Default Bayesian analysis of the Behrens–Fisher problem

In the Bayesian approach, the Behrens–Fisher problem has been posed as one of estimation for the difference of two means. No Bayesian solution to the Behrens–Fisher testing problem has yet been given due, perhaps, to the fact that the conventional priors used are improper. While default Bayesian analysis can be carried out for estimation purposes, it poses difficulties for testing problems. This paper generates sensible intrinsic and fractional prior distributions for the Behrens–Fisher testing problem from the improper priors commonly used for estimation. It allows us to compute the Bayes factor to compare the null and the alternative hypotheses. This default procedure of model selection is compared with a frequentist test and the Bayesian information criterion. We find discrepancy in the sense that frequentist and Bayesian information criterion reject the null hypothesis for data, that the Bayes factor for intrinsic or fractional priors do not.     

Testing equality of regression coefficients in heteroscedastic normal regression models

This article addresses the problem of testing whether the vectors of regression coefficients are equal for two independent normal regression models when the error variances are unknown. This problem poses severe difficulties both to the frequentist and Bayesian approaches to statistical inference. In the former approach, normal hypothesis testing theory does not apply because of the unrelated variances. In the latter, the prior distributions typically used for the parameters are improper and hence the Bayes factor-based solution cannot be used.We propose a Bayesian solution to this problem in which no subjective input is considered. We first generate “objective” proper prior distributions (intrinsic priors) for which the Bayes factor and model posterior probabilities are well defined. The posterior probability of each model is used as a model selection tool. This consistent procedure of testing hypotheses is compared with some of the frequentist approximate tests proposed in the literature.     

On empirical Bayes simultaneous selection procedures for comparing normal populations with a standard

In this paper, we derive statistical selection procedures to partition k normal populations into ‘good’ or ‘bad’ ones, respectively, using the nonparametric empirical Bayes approach. The relative regret risk of a selection procedure is used as a measure of its performance. We establish the asymptotic optimality of the proposed empirical Bayes selection procedures and investigate the associated rates of convergence. Under a very mild condition, the proposed empirical Bayes selection procedures are shown to have rates of convergence of order close to O(k^−1/2) where k is the number of populations involved in the selection problem. With further strong assumptions, the empirical Bayes selection procedures have rates of convergence of order O(k^{−α(r−1)/(2r+1)}), where 1<α<2 and r is an integer greater than 2.     

Empirical Bayes vs. fully Bayes variable selection

For the problem of variable selection for the normal linear model, fixed penalty selection criteria such as AIC, _Cp${\mathrm{C}}_p$, BIC and RIC correspond to the posterior modes of a hierarchical Bayes model for various fixed hyperparameter settings. Adaptive selection criteria obtained by empirical Bayes estimation of the hyperparameters have been shown by George and Foster [2000. Calibration and Empirical Bayes variable selection. Biometrika 87(4), 731–747] to improve on these fixed selection criteria. In this paper, we study the potential of alternative fully Bayes methods, which instead margin out the hyperparameters with respect to prior distributions. Several structured prior formulations are considered for which fully Bayes selection and estimation methods are obtained. Analytical and simulation comparisons with empirical Bayes counterparts are studied.     

Alternative Bayes factors for model selection

Several alternative Bayes factors have been recently proposed in order to solve the problem of the extreme sensitivity of the Bayes factor to the priors of models under comparison. Specifically, the impossibility of using the Bayes factor with standard noninformative priors for model comparison has led to the introduction of new automatic criteria, such as the posterior Bayes factor (Aitkin 1991), the intrinsic Bayes factors (Berger and Pericchi 1996b) and the fractional Bayes factor (O'Hagan 1995). We derive some interesting properties of the fractional Bayes factor that provide justifications for its use additional to the ones given by O'Hagan. We further argue that the use of the fractional Bayes factor, originally introduced to cope with improper priors, is also useful in a robust analysis. Finally, using usual classes of priors, we compare several alternative Bayes factors for the problem of testing the point null hypothesis in the univariate normal model.     

p-Values,Bayes Factors,and Sufficiency

ABSTRACT

Various approaches can be used to construct a model from a null distribution and a test statistic. I prove that one such approach, originating with D. R. Cox, has the property that the p-value is never greater than the Generalized Likelihood Ratio (GLR). When combined with the general result that the GLR is never greater than any Bayes factor, we conclude that, under Cox’s model, the p-value is never greater than any Bayes factor. I also provide a generalization, illustrations for the canonical Normal model, and an alternative approach based on sufficiency. This result is relevant for the ongoing discussion about the evidential value of small p-values, and the movement among statisticians to “redefine statistical significance.”     

