Joint modeling of spatially-oriented dependent variables is commonplace in the environmental sciences, where scientists seek to estimate the relationships among a set of environmental outcomes accounting for dependence among these outcomes and the spatial dependence for each outcome. Such modeling is now sought for massive data sets with variables measured at a very large number of locations. Bayesian inference, while attractive for accommodating uncertainties through hierarchical structures, can become computationally onerous for modeling massive spatial data sets because of its reliance on iterative estimation algorithms. This manuscript develops a conjugate Bayesian framework for analyzing multivariate spatial data using analytically tractable posterior distributions that obviate iterative algorithms. We discuss differences between modeling the multivariate response itself as a spatial process and that of modeling a latent process in a hierarchical model. We illustrate the computational and inferential benefits of these models using simulation studies and analysis of a Vegetation Index data set with spatially dependent observations numbering in the millions.
Preferential sampling is a common feature in geostatistics and occurs when the locations to be sampled are chosen based on information about the phenomena under study. In this case, point pattern models are commonly used as the probability law for the distribution of the locations. However, analytic intractability of the point process likelihood prevents its direct calculation. Many Bayesian (and non-Bayesian) approaches in non-parametric model specifications handle this difficulty with approximation-based methods. These approximations involve errors that are difficult to quantify and can lead…
We introduce a flexible and scalable class of Bayesian geostatistical models for discrete data, based on the class of nearest neighbor mixture transition distribution processes (NNMP), referred to as discrete NNMP. The proposed class characterizes spatial variability by a weighted combination of first-order conditional probability mass functions (pmfs) for each one of a given number of neighbors. The approach supports flexible modeling for multivariate dependence through specification of general bivariate discrete distributions that define the conditional pmfs. Moreover, the discrete NNMP allo…
Cokriging is the common method of spatial interpolation (best linear unbiased prediction) in multivariate geostatistics. While best linear prediction has been well understood in univariate spatial statistics, the literature for the multivariate case has been elusive so far. The new challenges provided by modern spatial datasets, being typically multivariate, call for a deeper study of cokriging. In particular, we deal with the problem of misspecified cokriging prediction within the framework of fixed domain asymptotics. Specifically, we provide conditions for equivalence of measures associated…
With the growing capabilities of Geographic Information Systems (GIS) and user-friendly software, statisticians today routinely encounter geographically referenced data containing observations from a large number of spatial locations and time points. Over the last decade, hierarchical spatiotemporal process models have become widely deployed statistical tools for researchers to better understand the complex nature of spatial and temporal variability. However, fitting hierarchical spatiotemporal models often involves expensive matrix computations with complexity increasing in cubic order for th…
We introduce a class of scalable Bayesian hierarchical models for the analysis of massive geostatistical datasets. The underlying idea combines ideas on high-dimensional geostatistics by partitioning the spatial domain and modeling the regions in the partition using a sparsity-inducing directed acyclic graph (DAG). We extend the model over the DAG to a well-defined spatial process, which we call the Meshed Gaussian Process (MGP). A major contribution is the development of a MGPs on tessellated domains, accompanied by a Gibbs sampler for the efficient recovery of spatial random effects. In part…
University of Exeter（埃克塞特大学）；University of Glasgow（格拉斯哥大学）
For geospatial modelling and mapping tasks, variants of kriging - the spatial interpolation technique developed by South African mining engineer Danie Krige - have long been regarded as the established geostatistical methods. However, kriging and its variants (such as regression kriging, in which auxiliary variables or derivatives of these are included as covariates) are relatively restrictive models and lack capabilities that have been afforded to us in the last decade by deep neural networks. Principal among these is feature learning - the ability to learn filters to recognise task-specific …
In geostatistics, the design for data collection is central for accurate prediction and parameter inference. One important class of geostatistical models is log-Gaussian Cox process (LGCP) which is used extensively, for example, in ecology. However, there are no formal analyses on optimal designs for LGCP models. In this work, we develop a novel model-based experimental design for LGCP modeling of spatiotemporal point process data. We propose a new spatially balanced rejection sampling design which directs sampling to spatiotemporal locations that are a priori expected to provide most informat…
