Analyses of array-valued datasets often involve reduced-rank array approximations, typically obtained via least-squares or truncations of array decompositions. However, least-squares approximations tend to be noisy in high-dimensional settings, and may not be appropriate for arrays that include discrete or ordinal measurements. This article develops methodology to obtain low-rank model-based representations of continuous, discrete and ordinal data arrays. The model is based on a parameterization of the mean array as a multilinear product of a reduced-rank core array and a set of index-specific orthogonal eigenvector matrices. It is shown how orthogonally equivariant parameter estimates can be obtained from Bayesian procedures under invariant prior distributions. Additionally, priors on the core array are developed that act as regularizers, leading to improved inference over the standard least-squares estimator, and providing robustness to misspecification of the array rank. This model-based approach is extended to accommodate discrete or ordinal data arrays using a semiparametric transformation model. The resulting low-rank representation is scale-free, in the sense that it is invariant to monotonic transformations of the data array. In an example analysis of a multivariate discrete network dataset, this scale-free approach provides a more complete description of data patterns.

Functional data, with basic observational units being functions (e.g., curves, surfaces) varying over a continuum, are frequently encountered in various applications. While many statistical tools have been developed for functional data analysis, the issue of smoothing all functional observations simultaneously is less studied. Existing methods often focus on smoothing each individual function separately, at the risk of removing important systematic patterns common across functions. We propose a nonparametric Bayesian approach to smooth all functional observations simultaneously and nonparametrically. In the proposed approach, we assume that the functional observations are independent Gaussian processes subject to a common level of measurement errors, enabling the borrowing of strength across all observations. Unlike most Gaussian process regression models that rely on pre-specified structures for the covariance kernel, we adopt a hierarchical framework by assuming a Gaussian process prior for the mean function and an Inverse-Wishart process prior for the covariance function. These prior assumptions induce an automatic mean–covariance estimation in the posterior inference in addition to the simultaneous smoothing of all observations. Such a hierarchical framework is flexible enough to incorporate functional data with different characteristics, including data measured on either common or uncommon grids, and data with either stationary or nonstationary covariance structures. Simulations and real data analysis demonstrate that, in comparison with alternative methods, the proposed Bayesian approach achieves better smoothing accuracy and comparable mean–covariance estimation results. Furthermore, it can successfully retain the systematic patterns in the functional observations that are usually neglected by the existing functional data analyses based on individual-curve smoothing.

We consider Bayesian linear inverse problems in infinite-dimensional separable Hilbert spaces, with a Gaussian prior measure and additive Gaussian noise model, and provide an extension of the concept of Bayesian D-optimality to the infinite-dimensional case. To this end, we derive the infinite-dimensional version of the expression for the Kullback–Leibler divergence from the posterior measure to the prior measure, which is subsequently used to derive the expression for the expected information gain. We also study the notion of Bayesian A-optimality in the infinite-dimensional setting, and extend the well known (in the finite-dimensional case) equivalence of the Bayes risk of the MAP estimator with the trace of the posterior covariance, for the Gaussian linear case, to the infinite-dimensional Hilbert space case.

In this paper, we consider homogeneous normalized random measures with independent increments (hNRMI), a class of nonparametric priors recently introduced in the literature. Many of their distributional properties are known by now but their stick-breaking representation is missing. Here we display such a representation, which will feature dependent stick-breaking weights, and then derive explicit versions for noteworthy special cases of hNRMI. Posterior characterizations are also discussed. Finally, we devise an algorithm for slice sampling mixture models based on hNRMIs, which relies on the representation we have obtained, and implement it to analyze real data.

While statisticians and quantitative social scientists typically study the “effects of causes” (EoC), Lawyers and the Courts are more concerned with understanding the “causes of effects” (CoE). EoC can be addressed using experimental design and statistical analysis, but it is less clear how to incorporate statistical or epidemiological evidence into CoE reasoning, as might be required for a case at Law. Some form of counterfactual reasoning, such as the “potential outcomes” approach championed by Rubin, appears unavoidable, but this typically yields “answers” that are sensitive to arbitrary and untestable assumptions. We must therefore recognise that a CoE question simply might not have a well-determined answer. It is nevertheless possible to use statistical data to set bounds within which any answer must lie. With less than perfect data these bounds will themselves be uncertain, leading to a compounding of different kinds of uncertainty. Still further care is required in the presence of possible confounding factors. In addition, even identifying the relevant “counterfactual contrast” may be a matter of Policy as much as of Science. Defining the question is as non-trivial a task as finding a route towards an answer.

This paper develops some technical elaborations of these philosophical points from a personalist Bayesian perspective, and illustrates them with a Bayesian analysis of a case study in child protection.

