In this work we propose a semiparametric bivariate copula whose density is defined by a piecewise constant function on disjoint squares. We obtain the maximum likelihood estimators of model parameters and prove that they reduce to the sample copula under specific conditions. We further propose to carry out a full Bayesian analysis of the model and introduce a spatial dependent prior distribution for the model parameters. This prior allows the parameters to borrow strength across neighbouring regions to produce smooth posterior estimates. To characterise the posterior distribution, via the full conditional distributions, we propose a data augmentation technique. A Metropolis-Hastings step is required and we propose a novel adaptation scheme for the random walk proposal distribution. We implement a simulation study and an analysis of a real dataset to illustrate the performance of our model and inference algorithms.
Copula models have become one of the most widely used tools in the applied modelling of multivariate data. Similarly, Bayesian methods are increasingly used to obtain efficient likelihood-based inference. However, to date, there has been only limited use of Bayesian approaches in the formulation and estimation of copula models. This article aims to address this shortcoming in two ways. First, to introduce copula models and aspects of copula theory that are especially relevant for a Bayesian analysis. Second, to outline Bayesian approaches to formulating and estimating copula models, and their …
Copula-based models provide a great deal of flexibility in modelling multivariate distributions, allowing for the specifications of models for the marginal distributions separately from the dependence structure (copula) that links them to form a joint distribution. Choosing a class of copula models is not a trivial task and its misspecification can lead to wrong conclusions. We introduce a novel class of grid-uniform copula functions, which is dense in the space of all continuous copula functions in a Hellinger sense. We propose a Bayesian model based on this class and develop an automatic Mar…
We propose a novel Dirichlet-based Pólya tree (D-P tree) prior on the copula and based on the D-P tree prior, a nonparametric Bayesian inference procedure. Through theoretical analysis and simulations, we are able to show that the flexibility of the D-P tree prior ensures its consistency in copula estimation, thus able to detect more subtle and complex copula structures than earlier nonparametric Bayesian models, such as a Gaussian copula mixture. Further, the continuity of the imposed D-P tree prior leads to a more favorable smoothing effect in copula estimation over classic frequentist metho…
We propose a class of dynamic vine copula models. This is an extension of static vine copulas and a generalization of dynamic C-vine and D-vine copulas studied by Almeida et al (2016) and Goel and Mehra (2019). Within this class, we allow for time-varying dependence by driving the vine copula parameters with latent AR(1) processes. This modeling approach is very flexible but estimation is not straightforward due to the high-dimensional parameter space. We propose a Bayesian estimation approach, which relies on a novel approximation of the posterior distribution. This approximation allows to us…
We show how to extract the implicit copula of a response vector from a Bayesian regularized regression smoother with Gaussian disturbances. The copula can be used to compare smoothers that employ different shrinkage priors and function bases. We illustrate with three popular choices of shrinkage priors --- a pairwise prior, the horseshoe prior and a g prior augmented with a point mass as employed for Bayesian variable selection --- and both univariate and multivariate function bases. The implicit copulas are high-dimensional, have flexible dependence structures that are far from that of a Gaus…
Pair-copula Bayesian networks (PCBNs) are a novel class of multivariate statistical models, which combine the distributional flexibility of pair-copula constructions (PCCs) with the parsimony of conditional independence models associated with directed acyclic graphs (DAG). We are first to provide generic algorithms for random sampling and likelihood inference in arbitrary PCBNs as well as for selecting orderings of the parents of the vertices in the underlying graphs. Model selection of the DAG is facilitated using a version of the well-known PC algorithm which is based on a novel test for con…
Copula models are flexible tools to represent complex structures of dependence for multivariate random variables. According to Sklar's theorem (Sklar, 1959), any d-dimensional absolutely continuous density can be uniquely represented as the product of the marginal distributions and a copula function which captures the dependence structure among the vector components. In real data applications, the interest of the analyses often lies on specific functionals of the dependence, which quantify aspects of it in a few numerical values. A broad literature exists on such functionals, however extension…
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…
In recent years, conditional copulas, that allow dependence between variables to vary according to the values of one or more covariates, have attracted increasing attention. In high dimension, vine copulas offer greater flexibility compared to multivariate copulas, since they are constructed using bivariate copulas as building blocks. In this paper we present a novel inferential approach for multivariate distributions, which combines the flexibility of vine constructions with the advantages of Bayesian nonparametrics, not requiring the specification of parametric families for each pair copula.…
Microorganisms play a critical role in host health. The advancement of high-throughput sequencing technology provides opportunities for a deeper understanding of microbial interactions. However, due to the limitations of 16S ribosomal RNA sequencing, microbiome data are zero-inflated, and a quantitative comparison of microbial abundances cannot be made across subjects. By leveraging a recent microbiome profiling technique that quantifies 16S ribosomal RNA microbial counts, we propose a novel Bayesian graphical model that incorporates microorganisms' evolutionary history through a phylogenetic …
We describe a simple method for making inference on a functional of a multivariate distribution. The method is based on a copula representation of the multivariate distribution and it is based on the properties of an Approximate Bayesian Monte Carlo algorithm, where the proposed values of the functional of interest are weighed in terms of their empirical likelihood. This method is particularly useful when the "true" likelihood function associated with the working model is too costly to evaluate or when the working model is only partially specified.
