We introduce a general Bayesian framework for graph matching grounded in a new theory of exchangeable random permutations. Leveraging the cycle representation of permutations and the literature on exchangeable random partitions, we define, characterize, and study the structural and predictive properties of these probabilistic objects. A novel sequential metaphor, the position-aware generalized Chinese restaurant process, provides a constructive foundation for this theory and supports practical algorithmic design. Exchangeable random permutations offer flexible priors for a wide range of inferential problems centered on permutations. As an application, we develop a Bayesian model for graph matching that integrates a correlated stochastic block model with our novel class of priors. The cycle structure of the matching is linked to latent node partitions that explain connectivity patterns, an assumption consistent with the homogeneity requirement underlying the graph matching task itself. Posterior inference is performed through a node-wise blocked Gibbs sampler directly enabled by the proposed sequential construction. To summarize posterior uncertainty, we introduce perSALSO, an adaptation of SALSO to the permutation domain that provides principled point estimation and interpretable posterior summaries. Together, these contributions establish a unified probabilistic framework for modeling, inference, and uncertainty quantification over permutations.
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}…
The natural habitat of most Bayesian methods is data represented by exchangeable sequences of observations, for which de Finetti's theorem provides the theoretical foundation. Dirichlet process clustering, Gaussian process regression, and many other parametric and nonparametric Bayesian models fall within the remit of this framework; many problems arising in modern data analysis do not. This article provides an introduction to Bayesian models of graphs, matrices, and other data that can be modeled by random structures. We describe results in probability theory that generalize de Finetti's theo…
Given a sequence ξ_1, ξ_2,... of X-valued, exchangeable random elements, let q(ξ^(n)) and p_m(ξ^(n)) stand for posterior and predictive distribution, respectively, given ξ^(n) = (ξ_1,..., ξ_n). We provide an upper bound for limsup b_n d_[[X]](q(ξ^(n)), δ_\empiricn) and limsup b_n d_[X^m](p_m(ξ^(n)), \empiricn^m), where \empiricn is the empirical measure, b_n is a suitable sequence of positive numbers increasing to +\infty, d_[[X]] and d_[X^m] denote distinguished weak probability distances on [[X]] and [X^m], respectively, with the proviso that [S] denotes the space of all probability measures…
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…
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 unknow…
We explore the effect of finite population sampling in design problems with many variables cross-classified in many ways. In particular, we investigate designs where we wish to sample individuals belonging to different groups for which the underlying covariance matrices are separable between groups and variables. We exploit the generalised conditional independence structure of the model to show how the analysis of the full model can be reduced to an interpretable series of lower dimensional problems. The types of information we gain by sampling are identified with the orthogonal canonical dire…
We define a conjugate prior for the reversible Markov chain of order $r$. The prior arises from a partially exchangeable reinforced random walk, in the same way that the Beta distribution arises from the exchangeable Polyá urn. An extension to variable-order Markov chains is also derived. We show the utility of this prior in testing the order and estimating the parameters of a reversible Markov model.
This paper explores the intrinsic connections between the Bayesian false discovery rate (FDR) control procedures and their counterpart of frequentist procedures. We attempt to offer a unified view of FDR control within and beyond the setting of testing exchangeable hypotheses. Under the standard two-groups model and the Oracle condition, we show that the Bayesian and the frequentist methods can achieve asymptotically equivalent FDR control at arbitrary levels. Built on this result, we further illustrate that rigorous post-fitting model diagnosis is necessary and effective to ensure robust FDR …
Entity resolution (record linkage or deduplication) is the process of identifying and linking duplicate records in databases. In this paper, we propose a Bayesian graphical approach for entity resolution that links records to latent entities, where the prior representation on the linkage structure is exchangeable. First, we adopt a flexible and tractable set of priors for the linkage structure, which corresponds to a special class of random partition models. Second, we propose a more realistic distortion model for categorical/discrete record attributes, which corrects a logical inconsistency w…
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 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.
