Large-scale interval and point estimates from an empirical Bayes extension of confidence posteriors
David R. Bickel
发表信息:
Bickel, D. R. (2012). Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals. Statistical Applications in Genetics and Molecular Biology, 11 (article 3)
The proposed approach extends the confidence posterior distribution to the semi-parametric empirical Bayes setting. Whereas the Bayesian posterior is defined in terms of a prior distribution conditional on the observed data, the confidence posterior is defined such that the probability that the parameter value lies in any fixed subset of parameter space, given the observed data, is equal to the coverage rate of the corresponding confidence interval. A confidence posterior that has correct frequentist coverage at each fixed parameter value is combined with the estimated local false discovery rate to yield a parameter distribution from which interval and point estimates are derived within the framework of minimizing expected loss. The point estimates exhibit suitable shrinkage toward the null hypothesis value, making them practical for automatically ranking features in order of priority. The corresponding confidence intervals are also shrunken and tend to be much shorter than their fixed-parameter counterparts, as illustrated with gene expression data. Further, simulations confirm a theoretical argument that the shrunken confidence intervals cover the parameter at a higher-than-nominal frequency.
Quantitative comparisons between finitary posterior distributions and Bayesian posterior distributions
贝叶斯统计推断的主要目的是确定后验分布。有时,这些定律是为缺乏经验值的量给出的。当我们只考虑有限视界框架时,这个严重的缺点就消失了。然而,假设无限的交换率会产生相当容易处理的{ \it a posteriori}量,这在应用中是非常有吸引力的。因此,为了调和这两个方面的贝叶斯推理方式,在本文中,我们提供了定量比较后验分布的有限参数和后验分布的盟军参数出现在通常的统计模型。
We consider the asymptotic behaviour of the marginal maximum likelihood empirical Bayes posterior distribution in general setting. First we characterize the set where the maximum marginal likelihood estimator is located with high probability. Then we provide oracle type of upper and lower bounds for the contraction rates of the empirical Bayes posterior. We also show that the hierarchical Bayes posterior achieves the same contraction rate as the maximum marginal likelihood empirical Bayes posterior. We demonstrate the applicability of our general results for various models and prior distributi…
Bayesian model selection is premised on the assumption that the data are generated from one of the postulated models. However, in many applications, all of these models are incorrect (that is, there is misspecification). When the models are misspecified, two or more models can provide a nearly equally good fit to the data, in which case Bayesian model selection can be highly unstable, potentially leading to self-contradictory findings. To remedy this instability, we propose to use bagging on the posterior distribution ("BayesBag") -- that is, to average the posterior model probabilities over m…
In the sparse normal means model, convergence of the Bayesian posterior distribution associated to spike and slab prior distributions is considered. The key sparsity hyperparameter is calibrated via marginal maximum likelihood empirical Bayes. The plug-in posterior squared-$L^2$ norm is shown to converge at the minimax rate for the euclidean norm for appropriate choices of spike and slab distributions. Possible choices include standard spike and slab with heavy tailed slab, and the spike and slab LASSO of Rocková and George with heavy tailed slab. Surprisingly, the popular Laplace slab is show…
Standard Bayesian inference is known to be sensitive to model misspecification, leading to unreliable uncertainty quantification and poor predictive performance. However, finding generally applicable and computationally feasible methods for robust Bayesian inference under misspecification has proven to be a difficult challenge. An intriguing, easy-to-use, and widely applicable approach is to use bagging on the Bayesian posterior ("BayesBag"); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. In this paper, we develop the asymptotic theory of BayesBag,…
Although Bayesian inference is an immensely popular paradigm among a large segment of scientists including statisticians, most applications consider objective priors and need critical investigations (Efron, 2013, Science). While it has several optimal properties, a major drawback of Bayesian inference is the lack of robustness against data contamination and model misspecification, which becomes pernicious in the use of objective priors. This paper presents the general formulation of a Bayes pseudo-posterior distribution yielding robust inference. Exponential convergence results related to the …
Optimality results for two outstanding Bayesian estimation problems are given in this paper: the estimation of the sampling distribution for the squared total variation function and the estimation of the density for the $L^1$-squared loss function. The posterior predictive distribution provides the solution to these problems. Some examples are presented to illustrate it. The Bayesian estimation problem of a distribution function is also addressed. Consistency of the estimator of the density is proved.
