Biometrika - current issue

Nonparametric Bayes local partition models for random effects

Dunson, D. B. — 2009-05-20

This paper focuses on the problem of choosing a prior for an unknown random effects distribution within a Bayesian hierarchical model. The goal is to obtain a sparse representation by allowing a combination of global and local borrowing of information. A local partition process prior is proposed, which induces dependent local clustering. Subjects can be clustered together for a subset of their parameters, and one learns about similarities between subjects increasingly as parameters are added. Some basic properties are described, including simple two-parameter expressions for marginal and conditional clustering probabilities. A slice sampler is developed which bypasses the need to approximate the countably infinite random measure in performing posterior computation. The methods are illustrated using simulation examples, and an application to hormone trajectory data.

Mixtures of Polya trees for flexible spatial frailty survival modelling

Zhao, L., Hanson, T. E., Carlin, B. P. — 2009-05-20

Mixtures of Polya trees offer a very flexible nonparametric approach for modelling time-to-event data. Many such settings also feature spatial association that requires further sophistication, either at the point level or at the lattice level. In this paper, we combine these two aspects within three competing survival models, obtaining a data analytic approach that remains computationally feasible in a fully hierarchical Bayesian framework using Markov chain Monte Carlo methods. We illustrate our proposed methods with an analysis of spatially oriented breast cancer survival data from the Surveillance, Epidemiology and End Results program of the National Cancer Institute. Our results indicate appreciable advantages for our approach over competing methods that impose unrealistic parametric assumptions, ignore spatial association or both.

Gamma frailty transformation models for multivariate survival times

Zeng, D., Chen, Q., Ibrahim, J. G. — 2009-05-20

We propose a class of transformation models for multivariate failure times. The class of transformation models generalize the usual gamma frailty model and yields a marginally linear transformation model for each failure time. Nonparametric maximum likelihood estimation is used for inference. The maximum likelihood estimators for the regression coefficients are shown to be consistent and asymptotically normal, and their asymptotic variances attain the semiparametric efficiency bound. Simulation studies show that the proposed estimation procedure provides asymptotically efficient estimates and yields good inferential properties for small sample sizes. The method is illustrated using data from a cardiovascular study.

Generalized method of moments estimation for linear regression with clustered failure time data

Li, H., Yin, G. — 2009-05-20

We propose a generalized method of moments approach to the accelerated failure time model with correlated survival data. We study the semiparametric rank estimator using martingale-based moments. We circumvent direct estimation of correlation parameters by concatenating the moments and minimizing a quadratic objective function. We establish the consistency and asymptotic normality of the parameter estimators, and derive the limiting distribution of the objective function. We carry out simulation studies to examine the finite-sample properties of the method, and demonstrate its substantial efficiency gain over the conventional method. Finally, we illustrate the new proposal with an example from a diabetic retinopathy study.

Hierarchically penalized Cox regression with grouped variables

Wang, S., Nan, B., Zhu, N., Zhu, J. — 2009-05-20

In many biological and other scientific applications, predictors are often naturally grouped. For example, in biological applications, assayed genes or proteins are grouped by biological roles or biological pathways. When studying the dependence of survival outcome on these grouped predictors, it is desirable to select variables at both the group level and the within-group level. In this article, we develop a new method to address the group variable selection problem in the Cox proportional hazards model. Our method not only effectively removes unimportant groups, but also maintains the flexibility of selecting variables within the identified groups. We also show that the new method offers the potential for achieving the asymptotic oracle property.

A generalized Dantzig selector with shrinkage tuning

James, G. M., Radchenko, P. — 2009-05-20

The Dantzig selector performs variable selection and model fitting in linear regression. It uses an L₁ penalty to shrink the regression coefficients towards zero, in a similar fashion to the lasso. While both the lasso and Dantzig selector potentially do a good job of selecting the correct variables, they tend to overshrink the final coefficients. This results in an unfortunate trade-off. One can either select a high shrinkage tuning parameter that produces an accurate model but poor coefficient estimates or a low shrinkage parameter that produces more accurate coefficients but includes many irrelevant variables. We extend the Dantzig selector to fit generalized linear models while eliminating overshrinkage of the coefficient estimates, and develop a computationally efficient algorithm, similar in nature to least angle regression, to compute the entire path of coefficient estimates. A simulation study illustrates the advantages of our approach relative to others. We apply the methodology to two datasets.