Conditional copulas are flexible statistical tools that couple joint conditional and marginal conditional distributions. In a linear regression setting with more than one covariate and two dependent outcomes, we propose the use of additive models for conditional bivariate copula models and discuss computation and model selection tools for performing Bayesian inference. The method is illustrated using simulations and a real example.
We study a broad class of asymmetric copulas introduced by Liebscher (2008) as a combination of multiple - usually symmetric - copulas. The main thrust of the paper is to provide new theoretical properties including exact tail dependence expressions and stability properties. A subclass of Liebscher copulas obtained by combining Fréchet copulas is studied in more details. We establish further dependence properties for copulas of this class and show that they are characterized by an arbitrary number of singular components. Furthermore, we introduce a novel iterative representation for general Li…
Several studies on heritability in twins aim at understanding the different contribution of environmental and genetic factors to specific traits. Considering the National Merit Twin Study, our purpose is to correctly analyse the influence of the socioeconomic status on the relationship between twins' cognitive abilities. Our methodology is based on conditional copulas, which allow us to model the effect of a covariate driving the strength of dependence between the main variables. We propose a flexible Bayesian nonparametric approach for the estimation of conditional copulas, which can model an…
Estimating the marginal and joint densities of the long-term average intakes of different dietary components is an important problem in nutritional epidemiology. Since these variables cannot be directly measured, data are usually collected in the form of 24-hour recalls of the intakes, which show marked patterns of conditional heteroscedasticity. Significantly compounding the challenges, the recalls for episodically consumed dietary components also include exact zeros. The problem of estimating the density of the latent long-time intakes from their observed measurement error contaminated proxi…
In this paper, a Bayesian semiparametric copula approach is used to model the underlying multivariate distribution $F_{true}$. First, the Dirichlet process is constructed on the unknown marginal distributions of $F_{true}$. Then a Gaussian copula model is utilized to capture the dependence structure of $F_{true}$. As a result, a Bayesian multivariate normality test is developed by combining the relative belief ratio and the Energy distance. Several interesting theoretical results of the approach are derived. Finally, through several simulated examples and a real data set, the proposed approach…
Regular vine copulas can describe a wider array of dependency patterns than the multivariate Gaussian copula or the multivariate Student's t copula. This paper presents two contributions related to model selection of regular vine copulas. First, our pair copula family selection procedure extends existing Bayesian family selection methods by allowing pair families to be chosen from an arbitrary set of candidate families. Second, our method represents the first Bayesian model selection approach to include the regular vine density construction in its scope of inference. The merits of our approach…
Cardiovascular disease lead the cause of death world wide and several studies have been carried out to understand and explore cardiovascular risk markers in normoglycemic and diabetic populations. In this work, we explore the association structure between hyperglycemic markers and cardiovascular risk markers controlled by triglycerides, body mass index, age and gender, for the normoglycemic population in The Mexico City Diabetes Study. Understanding the association structure could contribute to the assessment of additional cardiovascular risk markers in this low income urban population with a …
Bayesian model selection of vine copulas: a loss-based perspective
Università Cattolica del Sacro Cuore（天主教撒科鲁尔圣心大学）；University of Turin（都灵大学）；University of Exeter（埃克塞特大学）；King’s College London（伦敦国王学院）；Duke Kunshan University（杜克昆山大学）
We propose a flexible copula model to describe changes with a covariate in the dependence structure of (conditionally exchangeable) random variables. The starting point is a spline approximation to the generator of an Archimedean copula. Changes in the dependence structure with a covariate $x$ are modelled by flexible regression of the spline coefficients on $x$. The performances and properties of the spline estimate of the reference generator and the abilities of these conditional models to approximate conditional copulas are studied through simulations. Inference is made using Bayesian argum…
