Bayesian Nonparametric Instrumental Variables Regression Based on Penalized Splines and Dirichlet Process Mixtures

We propose a Bayesian nonparametric instrumental variable approach under additive separability that allows us to correct for endogeneity bias in regression models where the covariate effects enter with unknown functional form. Bias correction relies on a simultaneous equations specification with flexible modeling of the joint error distribution implemented via a Dirichlet process mixture prior. Both the structural and instrumental variable equation are specified in terms of additive predictors comprising penalized splines for nonlinear effects of continuous covariates. Inference is fully Bayesian, employing efficient Markov chain Monte Carlo simulation techniques. The resulting posterior samples do not only provide us with point estimates, but allow us to construct simultaneous credible bands for the nonparametric effects, including data-driven smoothing parameter selection. In addition, improved robustness properties are achieved due to the flexible error distribution specification. Both these features are challenging in the classical framework, making the Bayesian one advantageous. In simulations, we investigate small sample properties and an investigation of the effect of class size on student performance in Israel provides an illustration of the proposed approach which is implemented in an R package bayesIV. Supplementary materials for this article are available online.     

On selecting a prior for the precision parameter of Dirichlet process mixture models

In hierarchical mixture models the Dirichlet process is used to specify latent patterns of heterogeneity, particularly when the distribution of latent parameters is thought to be clustered (multimodal). The parameters of a Dirichlet process include a precision parameter α$\alpha$ and a base probability measure _G0$G_0$. In problems where α$\alpha$ is unknown and must be estimated, inferences about the level of clustering can be sensitive to the choice of prior assumed for α$\alpha$. In this paper an approach is developed for computing a prior for the precision parameter α$\alpha$ that can be used in the presence or absence of prior information about the level of clustering. This approach is illustrated in an analysis of counts of stream fishes. The results of this fully Bayesian analysis are compared with an empirical Bayes analysis of the same data and with a Bayesian analysis based on an alternative commonly used prior.     

A mixture of beta–Dirichlet processes prior for Bayesian analysis of event history data

In this paper, we propose a mixture of beta–Dirichlet processes as a nonparametric prior for the cumulative intensity functions of a Markov process. This family of priors is a natural extension of a mixture of Dirichlet processes or a mixture of beta processes which are devised to compromise advantages of parametric and nonparametric approaches. They give most of their prior mass to the small neighborhood of a specific parametric model. We show that a mixture of beta–Dirichlet processes prior is conjugate with Markov processes. Formulas for computing the posterior distribution are derived. Finally, results of analyzing credit history data are given.     

On several estimates to the precision parameter of Dirichlet process prior

The article presents careful comparisons among several empirical Bayes estimates to the precision parameter of Dirichlet process prior, with the setup of univariate observations and multigroup data. Specifically, the data are equipped with a two-stage compound sampling model, where the prior is assumed as a Dirichlet process that follows within a Bayesian nonparametric framework. The precision parameter α measures the strength of the prior belief and kinds of estimates are generated on the basis of observations, including the naive estimate, two calibrated naive estimates, and two different types of maximum likelihood estimates stemming from distinct distributions. We explore some theoretical properties and provide explicitly detailed comparisons among these estimates, in the perspectives of bias, variance, and mean squared error. Besides, we further present the corresponding calculation algorithms and numerical simulations to illustrate our theoretical achievements.     

A semiparametric stochastic mixed effects model for bivariate cyclic longitudinal data

We propose a flexible semiparametric stochastic mixed effects model for bivariate cyclic longitudinal data. The model can handle either single cycle or, more generally, multiple consecutive cycle data. The approach models the mean of responses by parametric fixed effects and a smooth nonparametric function for the underlying time effects, and the relationship across the bivariate responses by a bivariate Gaussian random field and a joint distribution of random effects. The proposed model not only can model complicated individual profiles, but also allows for more flexible within-subject and between-response correlations. The fixed effects regression coefficients and the nonparametric time functions are estimated using maximum penalized likelihood, where the resulting estimator for the nonparametric time function is a cubic smoothing spline. The smoothing parameters and variance components are estimated simultaneously using restricted maximum likelihood. Simulation results show that the parameter estimates are close to the true values. The fit of the proposed model on a real bivariate longitudinal dataset of pre-menopausal women also performs well, both for a single cycle analysis and for a multiple consecutive cycle analysis. The Canadian Journal of Statistics 48: 471–498; 2020 © 2020 Statistical Society of Canada     