A group bridge approach for variable selection

Huang, J., Ma, S., Xie, H., Zhang, C.-H. — 2009-05-20

In multiple regression problems when covariates can be naturally grouped, it is important to carry out feature selection at the group and within-group individual variable levels simultaneously. The existing methods, including the lasso and group lasso, are designed for either variable selection or group selection, but not for both. We propose a group bridge approach that is capable of simultaneous selection at both the group and within-group individual variable levels. The proposed approach is a penalized regularization method that uses a specially designed group bridge penalty. It has the oracle group selection property, in that it can correctly select important groups with probability converging to one. In contrast, the group lasso and group least angle regression methods in general do not possess such an oracle property in group selection. Simulation studies indicate that the group bridge has superior performance in group and individual variable selection relative to several existing methods.

Covariate-adjusted generalized linear models

Senturk, D., Muller, H.-G. — 2009-05-20

We propose covariate adjustment methodology for a situation where one wishes to study the dependence of a generalized response on predictors while both predictors and response are distorted by an observable covariate. The distorting covariate is thought of as a size measurement that affects predictors in a multiplicative fashion. The generalized response is modelled by means of a random threshold, where the subject-specific thresholds are affected by a multiplicative factor that is a function of the distorting covariate. While the various factors are modelled as smooth unknown functions of the distorting covariate, the underlying relationship between response and covariates is assumed to be governed by a generalized linear model with a known link function. This model provides an extension of a covariate-adjusted regression approach to the case of a generalized linear model. We demonstrate that this contamination model leads to a semiparametric varying-coefficient model. Numerical implementation is straightforward by combining binning, quasilikelihood, and smoothing steps. The asymptotic distribution of the proposed estimators for the regression coefficients of the latent generalized linear model is derived by means of a martingale central limit theorem. Combining this result with consistent estimators for the asymptotic variance makes it then possible to obtain asymptotic inference for the targeted parameters. Both real and simulated data are used in illustrating the proposed methodology.

Adjusting for covariate effects on classification accuracy using the covariate-adjusted receiver operating characteristic curve

Janes, H., Pepe, M. S. — 2009-05-20

Recent scientific and technological innovations have produced an abundance of potential markers that are being investigated for their use in disease screening and diagnosis. In evaluating these markers, it is often necessary to account for covariates associated with the marker of interest. Covariates may include subject characteristics, expertise of the test operator, test procedures or aspects of specimen handling. In this paper, we propose the covariate-adjusted receiver operating characteristic curve, a measure of covariate-adjusted classification accuracy. Nonparametric and semiparametric estimators are proposed, asymptotic distribution theory is provided and finite sample performance is investigated. For illustration we characterize the age-adjusted discriminatory accuracy of prostate-specific antigen as a biomarker for prostate cancer.

Nonparametric additive regression for repeatedly measured data

Carroll, R. J., Maity, A., Mammen, E., Yu, K. — 2009-05-20

We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements. We allow for a working covariance matrix for the regression errors, showing that our method is most efficient when the correct covariance matrix is used. The component functions achieve the known asymptotic variance lower bound for the scalar argument case. Smooth backfitting also leads directly to design-independent biases in the local linear case. Simulations show our estimator has smaller variance than the usual kernel estimator. This is also illustrated by an example from nutritional epidemiology.

Optimal testing of multiple hypotheses with common effect direction

Bittman, R. M., Romano, J. P., Vallarino, C., Wolf, M. — 2009-05-20

We present a theoretical basis for testing related endpoints. Typically, it is known how to construct tests of the individual hypotheses, but not how to combine them into a multiple test procedure that controls the familywise error rate. Using the closure method, we emphasize the role of consonant procedures, from an interpretive as well as a theoretical viewpoint. Surprisingly, even if each intersection test has an optimality property, the overall procedure obtained by applying closure to these tests may be inadmissible. We introduce a new procedure, which is consonant and has a maximin property under the normal model. The results are then applied to PROactive, a clinical trial designed to investigate the effectiveness of a glucose-lowering drug on macrovascular outcomes among patients with type 2 diabetes.

Non-finite Fisher information and homogeneity: an EM approach

Li, P., Chen, J., Marriott, P. — 2009-05-20

Even simple examples of finite mixture models can fail to fulfil the regularity conditions that are routinely assumed in standard parametric inference problems. Many methods have been investigated for testing for homogeneity in finite mixture models, for example, but all rely on regularity conditions including the finiteness of the Fisher information and the space of the mixing parameter being a compact subset of some Euclidean space. Very simple examples where such assumptions fail include mixtures of two geometric distributions and two exponential distributions, and, more generally, mixture models in scale distribution families. To overcome these difficulties, we propose and study an em-test statistic, which has a simple limiting distribution for examples in this paper. Simulations show that the em-test has accurate Type I errors and is more efficient than existing methods when they are applicable. A real example is included.