Recent advances in Bayesian models for random partitions have led to the formulation and exploration of Exchangeable Sequences of Clusters (ESC) models. Under ESC models, it is the cluster sizes that are exchangeable, rather than the observations themselves. This property is particularly useful for obtaining microclustering behavior, whereby cluster sizes grow sublinearly in the number of observations, as is common in applications such as record linkage, sparse networks and genomics. Unfortunately, the exchangeable clusters property comes at the cost of projectivity. As a consequence, in contr…
Gibbs partition models are the largest class of infinite exchangeable partitions of the positive integers generalizing the product form of the probability function of the two-parameter Poisson-Dirichlet family. Recently those models have been investigated in a Bayesian nonparametric approach to species sampling problems as alternatives to the Dirichlet and the Pitman-Yor process priors. Here we derive marginals of conditional and unconditional multivariate distributions arising from exchangeable Gibbs partitions to obtain explicit formulas for joint falling factorial moments of corresponding c…
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…
Gibbs-type exchangeable random partitions, which is a class of multiplicative measures on the set of positive integer partitions, appear in various contexts, including Bayesian statistics, random combinatorial structures, and stochastic models of diversity in various phenomena. Some distributional results on ordered sizes in the Gibbs partition are established by introducing associated partial Bell polynomials and analysis of the generating functions. The combinatorial approach is applied to derive explicit results on asymptotic behavior of the extreme sizes in the Gibbs partition. Especially,…
Gibbs-type random probability measures and the exchangeable random partitions they induce represent the subject of a rich and active literature. They provide a probabilistic framework for a wide range of theoretical and applied problems that are typically referred to as species sampling problems. In this paper, we consider the class of looking-backward species sampling problems introduced in Lijoi et al. (Ann. Appl. Probab. 18 (2008) 1519-1547) in Bayesian nonparametrics. Specifically, given some information on the random partition induced by an initial sample from a Gibbs-type random probabil…
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…
Discrete Bayesian nonparametric models whose expectation is a convex linear combination of a point mass at some point of the support and a diffuse probability distribution allow to incorporate strong prior information, while still being extremely flexible. Recent contributions in the statistical literature have successfully implemented such a modelling strategy in a variety of applications, including density estimation, nonparametric regression and model-based clustering. We provide a thorough study of a large class of nonparametric models we call inner spike and slab hNRMI models, which are o…
The paper discusses shrinkage priors which impose increasing shrinkage in a sequence of parameters. We review the cumulative shrinkage process (CUSP) prior of Legramanti et al. (2020), which is a spike-and-slab shrinkage prior where the spike probability is stochastically increasing and constructed from the stick-breaking representation of a Dirichlet process prior. As a first contribution, this CUSP prior is extended by involving arbitrary stick-breaking representations arising from beta distributions. As a second contribution, we prove that exchangeable spike-and-slab priors, which are popul…
The problem of inferring a clustering of a data set has been the subject of much research in Bayesian analysis, and there currently exists a solid mathematical foundation for Bayesian approaches to clustering. In particular, the class of probability distributions over partitions of a data set has been characterized in a number of ways, including via exchangeable partition probability functions (EPPFs) and the Kingman paintbox. Here, we develop a generalization of the clustering problem, called feature allocation, where we allow each data point to belong to an arbitrary, non-negative integer nu…
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…
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…
Nonparametric Bayesian models are often based on the assumption that the objects being modeled are exchangeable. While appropriate in some applications (e.g., bag-of-words models for documents), exchangeability is sometimes assumed simply for computational reasons; non-exchangeable models might be a better choice for applications based on subject matter. Drawing on ideas from graphical models and phylogenetics, we describe a non-exchangeable prior for a class of nonparametric latent feature models that is nearly as efficient computationally as its exchangeable counterpart. Our model is applica…
