Cox regression of clustered event times with covariates missing not at random

Motivated by a recent tuberculosis (TB) study, this paper is concerned with covariates missing not at random (MNAR) and models the potential intracluster correlation by a frailty. We consider the regression analysis of right‐censored event times from clustered subjects under a Cox proportional hazards frailty model and present the semiparametric maximum likelihood estimator (SPMLE) of the model parameters. An easy‐to‐implement pseudo‐SPMLE is then proposed to accommodate more realistic situations using readily available supplementary information on the missing covariates. Algorithms are provided to compute the estimators and their consistent variance estimators. We demonstrate that both the SPMLE and the pseudo‐SPMLE are consistent and asymptotically normal by the arguments based on the theory of modern empirical processes. The proposed approach is examined numerically via simulation and illustrated with an analysis of the motivating TB study data.     

Learning from a lot: Empirical Bayes for high‐dimensional model‐based prediction

Empirical Bayes is a versatile approach to “learn from a lot” in two ways: first, from a large number of variables and, second, from a potentially large amount of prior information, for example, stored in public repositories. We review applications of a variety of empirical Bayes methods to several well‐known model‐based prediction methods, including penalized regression, linear discriminant analysis, and Bayesian models with sparse or dense priors. We discuss “formal” empirical Bayes methods that maximize the marginal likelihood but also more informal approaches based on other data summaries. We contrast empirical Bayes to cross‐validation and full Bayes and discuss hybrid approaches. To study the relation between the quality of an empirical Bayes estimator and p, the number of variables, we consider a simple empirical Bayes estimator in a linear model setting. We argue that empirical Bayes is particularly useful when the prior contains multiple parameters, which model a priori information on variables termed “co‐data”. In particular, we present two novel examples that allow for co‐data: first, a Bayesian spike‐and‐slab setting that facilitates inclusion of multiple co‐data sources and types and, second, a hybrid empirical Bayes–full Bayes ridge regression approach for estimation of the posterior predictive interval.     

Confidence intervals based on the deviance statistic for the hyperparameters in state space models

The main objective of this work is to evaluate the performance of confidence intervals, built using the deviance statistic, for the hyperparameters of state space models. The first procedure is a marginal approximation to confidence regions, based on the likelihood test, and the second one is based on the signed root deviance profile. Those methods are computationally efficient and are not affected by problems such as intervals with limits outside the parameter space, which can be the case when the focus is on the variances of the errors. The procedures are compared to the usual approaches existing in the literature, which includes the method based on the asymptotic distribution of the maximum likelihood estimator, as well as bootstrap confidence intervals. The comparison is performed via a Monte Carlo study, in order to establish empirically the advantages and disadvantages of each method. The results show that the methods based on the deviance statistic possess a better coverage rate than the asymptotic and bootstrap procedures.     

On approximations via convolution-defined mixture models

An often-cited fact regarding mixing or mixture distributions is that their density functions are able to approximate the density function of any unknown distribution to arbitrary degrees of accuracy, provided that the mixing or mixture distribution is sufficiently complex. This fact is often not made concrete. We investigate and review theorems that provide approximation bounds for mixing distributions. Connections between the approximation bounds of mixing distributions and estimation bounds for the maximum likelihood estimator of finite mixtures of location-scale distributions are reviewed.     

An extended semiparametric model for short-term and long-term hazard ratios

In survival analysis, one way to deal with non-proportional hazards is to model short-term and long-term hazard ratios. The existing model of this nature has no control over how fast the hazard ratio is changing over time. We add a parameter to the existing model to allow the hazard ratio to change over time at different speed. A nonparametric maximum likelihood approach is used to estimate the model parameters. The existing model is a special case of the extended model when the speed parameter is 0, which leads naturally to a way of testing the adequacy of the existing model. Simulation results show that there can be substantial bias in the estimation of the short-term and long-term hazard ratio if the speed parameter is fixed incorrectly at 0 rather than estimated. The extended model is fitted to three real data sets to shed new insights, including the observation that converging hazards does not necessarily imply the odds are proportional.     