Asymptotic properties of the GMLE in the case 1 interval-censorship model with discrete inspection times

We consider the case 1 interval censorship model in which the survival time has an arbitrary distribution function F₀ and the inspection time has a discrete distribution function G. In such a model one is only able to observe the inspection time and whether the value of the survival time lies before or after the inspection time. We prove the strong consistency of the generalized maximum-likelihood estimate (GMLE) of the distribution function F₀ at the support points of G and its asymptotic normality and efficiency at what we call regular points. We also present a consistent estimate of the asymptotic variance at these points. The first result implies uniform strong consistency on [0, ∞) if F₀ is continuous and the support of G is dense in [0, ∞). For arbitrary F₀ and G, Peto (1973) and Tumbull (1976) conjectured that the convergence for the GMLE is at the usual parametric rate n½ Our asymptotic normality result supports their conjecture under our assumptions. But their conjecture was disproved by Groeneboom and Wellner (1992), who obtained the nonparametric rate ni under smoothness assumptions on the F₀ and G.     

Switching nonparametric regression models

We propose a methodology to analyse data arising from a curve that, over its domain, switches among J states. We consider a sequence of response variables, where each response y depends on a covariate x according to an unobserved state z. The states form a stochastic process and their possible values are j=1,?…?, J. If z equals j the expected response of y is one of J unknown smooth functions evaluated at x. We call this model a switching nonparametric regression model. We develop an Expectation–Maximisation algorithm to estimate the parameters of the latent state process and the functions corresponding to the J states. We also obtain standard errors for the parameter estimates of the state process. We conduct simulation studies to analyse the frequentist properties of our estimates. We also apply the proposed methodology to the well-known motorcycle dataset treating the data as coming from more than one simulated accident run with unobserved run labels.     

Constrained nonparametric maximum-likelihood estimation for mixture models

A nonparametric mixture model specifies that observations arise from a mixture distribution, ∫ f(x, θ) dG(θ), where the mixing distribution G is completely unspecified. A number of algorithms have been developed to obtain unconstrained maximum-likelihood estimates of G, but none of these algorithms lead to estimates when functional constraints are present. In many cases, there is a natural interest in functional ?(G), such as the mean and variance, of the mixing distribution, and profile likelihoods and confidence intervals for ?(G) are desired. In this paper we develop a penalized generalization of the ISDM algorithm of Kalbfleisch and Lesperance (1992) that can be used to solve the problem of constrained estimation. We also discuss its use in various different applications. Convergence results and numerical examples are given for the generalized ISDM algorithm, and asymptotic results are developed for the likelihood-ratio test statistics in the multinomial case.     

Optimal sampling for repeated binary measurements

The authors consider the optimal design of sampling schedules for binary sequence data. They propose an approach which allows a variety of goals to be reflected in the utility function by including deterministic sampling cost, a term related to prediction, and if relevant, a term related to learning about a treatment effect To this end, they use a nonparametric probability model relying on a minimal number of assumptions. They show how their assumption of partial exchangeability for the binary sequence of data allows the sampling distribution to be written as a mixture of homogeneous Markov chains of order k. The implementation follows the approach of Quintana & Müller (2004), which uses a Dirichlet process prior for the mixture.     

A comparison of nonparametric priors in hierarchical mixture modelling for AFT regression

We will pursue a Bayesian nonparametric approach in the hierarchical mixture modelling of lifetime data in two situations: density estimation, when the distribution is a mixture of parametric densities with a nonparametric mixing measure, and accelerated failure time (AFT) regression modelling, when the same type of mixture is used for the distribution of the error term. The Dirichlet process is a popular choice for the mixing measure, yielding a Dirichlet process mixture model for the error; as an alternative, we also allow the mixing measure to be equal to a normalized inverse-Gaussian prior, built from normalized inverse-Gaussian finite dimensional distributions, as recently proposed in the literature. Markov chain Monte Carlo techniques will be used to estimate the predictive distribution of the survival time, along with the posterior distribution of the regression parameters. A comparison between the two models will be carried out on the grounds of their predictive power and their ability to identify the number of components in a given mixture density.     

