We introduce a new class of semiparametric latent variable models for long memory discretized event data. The proposed methodology is motivated by a study of bird vocalizations in the Amazon rain forest; the timings of vocalizations exhibit self-similarity and long range dependence ruling out models based on Poisson processes. The proposed class of FRActional Probit (FRAP) models is based on thresholding of a latent process consisting of an additive expansion of a smooth Gaussian process with a fractional Brownian motion. We develop a Bayesian approach to inference using Markov chain Monte Carlo, and show good performance in simulation studies. Applying the methods to the Amazon bird vocalization data, we find substantial evidence for self-similarity and non-Markovian/Poisson dynamics. To accommodate the bird vocalization data, in which there are many different species of birds exhibiting their own vocalization dynamics, a hierarchical expansion of FRAP is provided in Supplementary Materials.
Item response theory (IRT) models typically rely on a normality assumption for subject-specific latent traits, which is often unrealistic in practice. Semiparametric extensions based on Dirichlet process mixtures offer a more flexible representation of the unknown distribution of the latent trait. However, the use of such models in the IRT literature has been extremely limited, in good part because of the lack of comprehensive studies and accessible software tools. This paper provides guidance for practitioners on semiparametric IRT models and their implementation. In particular, we rely on NI…
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…
In this paper we extend existing Bayesian methods for variable selection in Gaussian process regression, to select both the regression terms and the active covariates in the spatial correlation structure. We then use the estimated posterior probabilities to choose between relatively few modes through cross-validation, and consequently improve prediction.
Typical Bayesian inference requires parameter identification via likelihood parameterization, which has invited criticism for being less flexible than the Frequentist framework and subject to misspecification. Though misspecification may be avoided by functional parameter inference under a nonparametric model space, there does not exist a flexible Bayesian semiparametric model that would allow full control over the marginal prior over any general functional parameter. We present the technique of $θ$-augmentation which helps us manipulate nonparametric models into semiparametric ones that direc…
We propose a Bayesian semiparametric approach for registration of multiple point processes. Our approach entails modelling the mean measures of the phase-varying point processes with a Bernstein-Dirichlet prior, which induces a prior on the space of all warp functions. Theoretical results on the support of the induced priors are derived, and posterior consistency is obtained under mild conditions. Numerical experiments suggest a good performance of the proposed methods, and a climatology real-data example is used to showcase how the method can be employed in practice.
The cyclical and heterogeneous nature of many substance use disorders highlights the need to adapt the type or the dose of treatment to accommodate the specific and changing needs of individuals. The Adaptive Treatment for Alcohol and Cocaine Dependence study (ENGAGE) is a multi-stage randomized trial that aimed to provide longitudinal data for constructing treatment strategies to improve patients' engagement in therapy. However, the high rate of noncompliance and lack of analytic tools to account for noncompliance have impeded researchers from using the data to achieve the main goal of the tr…
When the target variable exhibits a semicontinuous behaviour (i.e. a point mass in a single value and a continuous distribution elsewhere) parametric `two-part regression models' have been extensively used and investigated. In this paper, a semiparametric Bayesian two-part regression model for dealing with such variables is proposed. The model allows a semiparametric expression for the two part of the model by using Dirichlet processes. A motivating example (in the `small area estimation' framework) based on pseudo-real data on grapewine production in Tuscany, is used to evaluate the capabilit…
Diffusion tensor imaging (DTI) is a popular magnetic resonance imaging technique used to characterize microstructural changes in the brain. DTI studies quantify the diffusion of water molecules in a voxel using an estimated 3x3 symmetric positive definite diffusion tensor matrix. Statistical analysis of DTI data is challenging because the data are positive definite matrices. Matrix-variate information is often summarized by a univariate quantity, such as the fractional anisotropy (FA), leading to a loss of information. Furthermore, DTI analyses often ignore the spatial association of neighbori…
In this paper we propose a model with a Dirichlet process mixture of gamma densities in the bulk part below threshold and a generalized Pareto density in the tail for extreme value estimation. The proposed model is simple and flexible allowing us posterior density estimation and posterior inference for high quantiles. The model works well even for small sample sizes and in the absence of prior information. We evaluate the performance of the proposed model through a simulation study. Finally, the proposed model is applied to a real environmental data.