We first review an approach that had been developed in the past years to introduce concepts of "bivariate ageing" for exchangeable lifetimes and to analyze mutual relations among stochastic dependence, univariate ageing, and bivariate ageing. A specific feature of such an approach dwells on the concept of semi-copula and in the extension, from copulas to semi-copulas, of properties of stochastic dependence. In this perspective, we aim to discuss some intricate aspects of conceptual character and to provide the readers with pertinent remarks from a Bayesian Statistics standpoint. In particular …
Prior distributions play a crucial role in Bayesian approaches to clustering. Two commonly-used prior distributions are the Dirichlet and Pitman-Yor processes. In this paper, we investigate the predictive probabilities that underlie these processes, and the implicit "rich-get-richer" characteristic of the resulting partitions. We explore an alternative prior for nonparametric Bayesian clustering -- the uniform process -- for applications where the "rich-get-richer" property is undesirable. We also explore the cost of this process: partitions are no longer exchangeable with respect to the order…
Motivated by the fundamental problem of measuring species diversity, this paper introduces the concept of a cluster structure to define an exchangeable cluster probability function that governs the joint distribution of a random count and its exchangeable random partitions. A cluster structure, naturally arising from a completely random measure mixed Poisson process, allows the probability distribution of the random partitions of a subset of a sample to be dependent on the sample size, a distinct and motivated feature that differs it from a partition structure. A generalized negative binomial …
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 develop constructions for exchangeable sequences of point processes that are rendered conditionally-i.i.d. negative binomial processes by a (possibly unknown) random measure called the base measure. Negative binomial processes are useful in Bayesian nonparametrics as models for random multisets, and in applications we are often interested in cases when the base measure itself is difficult to construct (for example when it has countably infinite support). While a finitary construction for an important case (corresponding to a beta process base measure) has appeared in the literature, our con…
We present the Gaussian process density sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a distribution defined by a density that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We describe two such MCMC methods. Both me…
Covariance estimation and selection for multivariate datasets in a high-dimensional regime is a fundamental problem in modern statistics. Gaussian graphical models are a popular class of models used for this purpose. Current Bayesian methods for inverse covariance matrix estimation under Gaussian graphical models require the underlying graph and hence the ordering of variables to be known. However, in practice, such information on the true underlying model is often unavailable. We therefore propose a novel permutation-based Bayesian approach to tackle the unknown variable ordering issue. In pa…
In literature there are several studies on the performance of Bayesian network structure learning algorithms. The focus of these studies is almost always the heuristics the learning algorithms are based on, i.e. the maximisation algorithms (in score-based algorithms) or the techniques for learning the dependencies of each variable (in constraint-based algorithms). In this paper we investigate how the use of permutation tests instead of parametric ones affects the performance of Bayesian network structure learning from discrete data. Shrinkage tests are also covered to provide a broad overview …
Measure-valued Markov chains have raised interest in Bayesian nonparametrics since the seminal paper by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579--585) where a Markov chain having the law of the Dirichlet process as unique invariant measure has been introduced. In the present paper, we propose and investigate a new class of measure-valued Markov chains defined via exchangeable sequences of random variables. Asymptotic properties for this new class are derived and applications related to Bayesian nonparametric mixture modeling, and to a generalization of the Markov chain proposed by (M…
Generalizations to the permutation test are introduced to allow for situations in which the null model is not exchangeable. It is shown that the generalized permutation tests are exact, and a partial converse: that any test function that is exact on all probability densities coincides with a generalized permutation test on a particular region, is established. A most powerful generalized permutation test is derived in closed form. Approximations to the most powerful generalized permutation test are proposed to reduce the computational burden required to compute the complete test. In particular,…