Nonparametric hierarchical Bayes analysis of binomial data via Bernstein polynomial priors

For binomial data analysis, many methods based on empirical Bayes interpretations have been developed, in which a variance‐stabilizing transformation and a normality assumption are usually required. To achieve the greatest model flexibility, we conduct nonparametric Bayesian inference for binomial data and employ a special nonparametric Bayesian prior—the Bernstein–Dirichlet process (BDP)—in the hierarchical Bayes model for the data. The BDP is a special Dirichlet process (DP) mixture based on beta distributions, and the posterior distribution resulting from it has a smooth density defined on [0, 1]. We examine two Markov chain Monte Carlo procedures for simulating from the resulting posterior distribution, and compare their convergence rates and computational efficiency. In contrast to existing results for posterior consistency based on direct observations, the posterior consistency of the BDP, given indirect binomial data, is established. We study shrinkage effects and the robustness of the BDP‐based posterior estimators in comparison with several other empirical and hierarchical Bayes estimators, and we illustrate through examples that the BDP‐based nonparametric Bayesian estimate is more robust to the sample variation and tends to have a smaller estimation error than those based on the DP prior. In certain settings, the new estimator can also beat Stein's estimator, Efron and Morris's limited‐translation estimator, and many other existing empirical Bayes estimators. The Canadian Journal of Statistics 40: 328–344; 2012 © 2012 Statistical Society of Canada     

Sampling schemes for generalized linear Dirichlet process random effects models

We evaluate MCMC sampling schemes for a variety of link functions in generalized linear models with Dirichlet process random effects. First, we find that there is a large amount of variability in the performance of MCMC algorithms, with the slice sampler typically being less desirable than either a Kolmogorov–Smirnov mixture representation or a Metropolis–Hastings algorithm. Second, in fitting the Dirichlet process, dealing with the precision parameter has troubled model specifications in the past. Here we find that incorporating this parameter into the MCMC sampling scheme is not only computationally feasible, but also results in a more robust set of estimates, in that they are marginalized-over rather than conditioned-upon. Applications are provided with social science problems in areas where the data can be difficult to model, and we find that the nonparametric nature of the Dirichlet process priors for the random effects leads to improved analyses with more reasonable inferences.     

Nonparametric Bayesian survival analysis using mixtures of Weibull distributions

Bayesian nonparametric methods have been applied to survival analysis problems since the emergence of the area of Bayesian nonparametrics. However, the use of the flexible class of Dirichlet process mixture models has been rather limited in this context. This is, arguably, to a large extent, due to the standard way of fitting such models that precludes full posterior inference for many functionals of interest in survival analysis applications. To overcome this difficulty, we provide a computational approach to obtain the posterior distribution of general functionals of a Dirichlet process mixture. We model the survival distribution employing a flexible Dirichlet process mixture, with a Weibull kernel, that yields rich inference for several important functionals. In the process, a method for hazard function estimation emerges. Methods for simulation-based model fitting, in the presence of censoring, and for prior specification are provided. We illustrate the modeling approach with simulated and real data.     

Bayesian semiparametric modeling and inference with mixtures of?symmetric distributions

We propose a semiparametric modeling approach for mixtures of symmetric distributions. The mixture model is built from a common symmetric density with different components arising through different location parameters. This structure ensures identifiability for mixture components, which is a key feature of the model as it allows applications to settings where primary interest is inference for the subpopulations comprising the mixture. We focus on the two-component mixture setting and develop a Bayesian model using parametric priors for the location parameters and for the mixture proportion, and a nonparametric prior probability model, based on Dirichlet process mixtures, for the random symmetric density. We present an approach to inference using Markov chain Monte Carlo posterior simulation. The performance of the model is studied with a simulation experiment and through analysis of a rainfall precipitation data set as well as with data on eruptions of the Old Faithful geyser.     