Double block bootstrap confidence intervals for dependent data

Lee, S. M. S., Lai, P. Y. — 2009-05-20

The block bootstrap confidence interval for dependent data can outperform the conventional normal approximation only with nontrivial studentization which, in the case of complicated statistics, calls for specialist treatment and often results in unstable endpoints. We propose two double block bootstrap approaches for improving the accuracy of the block bootstrap confidence interval under very general conditions. The first approach calibrates the nominal coverage level and the second calculates studentizing factors directly from a block bootstrap series without the need for nontrivial analytical treatment. We prove that the two approaches reduce the coverage error of the block bootstrap interval by an order of magnitude with simple tuning of block lengths at the two block bootstrapping levels. Empirical properties of the procedures are investigated by simulations and application to an econometric time series.

Marginal analysis of panel counts through estimating functions

Hu, X. J., Lagakos, S. W., Lockhart, R. A. — 2009-05-20

We develop nonparametric estimation procedures for the marginal mean function of a counting process based on periodic observations, using two types of self-consistent estimating equations. The first is derived from the likelihood studied by Wellner & Zhang (2000), assuming a Poisson counting process. It gives a nondecreasing estimator, which equals the nonparametric maximum likelihood estimator of Wellner & Zhang and is consistent without the Poisson assumption. Motivated by the construction of parametric generalized estimating equations, the second type is a set of data-adaptive quasi-score functions, which are likelihood estimating functions under a mixed-Poisson assumption. We evaluate the procedures using simulation, and illustrate them with the data from a bladder cancer study.

Jackknife estimation of mean squared error of small area predictors in nonlinear mixed models

Lohr, S. L., Rao, J. N. K. — 2009-05-20

Empirical Bayes predictors of small area parameters of interest are often obtained under a linear mixed model for continuous response data or a generalized linear mixed model for binary responses or count data. However, estimation of the unconditional mean squared error of prediction is complicated, particularly for a nonlinear mixed model. Jiang et al. (2002) proposed a jackknife method for estimating the unconditional mean squared error and showed that the resulting estimator is nearly unbiased. The leading term of this estimator does not depend on the area-specific responses in the nonlinear case, whereas the posterior variance of the small area parameter given the model parameters is area-specific. Rao (2003) proposed an alternative method that leads to a computationally simpler jackknife estimator with an area-specific leading term. We show that a modification of Rao's method leads to a nearly unbiased area-specific jackknife estimator, which is also nearly unbiased for the conditional mean squared error given the area-specific responses. We examine the relative performances of the jackknife estimators, conditionally as well as unconditionally, in a simulation study, and apply the proposed method to estimate small area mean squared errors in disease mapping problems.

Scale adjustments for classifiers in high-dimensional, low sample size settings

Chan, Y.-B., Hall, P. — 2009-05-20

Distance-based classifiers are generally considered to be effective at discriminating between populations that differ in location. Indeed, nearest-neighbour methods and the support vector machine are frequently used in very high-dimensional problems involving gene expression data, where it is believed that elevated levels of expression convey much of the information for classification. However, one problem inherent to distance-based classifiers is that scale differences can mask location differences. In consequence, such classifiers can have poor performance if the information for classification accumulates through a large number of relatively small location differences in data components, rather than via large differences. In this paper, we show that a simple adjustment for scale, applicable to a variety of distance-based classifiers, can remedy the problem. For some classifiers, such as those based on the support vector machine or the centroid method, scale corrections are important primarily in the case of small training-sample sizes. However, for other classifiers, including those based on nearest-neighbour and average-distance methods, scale adjustments are helpful more generally.

Saddlepoint approximation for mixture models

Davison, A. C., Mastropietro, D. — 2009-05-20

Two-component mixture distributions with one component a point mass and the other a continuous density may be used as priors for Bayesian inference when sparse representation of an underlying signal is required. We show how saddlepoint approximation in such models can yield highly accurate quantiles for posterior distributions, and illustrate this numerically, using wavelet regression with point mass/Laplace and point mass/normal prior distributions.

Some results on D-optimal designs for nonlinear models with applications

Li, G., Majumdar, D. — 2009-05-20

Sufficient conditions are established for the locally D$-optimal design for a nonlinear model to have a minimal number of support points. The conditions are applied to obtain locally D-optimal designs for a one-compartment pharmacokinetic model and a Poisson regression model.

Dimension reduction in time series and the dynamic factor model

Pena, D. — 2009-05-20

This note shows that the dimension reduction method proposed by Li & Shedden (2002) is equivalent to the dynamic factor model introduced by Peña & Box (1987).