For linear models with a diverging number of parameters, it has recently been shown that modified versions of Bayesian information criterion (BIC) can identify the true model consistently. However, in many cases there is little justification that the effects of the covariates are actually linear. Thus a semiparametric model such as the additive model studied here, is a viable alternative. We demonstrate that theoretical results on the consistency of BIC-type criterion can be extended to this more challenging situation, with dimension diverging exponentially fast with sample size. Besides, the …
A comprehensive, unified approach to modeling arbitrarily censored spatial survival data is presented for the three most commonly-used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. Unlike many other approaches, all manner of censored survival times are simultaneously accommodated including uncensored, interval censored, current-status, left and right censored, and mixtures of these. Left-truncated data are also accommodated leading to models for time-dependent covariates. Both georeferenced (location exactly observed) and areally observed (locati…
As the dynamic structure of the financial markets is subject to dramatic changes, a model capable of providing consistently accurate volatility estimates must not make strong assumptions on how prices change over time. Most volatility models impose a particular parametric functional form that relates an observed price change to a volatility forecast (news impact function). We propose a new class of functional coefficient semiparametric volatility models where the news impact function is allowed to be any smooth function, and study its ability to estimate volatilities compared to the well known…
Statistical inference with nonresponse is quite challenging, especially when the response mechanism is nonignorable. In this case, the validity of statistical inference depends on untestable correct specification of the response model. To avoid the misspecification, we propose semiparametric Bayesian estimation in which an outcome model is parametric, but the response model is semiparametric in that we do not assume any parametric form for the nonresponse variable. We adopt penalized spline methods to estimate the unknown function. We also consider a fully nonparametric approach to modeling th…
Bayesian Additive Regression Trees (BART) is a flexible machine learning algorithm capable of capturing nonlinearities between an outcome and covariates and interaction among covariates. We extend BART to a semiparametric regression framework in which the conditional expectation of an outcome is a function of treatment, its effect modifiers, and confounders. The confounders, not of scientific interest, are allowed to have unspecified functional form, while treatment and other covariates that do have scientific importance are given the usual linear form from parametric regression. The result is…
We consider incomplete observations of stochastic processes governing the spread of infectious diseases through finite populations by way of contact. We propose a flexible semiparametric modeling framework with at least three advantages. First, it enables researchers to study the structure of a population contact network and its impact on the spread of infectious diseases. Second, it can accommodate short- and long-tailed degree distributions and detect potential superspreaders, who represent an important public health concern. Third, it addresses the important issue of incomplete data. Starti…
Novelty detection methods aim at partitioning the test units into already observed and previously unseen patterns. However, two significant issues arise: there may be considerable interest in identifying specific structures within the novelty, and contamination in the known classes could completely blur the actual separation between manifest and new groups. Motivated by these problems, we propose a two-stage Bayesian semiparametric novelty detector, building upon prior information robustly extracted from a set of complete learning units. We devise a general-purpose multivariate methodology tha…
Understanding how adult humans learn non-native speech categories such as tone information has shed novel insights into the mechanisms underlying experience-dependent brain plasticity. Scientists have traditionally examined these questions using longitudinal learning experiments under a multi-category decision making paradigm. Drift-diffusion processes are popular in such contexts for their ability to mimic underlying neural mechanisms. Motivated by these problems, we develop a novel Bayesian semiparametric inverse Gaussian drift-diffusion mixed model for multi-alternative decision making in l…
This paper demonstrates the advantages of sharing information about unknown features of covariates across multiple model components in various nonparametric regression problems including multivariate, heteroscedastic, and semi-continuous responses. In this paper, we present methodology which allows for information to be shared nonparametrically across various model components using Bayesian sum-of-tree models. Our simulation results demonstrate that sharing of information across related model components is often very beneficial, particularly in sparse high-dimensional problems in which variabl…
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.
