A multivariate von mises distribution with applications to bioinformatics

Motivated by problems of modelling torsional angles in molecules, Singh, Hnizdo & Demchuk (2002) proposed a bivariate circular model which is a natural torus analogue of the bivariate normal distribution and a natural extension of the univariate von Mises distribution to the bivariate case. The authors present here a multivariate extension of the bivariate model of Singh, Hnizdo & Demchuk (2002). They study the conditional distributions and investigate the shapes of marginal distributions for a special case. The methods of moments and pseudo‐likelihood are considered for the estimation of parameters of the new distribution. The authors investigate the efficiency of the pseudo‐likelihood approach in three dimensions. They illustrate their methods with protein data of conformational angles     

ASYMPTOTIC DISTRIBUTIONS OF SEMIPARAMETRIC MAXIMUM LIKELIHOOD ESTIMATORS WITH ESTIMATING EQUATIONS FOR GROUP-CENSORED DATA

Semiparametric maximum likelihood estimation with estimating equations (SMLE) is more flexible than traditional methods; it has fewer restrictions on distributions and regression models. The required information about distribution and regression structures is incorporated in estimating equations of the SMLE to improve the estimation quality of non‐parametric methods. The likelihood of SMLE for censored data involves complicated implicit functions without closed‐form expressions, and the first derivatives of the log‐profile‐likelihood cannot be expressed as summations of independent and identically distributed random variables; it is challenging to derive asymptotic properties of the SMLE for censored data. For group‐censored data, the paper shows that all the implicit functions are well defined and obtains the asymptotic distributions of the SMLE for model parameters and lifetime distributions. With several examples the paper compares the SMLE, the regular non‐parametric likelihood estimation method and the parametric MLEs in terms of their asymptotic efficiencies, and illustrates application of SMLE. Various asymptotic distributions of the likelihood ratio statistics are derived for testing the adequacy of estimating equations and a partial set of parameters equal to some known values.     

Nonparametric estimation of the bivariate cdf for arbitrarily censored data

Right, left or interval censored multivariate data can be represented by an intersection graph. Focussing on the bivariate case, the authors relate the structure of such an intersection graph to the support of the nonparametric maximum likelihood estimate (NPMLE) of the cumulative distribution function (CDF) for such data. They distinguish two types of non‐uniqueness of the NPMLE: representational, arising when the likelihood is unaffected by the distribution of the estimated probability mass within regions, and mixture, arising when the masses themselves are not unique. The authors provide a brief overview of estimation techniques and examine three data sets.     

Testing for two states in a hidden Markov model

The authors consider hidden Markov models (HMMs) whose latent process has m ≥ 2 states and whose state‐dependent distributions arise from a general one‐parameter family. They propose a test of the hypothesis m = 2. Their procedure is an extension to HMMs of the modified likelihood ratio statistic proposed by Chen, Chen & Kalbfleisch (2004) for testing two states in a finite mixture. The authors determine the asymptotic distribution of their test under the hypothesis m = 2 and investigate its finite‐sample properties in a simulation study. Their test is based on inference for the marginal mixture distribution of the HMM. In order to illustrate the additional difficulties due to the dependence structure of the HMM, they show how to test general regular hypotheses on the marginal mixture of HMMs via a quasi‐modified likelihood ratio. They also discuss two applications.     

Orthogonalized Residuals for Estimation of Marginally Specified Association Parameters in Multivariate Binary Data

Abstract. This paper focuses on marginal regression models for correlated binary responses when estimation of the association structure is of primary interest. A new estimating function approach based on orthogonalized residuals is proposed. A special case of the proposed procedure allows a new representation of the alternating logistic regressions method through marginal residuals. The connections between second‐order generalized estimating equations, alternating logistic regressions, pseudo‐likelihood and other methods are explored. Efficiency comparisons are presented, with emphasis on variable cluster size and on the role of higher‐order assumptions. The new method is illustrated with an analysis of data on impaired pulmonary function.     