We present a Bayesian approach for modeling multivariate, dependent functional data. To account for the three dominant structural features in the data--functional, time dependent, and multivariate components--we extend hierarchical dynamic linear models for multivariate time series to the functional data setting. We also develop Bayesian spline theory in a more general constrained optimization framework. The proposed methods identify a time-invariant functional basis for the functional observations, which is smooth and interpretable, and can be made common across multivariate observations for …
In this paper we take up Bayesian inference in general multivariate stable distributions. We exploit the representation of Matsui and Takemura (2009) for univariate projections, and the representation of the distributions in terms of their spectral measure. We present efficient MCMC schemes to perform the computations when the spectral measure is approximated discretely or, as we propose, by a normal distribution. Appropriate latent variables are introduced to implement MCMC. In relation to the discrete approximation, we propose efficient computational schemes based on the characteristic funct…
Model-based geostatistical design involves the selection of locations to collect data to minimise an expected loss function over a set of all possible locations. The loss function is specified to reflect the aim of data collection, which, for geostatistical studies, could be to minimise the prediction uncertainty at unobserved locations. In this paper, we propose a new approach to design such studies via a loss function derived through considering the entropy about the model predictions and the parameters of the model. The approach also includes a multivariate extension to generalised linear s…
Multivariate functional data arise in a wide range of applications. One fundamental task is to understand the causal relationships among these functional objects of interest, which has not yet been fully explored. In this article, we develop a novel Bayesian network model for multivariate functional data where the conditional independence and causal structure are both encoded by a directed acyclic graph. Specifically, we allow the functional objects to deviate from Gaussian process, which is adopted by most existing functional data analysis models. The more reasonable non-Gaussian assumption i…
High resolution geospatial data are challenging because standard geostatistical models based on Gaussian processes are known to not scale to large data sizes. While progress has been made towards methods that can be computed more efficiently, considerably less attention has been devoted to big data methods that allow the description of complex relationships between several outcomes recorded at high resolutions by different sensors. Our Bayesian multivariate regression models based on spatial multivariate trees (SpamTrees) achieve scalability via conditional independence assumptions on latent r…
Multivariate categorical data are common in many fields. We are motivated by election polls studies assessing evidence of changes in voters opinions with their candidates preferences in the 2016 United States Presidential primaries or caucuses. Similar goals arise routinely in several applications, but current literature lacks a general methodology which combines flexibility, efficiency, and tractability in testing for group differences in multivariate categorical data at different---potentially complex---scales. We address this goal by leveraging a Bayesian representation which factorizes the…
A Bayesian approach is developed to analyze change points in multivariate time series and space-time data. The methodology is used to assess the impact of extended inundation on the ecosystem of the Gulf Plains bioregion in northern Australia. The proposed approach can be implemented for dynamic mixture models that have a conditionally Gaussian state space representation. Details are given on how to efficiently implement the algorithm for a general class of multivariate time series and space-time models. This efficient implementation makes it feasible to analyze high dimensional, but of realis…
We discuss probabilistic models of random covariance structures defined by distributions over sparse eigenmatrices. The decomposition of orthogonal matrices in terms of Givens rotations defines a natural, interpretable framework for defining distributions on sparsity structure of random eigenmatrices. We explore theoretical aspects and implications for conditional independence structures arising in multivariate Gaussian models, and discuss connections with sparse PCA, factor analysis and Gaussian graphical models. Methodology includes model-based exploratory data analysis and Bayesian analysis…
We consider the problem of multivariate density deconvolution where the distribution of a random vector needs to be estimated from replicates contaminated with conditionally heteroscedastic measurement errors. We propose a conceptually straightforward yet fundamentally novel and highly robust approach to multivariate density deconvolution by stochastically rotating the replicates toward the corresponding true latent values. We also address the additionally significantly challenging problem of accommodating conditionally heteroscedastic measurement errors in this newly introduced framework. We …