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The data sets typically comprise structured sequences of syllables or `songs' produced by animals from different genotypes under different social contexts. We develop a novel Bayesian semiparametric framework for inference in such data sets. Our approach is built on a novel class of mixed effects Markov transition models for the songs that accommodates exogenous influences of genotype and context as well as animal-specific het…
Popular parametric and semiparametric hazards regression models for clustered survival data are inappropriate and inadequate when the unknown effects of different covariates and clustering are complex. This calls for a flexible modeling framework to yield efficient survival prediction. Moreover, for some survival studies involving time to occurrence of some asymptomatic events, survival times are typically interval censored between consecutive clinical inspections. In this article, we propose a robust semiparametric model for clustered interval-censored survival data under a paradigm of Bayesi…
Disease subtype identification (clustering) is an important problem in biomedical research. Gene expression profiles are commonly utilized to infer disease subtypes, which often lead to biologically meaningful insights into disease. Despite many successes, existing clustering methods may not perform well when genes are highly correlated and many uninformative genes are included for clustering due to the high dimensionality. In this article, we introduce a novel subtype identification method in the Bayesian setting based on gene expression profiles. This method, called BCSub, adopts an innovati…
Undernutrition, resulting in restricted growth, and quantified here using height-for-age z-scores, is an important contributor to childhood morbidity and mortality. Since all levels of mild, moderate and severe undernutrition are of clinical and public health importance, it is of interest to estimate the shape of the z-scores' distributions. We present a finite normal mixture model that uses data on 4.3 million children to make annual country-specific estimates of these distributions for under-5-year-old children in the world's 141 low- and middle-income countries between 1985 and 2011. We inc…
We introduce semiparametric Bayesian networks that combine parametric and nonparametric conditional probability distributions. Their aim is to incorporate the advantages of both components: the bounded complexity of parametric models and the flexibility of nonparametric ones. We demonstrate that semiparametric Bayesian networks generalize two well-known types of Bayesian networks: Gaussian Bayesian networks and kernel density estimation Bayesian networks. For this purpose, we consider two different conditional probability distributions required in a semiparametric Bayesian network. In addition…
Multivariate nonnegative orthant data are real vectors bounded to the left by the null vector, and they can be continuous, discrete or mixed. We first review the recent relative variability indexes for multivariate nonnegative continuous and count distributions. As a prelude, the classification of two comparable distributions having the same mean vector is done through under-, equi- and over-variability with respect to the reference distribution. Multivariate associated kernel estimators are then reviewed with new proposals that can accommodate any nonnegative orthant dataset. We focus on band…
Fossil-based palaeoclimate reconstruction is an important area of ecological science that has gained momentum in the backdrop of the global climate change debate. The hierarchical Bayesian paradigm provides an interesting platform for studying such important scientific issue. However, our cross-validation based assessment of the existing Bayesian hierarchical models with respect to two modern proxy data sets based on chironomid and pollen, respectively, revealed that the models are inadequate for the data sets. In this paper, we model the species assemblages (compositional data) by the zero-in…
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…