Discrete random probability measures and the exchangeable random partitions they induce are key tools for addressing a variety of estimation and prediction problems in Bayesian inference. Indeed, many popular nonparametric priors, such as the Dirichlet and the Pitman-Yor process priors, select discrete probability distributions almost surely and, therefore, automatically induce exchangeable random partitions. Here we focus on the family of Gibbs-type priors, a recent and elegant generalization of the Dirichlet and the Pitman-Yor process priors. These random probability measures share propertie…
We introduce a three-parameter random walk with reinforcement, called the $(θ,α,β)$ scheme, which generalizes the linearly edge reinforced random walk to uncountable spaces. The parameter $β$ smoothly tunes the $(θ,α,β)$ scheme between this edge reinforced random walk and the classical exchangeable two-parameter Hoppe urn scheme, while the parameters $α$ and $θ$ modulate how many states are typically visited. Resorting to de Finetti's theorem for Markov chains, we use the $(θ,α,β)$ scheme to define a nonparametric prior for Bayesian analysis of reversible Markov chains. The prior is applied in…
University of Amsterdam（阿姆斯特丹大学）；Qualcomm AI Research（高通人工智能研究院）
In this work we propose a batch Bayesian optimization method for combinatorial problems on permutations, which is well suited for expensive-to-evaluate objectives. We first introduce LAW, an efficient batch acquisition method based on determinantal point processes using the acquisition weighted kernel. Relying on multiple parallel evaluations, LAW enables accelerated search on combinatorial spaces. We then apply the framework to permutation problems, which have so far received little attention in the Bayesian Optimization literature, despite their practical importance. We call this method LAW2…
The aim of this work is to study the problem of prior elicitation for the Mallows model with Spearman's distance, a popular distance-based model for rankings or permutation data. Previous Bayesian inference for such model has been limited to the use of the uniform prior over the space of permutations. We present a novel strategy to elicit subjective prior beliefs on the location parameter of the model, discussing the interpretation of hyper-parameters and the implication of prior choices for the posterior analysis.
An imprecise Bayesian nonparametric approach to system reliability with multiple types of components is developed. This allows modelling partial or imperfect prior knowledge on component failure distributions in a flexible way through bounds on the functioning probability. Given component level test data these bounds are propagated to bounds on the posterior predictive distribution for the functioning probability of a new system containing components exchangeable with those used in testing. The method further enables identification of prior-data conflict at the system level based on component …
We develop scalable methods for producing conformal Bayesian predictive intervals with finite sample calibration guarantees. Bayesian posterior predictive distributions, $p(y \mid x)$, characterize subjective beliefs on outcomes of interest, $y$, conditional on predictors, $x$. Bayesian prediction is well-calibrated when the model is true, but the predictive intervals may exhibit poor empirical coverage when the model is misspecified, under the so called ${\cal{M}}$-open perspective. In contrast, conformal inference provides finite sample frequentist guarantees on predictive confidence interva…
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…
We develop a general class of Bayesian repulsive Gaussian mixture models that encourage well-separated clusters, aiming at reducing potentially redundant components produced by independent priors for locations (such as the Dirichlet process). The asymptotic results for the posterior distribution of the proposed models are derived, including posterior consistency and posterior contraction rate in the context of nonparametric density estimation. More importantly, we show that compared to the independent prior on the component centers, the repulsive prior introduces additional shrinkage effect on…
We propose a flexible stochastic framework for modeling the market share dynamics over time in a multiple markets setting, where firms interact within and between markets. Firms undergo stochastic idiosyncratic shocks, which contract their shares, and compete to consolidate their position by acquiring new ones in both the market where they operate and in new markets. The model parameters can meaningfully account for phenomena such as barriers to entry and exit, fixed and sunk costs, costs of expanding to new sectors with different technologies and competitive advantage among firms. The constru…
Optimal Biological Dose Combination Finding: A Design Roadmap and Robust Cross-Indication Bayesian Borrowing
Population Health Sciences Institute, Newcastle University（纽卡斯尔大学人口健康科学研究所）；Quantitative Science and Evidence Generation, Astellas Pharma Global Development Inc.（安斯泰来全球开发公司定量科学与证据生成部）