We introduce efficient Markov chain Monte Carlo methods for inference and model determination in multivariate and matrix-variate Gaussian graphical models. Our framework is based on the G-Wishart prior for the precision matrix associated with graphs that can be decomposable or non-decomposable. We extend our sampling algorithms to a novel class of conditionally autoregressive models for sparse estimation in multivariate lattice data, with a special emphasis on the analysis of spatial data. These models embed a great deal of flexibility in estimating both the correlation structure across outcom…
We present a Bayesian mixture model for estimating the joint distribution of mixed ordinal, nominal, and continuous data conditional on a set of fixed variables. The model uses multivariate normal and categorical mixture kernels for the random variables. It induces dependence between the random and fixed variables through the means of the multivariate normal mixture kernels and via a truncated local Dirichlet process. The latter encourages observations with similar values of the fixed variables to share mixture components. Using a simulation of data fusion, we illustrate that the model can est…
While there is an increasing amount of literature about Bayesian time series analysis, only a few Bayesian nonparametric approaches to multivariate time series exist. Most methods rely on Whittle's Likelihood, involving the second order structure of a stationary time series by means of its spectral density matrix. This is often modeled in terms of the Cholesky decomposition to ensure positive definiteness. However, asymptotic properties such as posterior consistency or posterior contraction rates are not known. A different idea is to model the spectral density matrix by means of random measure…
We consider the problem of multivariate density deconvolution when the interest lies in estimating the distribution of a vector-valued random variable but precise measurements of the variable of interest are not available, observations being contaminated with additive measurement errors. The existing sparse literature on the problem assumes the density of the measurement errors to be completely known. We propose robust Bayesian semiparametric multivariate deconvolution approaches when the measurement error density is not known but replicated proxies are available for each unobserved value of t…
We develop the methodology and a detailed case study in use of a class of Bayesian predictive synthesis (BPS) models for multivariate time series forecasting. This extends the recently introduced foundational framework of BPS to the multivariate setting, with detailed application in the topical and challenging context of multi-step macroeconomic forecasting in a monetary policy setting. BPS evaluates-- sequentially and adaptively over time-- varying forecast biases and facets of miscalibration of individual forecast densities, and-- critically-- of time-varying inter-dependencies among them ov…
The problem of validating or criticising models for georeferenced data is challenging, since the conclusions can vary significantly depending on the locations of the validation set. This work proposes the use of cross-validation techniques to assess the goodness of fit of spatial models in different regions of the spatial domain to account for uncertainty in the choice of the validation sets. An obvious problem with the basic cross-validation scheme is that it is based on selecting only a few out of sample locations to validate the model, possibily making the conclusions sensitive to which par…
Univariate or multivariate ordinal responses are often assumed to arise from a latent continuous parametric distribution, with covariate effects which enter linearly. We introduce a Bayesian nonparametric modeling approach for univariate and multivariate ordinal regression, which is based on mixture modeling for the joint distribution of latent responses and covariates. The modeling framework enables highly flexible inference for ordinal regression relationships, avoiding assumptions of linearity or additivity in the covariate effects. In standard parametric ordinal regression models, computat…
Graphical models express conditional independence relationships among variables. Although methods for vector-valued data are well established, functional data graphical models remain underdeveloped. We introduce a notion of conditional independence between random functions, and construct a framework for Bayesian inference of undirected, decomposable graphs in the multivariate functional data context. This framework is based on extending Markov distributions and hyper Markov laws from random variables to random processes, providing a principled alternative to naive application of multivariate m…
The multivariate extended skew-normal distribution allows for accommodating raw data which are skewed and heavy tailed, and has at least three appealing statistical properties, namely closure under conditioning, affine transformations, and marginalization. In this paper we propose a Bayesian computational approach based on a sequential Monte Carlo (SMC) sampler to estimate such distributions. The practical implementation of each step of the algorithm is discussed and the elicitation of prior distributions takes into consideration some unusual behaviour of the likelihood function and the corres…