A Nonparametric Frailty Model for Clustered Survival Data

Clayton-type counting process formulations for survival data and parametric gamma models for cluster-specific frailty quantities are now routinely applied in analyses of clustered survival data. On the other hand, although nonparametric frailty models have been studied, they are not used much in practice. In this article, the distribution of the frailty terms is assumed to be an unknown random variable. The unknown frailty distribution is then modelled completely with a Dirichlet process prior. This prior assigns cluster units into sub-classes whose members have the same random frailty effect. The Gibbs sampler algorithm is used for computing posterior parameter estimates of the fixed effect hazards regression and the frailty distribution. The methodology is used to analyze community-clustered child survival in sub-Saharan Africa. The results show that the communities could be separated into fewer distinct classes of risk of childhood mortality; the fewer classes could be studied easily in order to provide useful guidance on the more effective use of resources for child health intervention programmes.     

A plug-in technique in nonparametric regression with dependence

The problem addressed is that of smoothing parameter selection in kernel nonparametric regression in the fixed design regression model with dependent noise. An asymptotic expression of the optimum bandwidth parameter has been obtained in recent studies, where this takes the form h = C ₀ n ^?1/5. This paper proposes to use a plug-in methodology, in order to obtain an optimum estimation of the bandwidth parameter, through preliminary estimation of the unknown value of C ₀.     

Mixture cure rate models with accelerated failures and nonparametric form of covariate effects

Two-component mixture cure rate model is popular in cure rate data analysis with the proportional hazards and accelerated failure time (AFT) models being the major competitors for modelling the latency component. [Wang, L., Du, P., and Liang, H. (2012), ‘Two-Component Mixture Cure Rate Model with Spline Estimated Nonparametric Components’, Biometrics, 68, 726–735] first proposed a nonparametric mixture cure rate model where the latency component assumes proportional hazards with nonparametric covariate effects in the relative risk. Here we consider a mixture cure rate model where the latency component assumes AFTs with nonparametric covariate effects in the acceleration factor. Besides the more direct physical interpretation than the proportional hazards, our model has an additional scalar parameter which adds more complication to the computational algorithm as well as the asymptotic theory. We develop a penalised EM algorithm for estimation together with confidence intervals derived from the Louis formula. Asymptotic convergence rates of the parameter estimates are established. Simulations and the application to a melanoma study shows the advantages of our new method.     

Asymptotic results for model robust regression

Since the mid 1980's many statisticians have studied methods for combining parametric and nonparametric models to improve the quality of fits in a regression problem. Notably Einsporn (1987) proposed the Model Robust Regression 1 estimate (MRRl) in which the parametric function, f, and the nonparametric functiong were combined in a straightforward fashion via the use of a mixing parameter, λ This technique was studied extensively atsmall samples and was shown to be quite effective at modeling various unusual functions. In this paper we have asymptotic results for the MRRl estimate in the case where λ is theoretically optimal, is asymptotically optimal and data driven, and is chosen with the PRESS statistic (Allen, 1971) We demonstrate that the MRRl estimate with λchosen by the PRESS statistic is slightly inferior asymptotically to the other two estimates, but, nevertheless possesses positive asymptotic qualities.     

Robust Bayesian analysis of the binomial empirical Bayes problem

Empirical Bayes estimation is considered for an i.i.d. sequence of binomial parameters θ_i arising from an unknown prior distribution G(.). This problem typically arises in industrial sampling, where samples from lots are routinely used to estimate the lot fraction defective of each lot. Two related issues are explored. The first concerns the fact that only the first few moments of G are typically estimable from the data. This suggests consideration of the interval of estimates (e.g., posterior means) corresponding to the different possible G with the specified moments. Such intervals can be obtained by application of well-known moment theory. The second development concerns the need to acknowledge the uncertainty in the estimation of the first few moments of G. Our proposal is to determine a credible set for the moments, and then find the range of estimates (e.g., posterior means) corresponding to the different possible G with moments in the credible set.