Spatial point pattern data are routinely encountered. A flexible regression model for the underlying intensity is essential to characterizing the spatial point pattern and understanding the impacts of potential risk factors on such pattern. We propose a Bayesian semiparametric regression model where the observed spatial points follow a spatial Poisson process with an intensity function which adjusts a nonparametric baseline intensity with multiplicative covariate effects. The baseline intensity is piecewise constant, approached with a powered Chinese restaurant process prior which prevents an …
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 …
Gene-gene interactions are often regarded as playing significant roles in influencing variabilities of complex traits. Although much research has been devoted to this area, to date a comprehensive statistical model that addresses the various sources of uncertainties, seem to be lacking. In this paper, we propose and develop a novel Bayesian semiparametric approach composed of finite mixtures based on Dirichlet processes and a hierarchical matrix-normal distribution that can comprehensively account for the unknown number of sub-populations and gene-gene interactions. Then, by formulating novel …
We introduce a general hierarchical Bayesian framework that incorporates a flexible nonparametric data model specification through the use of empirical likelihood methodology, which we term semiparametric hierarchical empirical likelihood (SHEL) models. Although general dependence structures can be readily accommodated, we focus on spatial modeling, a relatively underdeveloped area in the empirical likelihood literature. Importantly, the models we develop naturally accommodate spatial association on irregular lattices and irregularly spaced point-referenced data. We illustrate our proposed fra…
We propose a Bayesian hierarchical Jolly-Seber model that can account for individual heterogeneity in departure and the dependence of arrival time on covariates. Additionally, our model provides a semiparametric functional form for modeling capture probabilities. The model is flexible and can be used to estimate the stopover duration and stopover population size, which are key to stopover duration analysis. From the modeling perspective, our model allows for individual heterogeneity in departure due to a continuous intrinsic factor that varies with time and individual. A stochastic process is …
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…
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms is an important field of neuroscience. In the absence of high quality data on humans, mouse vocalization experiments in laboratory settings have been proven to be useful in providing valuable insights into mammalian vocal development and evolution, including especially the impact of certain genetic mutations. Data sets from mouse vocalization experiments usually consist of categorical syllable sequences along with continuous inter-syllable interval times for mice of different genotypes vocalizing …
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…
The R package BNSP provides a unified framework for semiparametric location-scale regression and stochastic search variable selection. The statistical methodology that the package is built upon utilizes basis function expansions to represent semiparametric covariate effects in the mean and variance functions, and spike-slab priors to perform selection and regularization of the estimated effects. In addition to the main function that performs posterior sampling, the package includes functions for assessing convergence of the sampler, summarizing model fits, visualizing covariate effects and obt…
University of Bonn（波恩大学）；CUHK Business School, Chinese University of Hong Kong（香港中文大学商学院）；Graduate School of Economics, University of Osaka（大阪大学经济学研究科）
For extreme value estimation we propose to use a model with a Dirichlet process mixture of gamma densities in the center and generalized Pareto densities for the tails. Due to the randomness in the center and a heavy tailed density in the tails density estimation and posterior inference for high quantiles are possible. The approach can be used in a "default" manner on the positive reals because it works when prior information is unavailable. The proposed model can be easy to implement and a sensitivity analysis is provided. We applied the proposed model for simulated and real data sets.