Bayes factor consistency for unbalanced ANOVA models

In practical situations, most experimental designs often yield unbalanced data which have different numbers of observations per unit because of cost constraints, missing data, etc. In this paper, we consider the Bayesian approach to hypothesis testing or model selection under the one-way unbalanced fixed-effects analysis-of-variance (ANOVA) model. We adopt Zellner's g-prior with the beta-prime distribution for g, which results in an explicit closed-form expression of the Bayes factor without integral representation. Furthermore, we investigate the model selection consistency of the Bayes factor under three different asymptotic scenarios: either the number of units goes to infinity, the number of observations per unit goes to infinity, or both go to infinity. The results presented extend some existing ones of the Bayes factor for the balanced ANOVA models in the literature.     

Objective Bayesian transformation and variable selection using default Bayes factors

In this work, the problem of transformation and simultaneous variable selection is thoroughly treated via objective Bayesian approaches by the use of default Bayes factor variants. Four uniparametric families of transformations (Box–Cox, Modulus, Yeo-Johnson and Dual), denoted by T, are evaluated and compared. The subjective prior elicitation for the transformation parameter \(\lambda _T\), for each T, is not a straightforward task. Additionally, little prior information for \(\lambda _T\) is expected to be available, and therefore, an objective method is required. The intrinsic Bayes factors and the fractional Bayes factors allow us to incorporate default improper priors for \(\lambda _T\). We study the behaviour of each approach using a simulated reference example as well as two real-life examples.     

Empirical Bayes testing for equivalence

For a fixed point θ₀ and a positive value c₀, this paper studies the problem of testing the hypotheses H₀:|θ−θ₀|≤c₀ against H₁:|θ−θ₀|>c₀ for the normal mean parameter θ using the empirical Bayes approach. With the accumulated past data, a monotone empirical Bayes test is constructed by mimicking the behavior of a monotone Bayes test. Such an empirical Bayes test is shown to be asymptotically optimal and its regret converges to zero at a rate (lnn)^2.5/n where n is the number of past data available, when the current testing problem is considered. A simulation study is also given, and the results show that the proposed empirical Bayes procedure has good performance for small to moderately large sample sizes. Our proposed method can be applied for testing close to a control problem or testing the therapeutic equivalence of one standard treatment compared to another in clinical trials.     

On the estimation of homogeneous population size from a complex dual-record system

ABSTRACT

A dual-record system (DRS) (equivalently two sample capture–recapture experiments) model, with time and behavioural response variation, has attracted much attention specifically in the domain of official statistics and epidemiology, as the assumption of list independence often fails. The relevant model suffers from parameter identifiability problem, and suitable Bayesian methodologies could be helpful. In this article, we formulate population size estimation in DRS as a missing data problem and two empirical Bayes approaches are proposed along with the discussion of an existing Bayes treatment. Some features and associated posterior convergence for these methods are mentioned. Investigation through an extensive simulation study finds that our proposed approaches compare favourably with the existing Bayes approach for this complex model depending upon the availability of directional nature of underlying behavioural response effect. A real-data example is given to illustrate these methods.     

Generalized ridge regression and a generalization of the CP statistic

We consider a generalization of ridge regression and demonstrate advantages over ridge regression. We provide an empirical Bayes method for determining the ridge constants, using the Bayesian interpretation of ridge estimators, and show that this coincides with a method based on a generalization of the C_P statistic and the non-negative garrote. These provide an automatic variable selection procedure for the canonical variables.     

The superharmonic condition for simultaneous estimation of means in exponential familles

The mean vector associated with several independent variates from the exponential subclass of Hudson (1978) is estimated under weighted squared error loss. In particular, the formal Bayes and “Stein-like” estimators of the mean vector are given. Conditions are also given under which these estimators dominate any of the “natural estimators”. Our conditions for dominance are motivated by a result of Stein (1981), who treated the N_p (θ, I) case with p ≥ 3. Stein showed that formal Bayes estimators dominate the usual estimator if the marginal density of the data is superharmonic. Our present exponential class generalization entails an elliptic differential inequality in some natural variables. Actually, we assume that each component of the data vector has a probability density function which satisfies a certain differential equation. While the densities of Hudson (1978) are particular solutions of this equation, other solutions are not of the exponential class if certain parameters are unknown. Our approach allows for the possibility of extending the parametric Stein-theory to useful nonexponential cases, but the problem of nuisance parameters is not treated here.     

Objective Bayesian multiple comparisons for normal variances

This paper considers the multiple comparisons problem for normal variances. We propose a solution based on a Bayesian model selection procedure to this problem in which no subjective input is considered. We construct the intrinsic and fractional priors for which the Bayes factors and model selection probabilities are well defined. The posterior probability of each model is used as a model selection tool. The behaviour of these Bayes factors is compared with the Bayesian information criterion of Schwarz and some frequentist tests.     

Different definitions of Δ-correct selection for the indifference zone formulation

The goal of the indifference zone formulation of selection (Bechhofer, 1954) consists of selecting the t best variants out of k variants with a probability of at least 1 − β if the parameter difference between the t ‘good’ variants and the k − t ‘bad’ variants is not less than Δ. A review of generalized selection goals not using this difference condition is presented. Within some general classes of distributions, the suitable experimental designs for all these selection goals are identical. Similar results are described for the problem of selecting the best variant in comparison with a control, or standard.     