Parametric conditional copula models allow the copula parameters to vary with a set of covariates according to an unknown calibration function. Flexible Bayesian inference for the calibration function of a bivariate conditional copula is proposed via a sparse Gaussian process (GP) prior distribution over the set of smooth calibration functions for the single index model (SIM). The estimation of parameters from the marginal distributions and the calibration function is done jointly via Markov Chain Monte Carlo sampling from the full posterior distribution. A new Conditional Cross Validated Pseu…
Copulas provide an attractive approach for constructing multivariate distributions with flexible marginal distributions and different forms of dependences. Of particular importance in many areas is the possibility of explicitly forecasting the tail-dependences. Most of the available approaches are only able to estimate tail-dependences and correlations via nuisance parameters, but can neither be used for interpretation, nor for forecasting. Aiming to improve copula forecasting performance, we propose a general Bayesian approach for modeling and forecasting tail-dependences and correlations as …
In this article, we analyze perinatal data with birth weight (BW) as primarily interesting response variable. Gestational age (GA) is usually an important covariate and included in polynomial form. However, in opposition to this univariate regression, bivariate modeling of BW and GA is recommended to distinguish effects on each, on both, and between them. Rather than a parametric bivariate distribution, we apply conditional copula regression, where marginal distributions of BW and GA (not necessarily of the same form) can be estimated independently, and where the dependence structure is modele…
An Archimedean copula is characterised by its generator. This is a real function whose inverse behaves as a survival function. We propose a semiparametric generator based on a quadratic spline. This is achieved by modelling the first derivative of a hazard rate function, in a survival analysis context, as a piecewise constant function. Convexity of our semiparametric generator is obtained by imposing some simple constraints. The induced semiparametric Archimedean copula produces Kendall's tau association measure that covers the whole range $(-1,1)$. Inference on the model is done under a Bayes…
Copula-based methods provide a flexible approach to build missing data imputation models of multivariate data of mixed types. However, the choice of copula function is an open question. We consider a Bayesian nonparametric approach by using an infinite mixture of elliptical copulas induced by a Dirichlet process mixture to build a flexible copula function. A slice sampling algorithm is used to sample from the infinite dimensional parameter space. We extend the work on prior parallel tempering used in finite mixture models to the Dirichlet process mixture model to overcome the mixing issue in m…
Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we prop…
The first investigation is made of designs for screening experiments where the response variable is approximated by a generalised linear model. A Bayesian information capacity criterion is defined for the selection of designs that are robust to the form of the linear predictor. For binomial data and logistic regression, the effectiveness of these designs for screening is assessed through simulation studies using all-subsets regression and model selection via maximum penalised likelihood and a generalised information criterion. For Poisson data and log-linear regression, similar assessments are…
A bivariate distribution with continuous margins can be uniquely decomposed via a copula and its marginal distributions. We consider the problem of estimating the copula function and adopt a Bayesian approach. On the space of copula functions, we construct a finite-dimensional approximation subspace that is parametrized by a doubly stochastic matrix. A major problem here is the selection of a prior distribution on the space of doubly stochastic matrices also known as the Birkhoff polytope. The main contributions of this paper are the derivation of a simple formula for the Jeffreys prior and sh…
In this paper, we discuss a method to define prior distributions for the threshold of a generalised Pareto distribution, in particular when its applications are directed to heavy-tailed data. We propose to assign prior probabilities to the order statistics of a given set of observations. In other words, we assume that the threshold coincides to one of the data points. We show two ways of defining a prior: by assigning equal mass to each order statistic, that is a uniform prior, and by considering the worth that every order statistic has in representing the true threshold. Both proposed priors …