We consider Bayesian inference in inverse regression problems where the objective is to infer about unobserved covariates from observed responses and covariates. We establish posterior consistency of such unobserved covariates in Bayesian inverse regression problemsunder appropriate priors in a leave-one-out cross-validation setup. We relate this to posterior consistency of inverse reference distributions (Bhattacharya (2013)) for assessing model adequacy. We illustrate our theory and methods with various examples of Bayesian inverse regression, along with adequate simulation experiments.
We propose a new empirical Bayes approach for inference in the $p \gg n$ normal linear model. The novelty is the use of data in the prior in two ways, for centering and regularization. Under suitable sparsity assumptions, we establish a variety of concentration rate results for the empirical Bayes posterior distribution, relevant for both estimation and model selection. Computation is straightforward and fast, and simulation results demonstrate the strong finite-sample performance of the empirical Bayes model selection procedure.
Recently, several researchers have claimed that conclusions obtained from a Bayes factor (or the posterior odds) may contradict those obtained from Bayesian posterior estimation. In this short paper, we wish to point out that no such "incompatibility" exists if one is willing to consistently define one's priors and posteriors. The key for compatibility is that the (implied) prior model odds used for testing are the same as those used for estimation. Our recommendation is simple: If one reports a Bayes factor comparing two models, then one should also report posterior estimates which appropriat…
Maximum a posteriori and Bayes estimators are two common methods of point estimation in Bayesian Statistics. It is commonly accepted that maximum a posteriori estimators are a limiting case of Bayes estimators with 0-1 loss. In this paper, we provide a counterexample which shows that in general this claim is false. We then correct the claim that by providing a level-set condition for posterior densities such that the result holds. Since both estimators are defined in terms of optimization problems, the tools of variational analysis find a natural application to Bayesian point estimation.
In a sparse stochastic block model with two communities of unequal sizes we derive two posterior concentration inequalities, that imply (1) posterior (almost-)exact recovery of the community structure under sparsity bounds comparable to well-known sharp bounds in the planted bi-section model; (2) a construction of confidence sets for the community assignment from credible sets, with finite graph sizes. The latter enables exact frequentist uncertain quantification with Bayesian credible sets at non-asymptotic graph sizes, where posteriors can be simulated well. There turns out to be no proporti…
We derive the posteror contraction rate for non-parametric Bayesian estimation of a deterministic dispersion coefficient of a linear stochastic differential equation.
Variational and Bayesian methods are two approaches that have been widely used to solve image reconstruction problems. In this paper, we propose original connections between Hamilton--Jacobi (HJ) partial differential equations and a broad class of Bayesian methods and posterior mean estimators with Gaussian data fidelity term and log-concave prior. Whereas solutions to certain first-order HJ PDEs with initial data describe maximum a posteriori estimators in a Bayesian setting, here we show that solutions to some viscous HJ PDEs with initial data describe a broad class of posterior mean estimat…
A Beta-Binomial-Logit model is a Beta-Binomial model with covariate information incorporated via a logistic regression. Posterior propriety of a Bayesian Beta-Binomial-Logit model can be data-dependent for improper hyper-prior distributions. Various researchers in the literature have unknowingly used improper posterior distributions or have given incorrect statements about posterior propriety because checking posterior propriety can be challenging due to the complicated functional form of a Beta-Binomial-Logit model. We derive data-dependent necessary and sufficient conditions for posterior pr…
We study the convergence rates of empirical Bayes posterior distributions for nonparametric and high-dimensional inference. We show that as long as the hyperparameter set is discrete, the empirical Bayes posterior distribution induced by the maximum marginal likelihood estimator can be regarded as a variational approximation to a hierarchical Bayes posterior distribution. This connection between empirical Bayes and variational Bayes allows us to leverage the recent results in the variational Bayes literature, and directly obtains the convergence rates of empirical Bayes posterior distributions…
Sparse Bayesian learning models are typically used for prediction in datasets with significantly greater number of covariates than observations. Such models often take a reproducing kernel Hilbert space (RKHS) approach to carry out the task of prediction and can be implemented using either proper or improper priors. In this article we show that a few sparse Bayesian learning models in the literature, when implemented using improper priors, lead to improper posteriors.