Family planning has been characterized by highly different strategic programs in India, including method-specific contraceptive targets, coercive sterilization, and more recent target-free approaches. These major changes in family planning policies over time have motivated a considerable interest towards assessing the effectiveness of the different programs, while understanding which subsets of the population have not been properly addressed. Current studies consider specific aspects of the above policies, including, for example, the factors associated with the choice of alternative contracept…
The standard noise model in gravitational wave (GW) data analysis assumes detector noise is stationary and Gaussian distributed, with a known power spectral density (PSD) that is usually estimated using clean off-source data. Real GW data often depart from these assumptions, and misspecified parametric models of the PSD could result in misleading inferences. We propose a Bayesian semiparametric approach to improve this. We use a nonparametric Bernstein polynomial prior on the PSD, with weights attained via a Dirichlet process distribution, and update this using the Whittle likelihood. Posterio…
The outbreak of Coronavirus Disease 2019 (COVID-19) is an ongoing pandemic affecting over 200 countries and regions. Inference about the transmission dynamics of COVID-19 can provide important insights into the speed of disease spread and the effects of mitigation policies. We develop a novel Bayesian approach to such inference based on a probabilistic compartmental model using data of daily confirmed COVID-19 cases. In particular, we consider a probabilistic extension of the classical susceptible-infectious-recovered model, which takes into account undocumented infections and allows the epide…
Functional data are frequently accompanied by a parametric template that describes the typical shapes of the functions. However, these parametric templates can incur significant bias, which undermines both utility and interpretability. To correct for model misspecification, we augment the parametric template with an infinite-dimensional nonparametric functional basis. The nonparametric basis functions are learned from the data and constrained to be orthogonal to the parametric template, which preserves distinctness between the parametric and nonparametric terms. This distinctness is essential …
This paper proposes a flexible Bayesian approach to multiple imputation using conditional Gaussian mixtures. We introduce novel shrinkage priors for covariate-dependent mixing proportions in the mixture models to automatically select the suitable number of components used in the imputation step. We develop an efficient sampling algorithm for posterior computation and multiple imputation via Markov Chain Monte Carlo methods. The proposed method can be easily extended to the situation where the data contains not only continuous variables but also discrete variables such as binary and count value…
We consider the problem of estimation in Hidden Markov models with finite state space and nonparametric emission distributions. Efficient estimators for the transition matrix are exhibited, and a semiparametric Bernstein-von Mises result is deduced. Following from this, we propose a modular approach using the cut posterior to jointly estimate the transition matrix and the emission densities. We derive a general theorem on contraction rates for this approach. We then show how this result may be applied to obtain a contraction rate result for the emission densities in our setting; a key intermed…
Multivariate data that combine binary, categorical, count and continuous outcomes are common in the social and health sciences. We propose a semiparametric Bayesian latent variable model for multivariate data of arbitrary type that does not require specification of conditional distributions. Drawing on the extended rank likelihood method by Hoff [Ann. Appl. Stat. 1 (2007) 265-283], we develop a semiparametric approach for latent variable modeling with mixed outcomes and propose associated Markov chain Monte Carlo estimation methods. Motivated by cognitive testing data, we focus on bifactor mod…
Storm surge, the onshore rush of sea water caused by the high winds and low pressure associated with a hurricane, can compound the effects of inland flooding caused by rainfall, leading to loss of property and loss of life for residents of coastal areas. Numerical ocean models are essential for creating storm surge forecasts for coastal areas. These models are driven primarily by the surface wind forcings. Currently, the gridded wind fields used by ocean models are specified by deterministic formulas that are based on the central pressure and location of the storm center. While these equations…
Many applications in medical statistics as well as in other fields can be described by transitions between multiple states (e.g. from health to disease) experienced by individuals over time. In this context, multi-state models are a popular statistical technique, in particular when the exact transition times are not observed. The key quantities of interest are the transition rates, capturing the instantaneous risk of moving from one state to another. The main contribution of this work is to propose a joint semiparametric model for several possibly related multi-state processes (Seemingly Unrel…
We show how the notion of message passing can be used to streamline the algebra and computer coding for fast approximate inference in large Bayesian semiparametric regression models. In particular, this approach is amenable to handling arbitrarily large models of particular types once a set of primitive operations is established. The approach is founded upon a message passing formulation of mean field variational Bayes that utilizes factor graph representations of statistical models. The underlying principles apply to general Bayesian hierarchical models although we focus on semiparametric reg…
Cognizance of gene-environment interactions may help prevent or detain the onset of complex diseases like cardiovascular disease, cancer, type2 diabetes, autism or asthma by adjustments to lifestyle. In this regard, we extend the Bayesian semiparametric gene-gene interaction model of Bhattacharya & Bhattacharya (2015) to include the possibility of influencing gene-gene interactions by environmental variables and possible mutations caused by the environment. Our model accounts for the unknown number of genetic sub-populations via finite mixtures composed of Dirichlet processes, which are relate…