We propose a model for unbalanced longitudinal data, where the univariate margins can be selected arbitrarily and the dependence structure is described with the help of a D-vine copula. We show that our approach is an extremely flexible extension of the widely used linear mixed model if the correlation is homogeneous over the considered individuals. As an alternative to joint maximum-likelihood a sequential estimation approach for the D-vine copula is provided and validated in a simulation study. The model can handle missing values without being forced to discard data. Since conditional distri…
This paper provides a simple, yet reliable, alternative to the (Bayesian) estimation of large multivariate VARs with time variation in the conditional mean equations and/or in the covariance structure. With our new methodology, the original multivariate, n dimensional model is treated as a set of n univariate estimation problems, and cross-dependence is handled through the use of a copula. Thus, only univariate distribution functions are needed when estimating the individual equations, which are often available in closed form, and easy to handle with MCMC (or other techniques). Estimation is c…
Dupuytren disease is a fibroproliferative disorder with unknown etiology that often progresses and eventually can cause permanent contractures of the affected fingers. In this paper, we provide a computationally efficient Bayesian framework to discover potential risk factors and investigate which fingers are jointly affected. Our Bayesian approach is based on Gaussian copula graphical models, which are one potential way to discover the underlying conditional independence structure of variables in multivariate mixed data. In particular, we combine the semiparametric Gaussian copula with extende…
One approach for constructing copula functions is by multiplication. Given that products of cumulative distribution functions (CDFs) are also CDFs, an adjustment to this multiplication will result in a copula model, as discussed by Liebscher (J Mult Analysis, 2008). Parameterizing models via products of CDFs has some advantages, both from the copula perspective (e.g., it is well-defined for any dimensionality) and from general multivariate analysis (e.g., it provides models where small dimensional marginal distributions can be easily read-off from the parameters). Independently, Huang and Frey…
The design of an experiment can be always be considered at least implicitly Bayesian, with prior knowledge used informally to aid decisions such as the variables to be studied and the choice of a plausible relationship between the explanatory variables and measured responses. Bayesian methods allow uncertainty in these decisions to be incorporated into design selection through prior distributions that encapsulate information available from scientific knowledge or previous experimentation. Further, a design may be explicitly tailored to the aim of the experiment through a decision-theoretic app…
Approximate Bayesian computation (ABC) refers to a family of inference methods used in the Bayesian analysis of complex models where evaluation of the likelihood is difficult. Conventional ABC methods often suffer from the curse of dimensionality, and a marginal adjustment strategy was recently introduced in the literature to improve the performance of ABC algorithms in high-dimensional problems. The marginal adjustment approach is extended using a Gaussian copula approximation. The method first estimates the bivariate posterior for each pair of parameters separately using a 2-dimensional Gaus…
Clustering task of mixed data is a challenging problem. In a probabilistic framework, the main difficulty is due to a shortage of conventional distributions for such data. In this paper, we propose to achieve the mixed data clustering with a Gaussian copula mixture model, since copulas, and in particular the Gaussian ones, are powerful tools for easily modelling the distribution of multivariate variables. Indeed, considering a mixing of continuous, integer and ordinal variables (thus all having a cumulative distribution function), this copula mixture model defines intra-component dependencies …
A2 Copula-Driven Spatial Bayesian Neural Network For Modeling Non-Gaussian Dependence: A Simulation Study
Department of Mathematics, University of Louisiana at Lafayette（数学系，路易斯安那州立大学拉斐特分校）；Department of Physical Sciences & Mathematics, West Liberty University（物理科学与数学系，韦斯特利比大学）；Department of Mathematics and Statistics, Minnesota State University（数学与统计学系，明尼苏达州立大学）；Department of Statistics, formerly of Presidency College, Kolkata, India（统计学系，原加尔各答 Presidency College）；Department of Kinesiology, University of Louisiana at Lafayette（运动科学系，路易斯安那州立大学拉斐特分校）；Department of Mathematics and Statistics, Texas Tech University（数学与统计学系，德克萨斯技术大学）；The Office of Vice President for Research, Innovation, and Economic Development, University of Louisiana at Lafayette（研究、创新与经济发展副总监办公室，路易斯安那州立大学拉斐特分校）