Regional aggregates of health outcomes over delineated administrative units (e.g., states, counties, zip codes), or areal units, are widely used by epidemiologists to map mortality or incidence rates and capture geographic variation. To capture health disparities over regions, we seek "difference boundaries" that separate neighboring regions with significantly different spatial effects. Matters are more challenging with multiple outcomes over each unit, where we capture dependence among diseases as well as across the areal units. Here, we address multivariate difference boundary detection for …
We propose a method for estimating the posterior distribution of a standard geostatistical model. After choosing the model formulation and specifying a prior, we use normal mixture densities to approximate the posterior distribution. The approximation is improved iteratively. Some difficulties in estimating the normal mixture densities, including determining tuning parameters concerning bandwidth and localization, are addressed. The method is applicable to other model formulations as long as all the parameters, or transforms thereof, are defined on the whole real line, $(-\infty, \infty)$. Ad …
This paper discusses the efficient Bayesian estimation of a multivariate factor stochastic volatility (Factor MSV) model with leverage. We propose a novel approach to construct the sampling schemes that converges to the posterior distribution of the latent volatilities and the parameters of interest of the Factor MSV model based on recent advances in Particle Markov chain Monte Carlo (PMCMC). As opposed to the approach of Chib et al. (2006} and Omori et al. (2007}, our approach does not require approximating the joint distribution of outcome and volatility innovations by a mixture of bivariate…
Given the cost and duration of phase III and phase IV clinical trials, the development of statistical methods for go/no-go decisions is vital. In this paper, we introduce a Bayesian methodology to compute the probability of success based on the current data of a treatment regimen for the multivariate linear model. Our approach utilizes a Bayesian seemingly unrelated regression model, which allows for multiple endpoints to be modeled jointly even if the covariates between the endpoints are different. Correlations between endpoints are explicitly modeled. This Bayesian joint modeling approach un…
Many modern data sets require inference methods that can estimate the shared and individual-specific components of variability in collections of matrices that change over time. Promising methods have been developed to analyze these types of data in static cases, but very few approaches are available for dynamic settings. To address this gap, we consider novel models and inference methods for pairs of matrices in which the columns correspond to multivariate observations at different time points. In order to characterize common and individual features, we propose a Bayesian dynamic factor modeli…
Near real time change detection is important for a variety of Earth monitoring applications and remains a high priority for remote sensing science. Data sparsity, subtle changes, seasonal trends, and the presence of outliers make detecting actual landscape changes challenging. Adams and MacKay (2007) introduced Bayesian Online Changepoint Detection (BOCPD), a computationally efficient, exact Bayesian method for change detection. Incorporation of prior information allows for relaxed dependence on dense data and an extensive stable period, making this method applicable to relatively short time s…
In this article, we consider a non-parametric Bayesian approach to multivariate quantile regression. The collection of related conditional distributions of a response vector Y given a univariate covariate X is modeled using a Dependent Dirichlet Process (DDP) prior. The DDP is used to introduce dependence across x. As the realizations from a Dirichlet process prior are almost surely discrete, we need to convolve it with a kernel. To model the error distribution as flexibly as possible, we use a countable mixture of multidimensional normal distributions as our kernel. For posterior computations…
A Bayesian design is given by maximising an expected utility over a design space. The utility is chosen to represent the aim of the experiment and its expectation is taken with respect to all unknowns: responses, parameters and/or models. Although straightforward in principle, there are several challenges to finding Bayesian designs in practice. Firstly, the utility and expected utility are rarely available in closed form and require approximation. Secondly, the design space can be of high-dimensionality. In the case of intractable likelihood models, these problems are compounded by the fact t…
The article develops marginal models for multivariate longitudinal responses. Overall, the model consists of five regression submodels, one for the mean and four for the covariance matrix, with the latter resulting by considering various matrix decompositions. The decompositions that we employ are intuitive, easy to understand, and they do not rely on any assumptions such as the presence of an ordering among the multivariate responses. The regression submodels are semiparametric, with unknown functions represented by basis function expansions. We use spike-slap priors for the regression coeffi…
