Such a posterior is determined together by a generative model imposed on data and the selection event that enforces a truncation on the assumed law. The effective difference between the selective posterior and the usual Bayesian framework is reflected in the use of a truncated likelihood. The normalizer of the truncated law in the adjusted framework is the probability of the selection event; this is typically intractable and it leads to the computationa…
We address the problem of providing inference from a Bayesian perspective for parameters selected after viewing the data. We present a Bayesian framework for providing inference for selected parameters, based on the observation that providing Bayesian inference for selected parameters is a truncated data problem. We show that if the prior for the parameter is non-informative, or if the parameter is a "fixed" unknown constant, then it is necessary to adjust the Bayesian inference for selection. Our second contribution is the introduction of Bayesian False Discovery Rate controlling methodology,…
Makerere University（马凯雷雷大学）；University of Sheffield（谢菲尔德大学）；University of Manchester（曼彻斯特大学）；University of Nottingham（诺丁汉大学）
Linear systems occur throughout engineering and the sciences, most notably as differential equations. In many cases the forcing function for the system is unknown, and interest lies in using noisy observations of the system to infer the forcing, as well as other unknown parameters. In differential equations, the forcing function is an unknown function of the independent variables (typically time and space), and can be modelled as a Gaussian process (GP). In this paper we show how the adjoint of a linear system can be used to efficiently infer forcing functions modelled as GPs, using a truncate…
A natural Bayesian approach for mixture models with an unknown number of components is to take the usual finite mixture model with Dirichlet weights, and put a prior on the number of components---that is, to use a mixture of finite mixtures (MFM). While inference in MFMs can be done with methods such as reversible jump Markov chain Monte Carlo, it is much more common to use Dirichlet process mixture (DPM) models because of the relative ease and generality with which DPM samplers can be applied. In this paper, we show that, in fact, many of the attractive mathematical properties of DPMs are als…
We present a scalable Bayesian model for low-rank factorization of massive tensors with binary observations. The proposed model has the following key properties: (1) in contrast to the models based on the logistic or probit likelihood, using a zero-truncated Poisson likelihood for binary data allows our model to scale up in the number of \emph{ones} in the tensor, which is especially appealing for massive but sparse binary tensors; (2) side-information in form of binary pairwise relationships (e.g., an adjacency network) between objects in any tensor mode can also be leveraged, which can be es…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach uses a phylogenetic multivariate probit model to accommodate binary and continuous traits via a latent variable framework, and utilizes an efficient bouncy particle sampler (BPS) to tackle the computational bottleneck -- integrating many latent variables from a high-dimensional truncated normal distribution. This approach breaks down as the number…