A dimensionality reduction method of continuous dependent variables based supervised Laplacian eigenmaps

Dimensionality reduction is one of the important preprocessing steps in high-dimensional data analysis. In this paper we propose a supervised manifold learning method, it makes use of the information of continuous dependent variables to distinguish intrinsic neighbourhood and extrinsic neighbourhood of data samples, and construct two graphs according to these two kinds of neighbourhoods. Following the idea of Laplacian eigenmaps, we reveal that on the low-dimensional manifold the neighbourhood structure can be preserved or even improved. Our approach has two important characteristics: (i) it uses dependent variables to find an informative low-dimensional projection which is robust to noisy independent variables and (ii) the objective function simultaneously enlarges the distance between dissimilar samples and pushes similar samples close to each other according to the graph constructed with the help of continuous dependent variables. Our experiments demonstrate that the effectiveness of our method is over their traditional rivals.     

Progressive censoring with fixed censoring times

In this paper, we revisit the progressive Type-I censoring scheme as it has originally been introduced by Cohen [Progressively censored samples in life testing. Technometrics. 1963;5(3):327–339]. In fact, original progressive Type-I censoring proceeds as progressive Type-II censoring but with fixed censoring times instead of failure time based censoring times. Apparently, a time truncation has been added to this censoring scheme by interpreting the final censoring time as a termination time. Therefore, not much work has been done on Cohens's original progressive censoring scheme with fixed censoring times. Thus, we discuss distributional results for this scheme and establish exact distributional results in likelihood inference for exponentially distributed lifetimes. In particular, we obtain the exact distribution of the maximum likelihood estimator (MLE). Further, the stochastic monotonicity of the MLE is verified in order to construct exact confidence intervals for both the scale parameter and the reliability.     

Theoretical results on the discrete Weibull distribution of Nakagawa and Osaki

In this paper, we discuss some theoretical results and properties of the discrete Weibull distribution, which was introduced by Nakagawa and Osaki [The discrete Weibull distribution. IEEE Trans Reliab. 1975;24:300–301]. We study the monotonicity of the probability mass, survival and hazard functions. Moreover, reliability, moments, p-quantiles, entropies and order statistics are also studied. We consider likelihood-based methods to estimate the model parameters based on complete and censored samples, and to derive confidence intervals. We also consider two additional methods to estimate the model parameters. The uniqueness of the maximum likelihood estimate of one of the parameters that index the discrete Weibull model is discussed. Numerical evaluation of the considered model is performed by Monte Carlo simulations. For illustrative purposes, two real data sets are analyzed.     

Semiparametric regression of clustered current status data

This paper discusses regression analysis of clustered current status data under semiparametric additive hazards models. In particular, we consider the situation when cluster sizes can be informative about correlated failure times from the same cluster. To address the problem, we present estimating equation-based estimation procedures and establish asymptotic properties of the resulting estimates. Finite sample performance of the proposed method is assessed through an extensive simulation study, which indicates the procedure works well. The method is applied to a motivating data set from a lung tumorigenicity study.     

Improved two-parameter estimators for the negative binomial and Poisson regression models

Negative binomial regression (NBR) and Poisson regression (PR) applications have become very popular in the analysis of count data in recent years. However, if there is a high degree of relationship between the independent variables, the problem of multicollinearity arises in these models. We introduce new two-parameter estimators (TPEs) for the NBR and the PR models by unifying the two-parameter estimator (TPE) of Özkale and Kaç?ranlar [The restricted and unrestricted two-parameter estimators. Commun Stat Theory Methods. 2007;36:2707–2725]. These new estimators are general estimators which include maximum likelihood (ML) estimator, ridge estimator (RE), Liu estimator (LE) and contraction estimator (CE) as special cases. Furthermore, biasing parameters of these estimators are given and a Monte Carlo simulation is done to evaluate the performance of these estimators using mean square error (MSE) criterion. The benefits of the new TPEs are also illustrated in an empirical application. The results show that the new proposed TPEs for the NBR and the PR models are better than the ML estimator, the RE and the LE.