Asymptotic theory of tail index estimation has been studied extensively in the frequentist literature on extreme values, but rarely in the Bayesian context. We investigate whether popular Bayesian kernel mixture models are able to support heavy tailed distributions and consistently estimate the tail index. We show that posterior inconsistency in tail index is surprisingly common for both parametric and nonparametric mixture models. We then present a set of sufficient conditions under which posterior consistency in tail index can be achieved, and verify these conditions for Pareto mixture model…
We consider the fractional posterior distribution that is obtained by updating a prior distribution via Bayes theorem with a fractional likelihood function, a usual likelihood function raised to a fractional power. First, we analyze the contraction property of the fractional posterior in a general misspecified framework. Our contraction results only require a prior mass condition on certain Kullback-Leibler (KL) neighborhood of the true parameter (or the KL divergence minimizer in the misspecified case), and obviate constructions of test functions and sieves commonly used in the literature for…
Posterior contractions rates (PCRs) strengthen the notion of Bayesian consistency, quantifying the speed at which the posterior distribution concentrates on arbitrarily small neighborhoods of the true model, with probability tending to 1 or almost surely, as the sample size goes to infinity. Under the Bayesian nonparametric framework, a common assumption in the study of PCRs is that the model is dominated for the observations; that is, it is assumed that the posterior can be written through the Bayes formula. In this paper, we consider the problem of establishing PCRs in Bayesian nonparametric…
In this paper, we are concerned with attributing meaning to the results of a Bayesian analysis for a problem which is sufficiently complex that we are unable to assert a precise correspondence between the expert probabilistic judgements of the analyst and the particular forms chosen for the prior specification and the likelihood for the analysis. In order to do this, we propose performing a finite collection of additional Bayesian analyses under alternative collections of prior and likelihood modelling judgements that we may also view as representative of our prior knowledge and the problem st…
Despite their widespread use in practice, the asymptotic properties of Bayesian penalized splines have not been investigated so far. We close this gap and study posterior concentration rates for Bayesian penalized splines in a Gaussian nonparametric regression model. A key feature of the approach is the hyperprior on the smoothing variance, which allows for adaptive smoothing in practice but complicates the theoretical analysis considerably as it destroys conjugacy and precludes analytic expressions for the posterior moments. To derive our theoretical results, we rely on several new concepts i…
Marginalization techniques are presented for the Bayesian filtering problem under the assumption of Gaussian priors and posteriors and a set of sequentially more constraining state space model assumptions. The techniques provide the capabilities to 1) reduce the filtering problem to essential marginal moment integrals, 2) combine model and numerical approximations to the moment integrals, and 3) decouple modelling and system composition. Closed-form expressions of the posterior means and covariances are developed as functions of subspace projection matrices, subsystem models, and the marginal …
Statistical inference can be seen as information processing involving input information and output information that updates belief about some unknown parameters. We consider the Bayesian framework for making inferences about dynamical systems from ergodic observations, where the Bayesian procedure is based on the Gibbs posterior inference, a decision process generalization of standard Bayesian inference where the likelihood is replaced by the exponential of a loss function. In the case of direct observation and almost-additive loss functions, we prove an exponential convergence of the a poster…
Selecting a subset of variables for linear models remains an active area of research. This paper reviews many of the recent contributions to the Bayesian model selection and shrinkage prior literature. A posterior variable selection summary is proposed, which distills a full posterior distribution over regression coefficients into a sequence of sparse linear predictors.