Consider the problem of simultaneous testing for the means of independent normal observations. In this paper, we study some asymptotic optimality properties of certain multiple testing rules induced by a general class of one-group shrinkage priors in a Bayesian decision theoretic framework, where the overall loss is taken as the number of misclassified hypotheses. We assume a two-groups normal mixture model for the data and consider the asymptotic framework adopted in Bogdan et al. (2011) who introduced the notion of asymptotic Bayes optimality under sparsity in the context of multiple testing. The general class of one-group priors under study is rich enough to include, among others, the families of three parameter beta, generalized double Pareto priors, and in particular the horseshoe, the normal–exponential–gamma and the Strawderman–Berger priors. We establish that within our chosen asymptotic framework, the multiple testing rules under study asymptotically attain the risk of the Bayes Oracle up to a multiplicative factor, with the constant in the risk close to the constant in the Oracle risk. This is similar to a result obtained in Datta and Ghosh (2013) for the multiple testing rule based on the horseshoe estimator introduced in Carvalho et al. (2009, 2010). We further show that under very mild assumption on the underlying sparsity parameter, the induced decisions using an empirical Bayes estimate of the corresponding global shrinkage parameter proposed by van der Pas et al. (2014), asymptotically attain the optimal Bayes risk up to the same multiplicative factor. We provide a unifying argument applicable for the general class of priors under study. In the process, we settle a conjecture regarding optimality property of the generalized double Pareto priors made in Datta and Ghosh (2013). Our work also shows that the result in Datta and Ghosh (2013) can be improved further.

We propose a new model for correlated outputs of mixed type, such as continuous and binary outputs, with a particular focus on joint regression and classification, motivated by an application in constrained optimization for computer simulation modeling. Our framework is based upon multivariate stochastic processes, extending Gaussian process methodology for modeling of continuous multivariate spatial outputs by adding a latent process structure that allows for joint modeling of a variety of types of correlated outputs. In addition, we implement fully Bayesian inference using particle learning, which allows us to conduct fast sequential inference. We demonstrate the effectiveness of our proposed methods on both synthetic examples and a real world hydrology computer experiment optimization problem where it is helpful to model the black box objective function as correlated with satisfaction of the constraint.

In this paper, we consider nonparametric Bayesian variable selection in quantile regression. The Bayesian model is based on the empirical likelihood, and the prior is chosen as the “spike-and-slab” prior–a mixture of a point mass at zero and a normal distribution. We show that the posterior distribution of the zero coefficients converges to a point mass at zero and that of the nonzero coefficients converges to a normal distribution. To further address the problem of low statistical efficiency in extreme quantile regression, we extend the Bayesian model such that it can integrate information at multiple quantiles to provide more accurate inference of extreme quantiles for homogenous error models. Simulation studies demonstrate that the proposed methods outperform or perform equally well compared with existing methods. We apply this Bayesian method to study the role of microRNAs on regulating gene expression and find that the regulation of microRNA may have a positive effect on the gene expression variation.

This paper addresses the problem of determining optimal designs for biological process models with intractable likelihoods, with the goal of parameter inference. The Bayesian approach is to choose a design that maximises the mean of a utility, and the utility is a function of the posterior distribution. Therefore, its estimation requires likelihood evaluations. However, many problems in experimental design involve models with intractable likelihoods, that is, likelihoods that are neither analytic nor can be computed in a reasonable amount of time. We propose a novel solution using indirect inference (II), a well established method in the literature, and the Markov chain Monte Carlo (MCMC) algorithm of Müller et al. (2004). Indirect inference employs an auxiliary model with a tractable likelihood in conjunction with the generative model, the assumed true model of interest, which has an intractable likelihood. Our approach is to estimate a map between the parameters of the generative and auxiliary models, using simulations from the generative model. An II posterior distribution is formed to expedite utility estimation. We also present a modification to the utility that allows the Müller algorithm to sample from a substantially sharpened utility surface, with little computational effort. Unlike competing methods, the II approach can handle complex design problems for models with intractable likelihoods on a continuous design space, with possible extension to many observations. The methodology is demonstrated using two stochastic models; a simple tractable death process used to validate the approach, and a motivating stochastic model for the population evolution of macroparasites.

Bayesian regression trees are flexible non-parametric models that are well suited to many modern statistical regression problems. Many such tree models have been proposed, from the simple single-tree model to more complex tree ensembles. Their nonparametric formulation allows one to model datasets exhibiting complex non-linear relationships between the model predictors and observations. However, the mixing behavior of the Markov Chain Monte Carlo (MCMC) sampler is sometimes poor, frequently suffering from local mode stickiness and poor mixing. This is because existing Metropolis–Hastings proposals do not allow for efficient traversal of the model space. We develop novel Metropolis–Hastings proposals that account for the topological structure of regression trees. The first is a novel tree rotation proposal that only requires local changes to the regression tree structure, yet efficiently traverses disparate regions of the model space along contours of high likelihood. The second is a rule perturbation proposal which can be seen as an efficient variation of the change proposal found in existing literature. We implement these samplers and demonstrate their effectiveness on a prediction problem from computer experiments, a test function where structural tree variability is needed to fully explore the posterior and data from a heart rate study.