Forecasting enterprise-wide revenue is critical to many companies and presents several challenges and opportunities for significant business impact. This case study is based on model developments to address these challenges for forecasting in a large-scale retail company. Focused on multivariate revenue forecasting across collections of supermarkets and product Categories, hierarchical dynamic models are natural: these are able to couple revenue streams in an integrated forecasting model, while allowing conditional decoupling to enable relevant and sensitive analysis together with scalable com…
This paper describes a method for a model-based analysis of clinical safety data called multivariate Bayesian logistic regression (MBLR). Parallel logistic regression models are fit to a set of medically related issues, or response variables, and MBLR allows information from the different issues to "borrow strength" from each other. The method is especially suited to sparse response data, as often occurs when fine-grained adverse events are collected from subjects in studies sized more for efficacy than for safety investigations. A combined analysis of data from multiple studies can be perform…
In this work we present full Bayesian inference for a new flexible nonseparable class of cross-covariance functions for multivariate spatial data. A Bayesian test is proposed for separability of covariance functions which is much more interpretable than parameters related to separability. Spatial models have been increasingly applied in several areas, such as environmental science, climate science and agriculture. These data are usually available in space, time and possibly for several processes. In this context the modeling of dependence is crucial for correct uncertainty quantification and r…
This paper analyses the effect of preferential sampling in Geostatistics when the choice of new sampling locations is the main interest of the researcher. A Bayesian criterion based on maximizing utility functions is used. Simulated studies are presented and highlight the strong influence of preferential sampling in the decisions. The computational complexity is faced by treating the new local sampling locations as a model parameter and the optimal choice is then made by analysing its posterior distribution. Finally, an application is presented using rainfall data collected during spring in Ri…
In this paper we propose a flexible class of multivariate nonlinear non-Gaussian state space models, based on copulas. More precisely, we assume that the observation equation and the state equation are defined by copula families that are not necessarily equal. For each time point, the resulting model can be described by a C-vine copula truncated after the first tree, where the root node is represented by the latent state. Inference is performed within the Bayesian framework, using the Hamiltonian Monte Carlo method, where a further D-vine truncated after the first tree is used as prior distrib…
We develop Bayesian models for density regression with emphasis on discrete outcomes. The problem of density regression is approached by considering methods for multivariate density estimation of mixed scale variables, and obtaining conditional densities from the multivariate ones. The approach to multivariate mixed scale outcome density estimation that we describe represents discrete variables, either responses or covariates, as discretised versions of continuous latent variables. We present and compare several models for obtaining these thresholds in the challenging context of count data ana…
The problem we consider considers estimating a multivariate longitudinal panel data model whose outcomes can be a combination of discrete and continuous variables. This problem is challenging because the likelihood is usually analytically intractable. Our article makes both a methodological contribution and also a substantive contribution to the application. The methodological contribution is to introduce into the panel data literature a particle Metropolis within Gibbs method to carry out Bayesian inference, using a Hamiltonian Monte Carlo (Neal 2011} proposal for sampling the vector of unkno…
Recent technological advances have enabled researchers in a variety of fields to collect accurately geocoded data for several variables simultaneously. In many cases it may be most appropriate to jointly model these multivariate spatial processes without constraints on their conditional relationships. When data have been collected on a regular lattice, the multivariate conditionally autoregressive (MCAR) models are a common choice. However, inference from these MCAR models relies heavily on the pre-specified neighborhood structure and often assumes a separable covariance structure. Here, we pr…
Geostatistical modeling of the reservoir intrinsic properties starts only with sparse data available. These estimates will depend largely on the number of wells and their location. The drilling costs are so high that they do not allow new wells to be placed for uncertainty assessment. Besides that difficulty, usual geostatistical models do not account for the uncertainty of conceptual models, which should be considered. Spatial bootstrap is applied to assess the estimate reliability when resampling from original field is not an option. Considering different realities (conceptual models) and di…