We consider Bayesian sample size determination using a criterion that utilizes the first two moments of the expected posterior variance. We study the resulting sample size in dependence on the chosen prior and explore the success rate for bounding the posterior variance below a prescribed limit under the true sampling distribution. Compared with sample size determination based on the expected average of the posterior variance the proposed criterion leads to an increase in sample size and significantly improved success rates. Generic asymptotic properties are proven, such as an asymptotic expre…
We consider inference in the scalar diffusion model $dX_t=b(X_t)dt+σ(X_t)dW_t$ with discrete data $(X_{jΔ_n})_{0\leq j \leq n}$, $n\to \infty,~Δ_n\to 0$ and periodic coefficients. For $σ$ given, we prove a general theorem detailing conditions under which Bayesian posteriors will contract in $L^2$-distance around the true drift function $b_0$ at the frequentist minimax rate (up to logarithmic factors) over Besov smoothness classes. We exhibit natural nonparametric priors which satisfy our conditions. Our results show that the Bayesian method adapts both to an unknown sampling regime and to unkn…
Many modern experiments, such as microarray gene expression and genome-wide association studies, present the problem of estimating a large number of parallel effects. Bayesian inference is a popular approach for analyzing such data by modeling the large number of unknown parameters as random effects from a common prior distribution. However, misspecification of the prior distribution can lead to erroneous estimates of the random effects, especially for the largest and most interesting effects. This paper has two aims. First, we propose a robustified posterior distribution for a parametric Baye…
The asymmetric Laplace density (ALD) is used as a working likelihood for Bayesian quantile regression. Sriram et al.(2013) derived posterior consistency for Bayesian linear quantile regression based on the misspecified ALD. While their paper also argued for $\sqrt{n}-$consistency, Sriram and Ramamoorthi (2017) highlighted that the argument was only valid for a rate less than $\sqrt{n}$. So, the question of $\sqrt{n}-$rate has remained unaddressed, but is necessary to carry out meaningful Bayesian inference based on the ALD. In this paper, we derive results to obtain posterior consistency rates…
We study the posterior contraction rates of a Bayesian method with Gaussian process priors in nonparametric regression and its plug-in property for differential operators. For a general class of kernels, we establish convergence rates of the posterior measure of the regression function and its derivatives, which are both minimax optimal up to a logarithmic factor for functions in certain classes. Our calculation shows that the rate-optimal estimation of the regression function and its derivatives share the same choice of hyperparameter, indicating that the Bayes procedure remarkably adapts to …
This paper proposes Bayesian mosaic, a parallelizable composite posterior, for scalable Bayesian inference on a broad class of multivariate discrete data models. Sampling is embarrassingly parallel since Bayesian mosaic is a multiplication of component posteriors that can be independently sampled from. Analogous to composite likelihood methods, these component posteriors are based on univariate or bivariate marginal densities. Utilizing the fact that the score functions of these densities are unbiased, we show that Bayesian mosaic is consistent and asymptotically normal under mild conditions. …
Although linear regression models are fundamental tools in statistical science, the estimation results can be sensitive to outliers. While several robust methods have been proposed in frequentist frameworks, statistical inference is not necessarily straightforward. We here propose a Bayesian approach to robust inference on linear regression models using synthetic posterior distributions based on $γ$-divergence, which enables us to naturally assess the uncertainty of the estimation through the posterior distribution. We also consider the use of shrinkage priors for the regression coefficients t…
PAC-Bayesian algorithms and Gibbs posteriors are gaining popularity due to their robustness against model misspecification even when Bayesian inference is inconsistent. The PAC-Bayesian alpha-posterior is a generalization of the standard Bayes posterior which can be tempered with a parameter alpha to handle inconsistency. Data driven methods for tuning alpha have been proposed but are still few, and are often computationally heavy. Additionally, the adequacy of these methods in cases where we use variational approximations instead of exact alpha-posteriors is not clear. This narrows their usag…
Incorporating a contrast in the Bayesian formula: What consequences for the MAP estimator and the posterior distribution? Applications in spatial statistics