A Bayesian test of independence in a two-way contingency table using surrogate sampling

We consider a Bayesian approach to the study of independence in a two-way contingency table which has been obtained from a two-stage cluster sampling design. If a procedure based on single-stage simple random sampling (rather than the appropriate cluster sampling) is used to test for independence, the p-value may be too small, resulting in a conclusion that the null hypothesis is false when it is, in fact, true. For many large complex surveys the Rao–Scott corrections to the standard chi-squared (or likelihood ratio) statistic provide appropriate inference. For smaller surveys, though, the Rao–Scott corrections may not be accurate, partly because the chi-squared test is inaccurate. In this paper, we use a hierarchical Bayesian model to convert the observed cluster samples to simple random samples. This provides surrogate samples which can be used to derive the distribution of the Bayes factor. We demonstrate the utility of our procedure using an example and also provide a simulation study which establishes our methodology as a viable alternative to the Rao–Scott approximations for relatively small two-stage cluster samples. We also show the additional insight gained by displaying the distribution of the Bayes factor rather than simply relying on a summary of the distribution.     

Bayesian Approach in Nonparametric Count Regression with Binomial Kernel

Recently, Kokonendji et al. have adapted the well-known Nadaraya–Watson kernel estimator for estimating the count function m in the context of nonparametric discrete regression. The authors have also investigated the bandwidth selection using the cross-validation method. In this article, we propose a Bayesian approach in the context of nonparametric count regression for estimating the bandwidth and the variance of the model error, which has not been estimated in Kokonendji et al. The model error is considered as Gaussian with mean of zero and a variance of σ². The Bayes estimates cannot be obtained in closed form and then, we use the well-known Markov chain Monte Carlo (MCMC) technique to compute the Bayes estimates under the squared errors loss function. The performance of this proposed approach and the cross-validation method are compared through simulation and real count data.     

A Bayesian mixture model for differential gene expression

Summary.  We propose model-based inference for differential gene expression, using a nonparametric Bayesian probability model for the distribution of gene intensities under various conditions. The probability model is a mixture of normal distributions. The resulting inference is similar to a popular empirical Bayes approach that is used for the same inference problem. The use of fully model-based inference mitigates some of the necessary limitations of the empirical Bayes method. We argue that inference is no more difficult than posterior simulation in traditional nonparametric mixture-of-normal models. The approach proposed is motivated by a microarray experiment that was carried out to identify genes that are differentially expressed between normal tissue and colon cancer tissue samples. Additionally, we carried out a small simulation study to verify the methods proposed. In the motivating case-studies we show how the nonparametric Bayes approach facilitates the evaluation of posterior expected false discovery rates. We also show how inference can proceed even in the absence of a null sample of known non-differentially expressed scores. This highlights the difference from alternative empirical Bayes approaches that are based on plug-in estimates.     

An application of a minimax Bayes rule and shrinkage estimators to the portofolio selection problem under the Bayesian approach

This paper shows that a minimax Bayes rule and shrinkage estimators can be effectively applied to portfolio selection under the Bayesian approach. Specifically, it is shown that the portfolio selection problem can result in a statistical decision problem in some situations. Following that, we present a method for solving a problem involved in portfolio selection under the Bayesian approach.     

Estimating the Proportion of True Null Hypotheses in Nonparametric Exponential Mixture Model with Appication to the Leukemia Gene Expression Data

We revisit the problem of estimating the proportion π of true null hypotheses where a large scale of parallel hypothesis tests are performed independently. While the proportion is a quantity of interest in its own right in applications, the problem has arisen in assessing or controlling an overall false discovery rate. On the basis of a Bayes interpretation of the problem, the marginal distribution of the p-value is modeled in a mixture of the uniform distribution (null) and a non-uniform distribution (alternative), so that the parameter π of interest is characterized as the mixing proportion of the uniform component on the mixture. In this article, a nonparametric exponential mixture model is proposed to fit the p-values. As an alternative approach to the convex decreasing mixture model, the exponential mixture model has the advantages of identifiability, flexibility, and regularity. A computation algorithm is developed. The new approach is applied to a leukemia gene expression data set where multiple significance tests over 3,051 genes are performed. The new estimate for π with the leukemia gene expression data appears to be about 10% lower than the other three estimates that are known to be conservative. Simulation results also show that the new estimate is usually lower and has smaller bias than the other three estimates.     

Bayes A-optimal designs for comparing test treatments with a control

The problem of comparing v test treatments simultaneously with a control treatment when k, v ⩾ 3 is considered. Following the work of Majumdar (1992), we use exact design theory to derive Bayes A-optimal block designs and optimal Г-minimax designs for a more general prior assumption for the one-way elimination of heterogeneity model. Examples of robust optimal designs, highly efficient designs, and the comparisons of the approximate optimal designs that are derived by our methods and by some other existing rounding-off schemes when using Owen's procedure are also provided.