Modelling and analysis of recall-based competing risks data

In this paper we consider the analysis of recall-based competing risks data. The chance of an individual recalling the exact time to event depends on the time of occurrence of the event and time of observation of the individual. In particular, it is assumed that the probability of recall depends on the time elapsed since the occurrence of an event. In this study we consider the likelihood-based inference for the analysis of recall-based competing risks data. The likelihood function is constructed by incorporating the information about the probability of recall. We consider the maximum likelihood estimation of parameters. Simulation studies are carried out to examine the performance of the estimators. The proposed estimation procedure is applied to a real life data set.     

SIMULATED MAXIMUM LIKELIHOOD APPLIED TO NON-GAUSSIAN AND NONLINEAR MIXED EFFECTS AND STATE–SPACE MODELS

The paper presents an overview of maximum likelihood estimation using simulated likelihood, including the use of antithetic variables and evaluation of the simulation error of the resulting estimates. It gives a general purpose implementation of simulated maximum likelihood and uses it to re‐visit four models that have previously appeared in the published literature: a state–space model for count data; a nested random effects model for binomial data; a nonlinear growth model with crossed random effects; and a crossed random effects model for binary salamander‐mating data. In the case of the last three examples, this appears to be the first time that maximum likelihood fits of these models have been presented.     

A weighted Poisson distribution and its application to cure rate models

The family of weighted Poisson distributions offers great flexibility in modeling discrete data due to its potential to capture over/under-dispersion by an appropriate selection of the weight function. In this paper, we introduce a flexible weighted Poisson distribution and further study its properties by using it in the context of cure rate modeling under a competing cause scenario. A special case of the new distribution is the COM-Poisson distribution which in turn encompasses the Bernoulli, Poisson, and geometric distributions; hence, many of the well-studied cure rate models may be seen as special cases of the proposed model. We focus on the estimation, through the maximum likelihood method, of the cured proportion and the properties of the failure time of the susceptibles/non cured individuals; a profile likelihood approach is also adopted for estimating the parameters of the weighted Poisson distribution. A Monte Carlo simulation study demonstrates the accuracy of the proposed inferential method. Finally, as an illustration, we fit the proposed model to a cutaneous melanoma data set.     

Interval censoring: Model characterizations for the validity of the simplified likelihood

In survival data analysis, the interval censoring problem has generally been treated via likelihood methods. Because this likelihood is complex, it is often assumed that the censoring mechanisms do not affect the mortality process. The authors specify conditions that ensure the validity of such a simplified likelihood. They prove the equivalence between different characterizations of noninformative censoring and define a constant‐sum condition analogous to the one derived in the context of right censoring. They also prove that when the noninformative or constant‐sum condition holds, the simplified likelihood can be used to obtain the nonparametric maximum likelihood estimator of the death time distribution function.     

A New Model for Multivariate Markov Chains

We propose a new model for multivariate Markov chains of order one or higher on the basis of the mixture transition distribution (MTD) model. We call it the MTD‐Probit. The proposed model presents two attractive features: it is completely free of constraints, thereby facilitating the estimation procedure, and it is more precise at estimating the transition probabilities of a multivariate or higher‐order Markov chain than the standard MTD model.     

General mixed‐data model: Extension of general location and grouped continuous models

The authors propose a general model for the joint distribution of nominal, ordinal and continuous variables. Their work is motivated by the treatment of various types of data. They show how to construct parameter estimates for their model, based on the maximization of the full likelihood. They provide algorithms to implement it, and present an alternative estimation method based on the pairwise likelihood approach. They also touch upon the issue of statistical inference. They illustrate their methodology using data from a foreign language achievement study.     

Computing Critical Values of Exact Tests by Incorporating Monte Carlo Simulations Combined with Statistical Tables

Various exact tests for statistical inference are available for powerful and accurate decision rules provided that corresponding critical values are tabulated or evaluated via Monte Carlo methods. This article introduces a novel hybrid method for computing p‐values of exact tests by combining Monte Carlo simulations and statistical tables generated a priori. To use the data from Monte Carlo generations and tabulated critical values jointly, we employ kernel density estimation within Bayesian‐type procedures. The p‐values are linked to the posterior means of quantiles. In this framework, we present relevant information from the Monte Carlo experiments via likelihood‐type functions, whereas tabulated critical values are used to reflect prior distributions. The local maximum likelihood technique is employed to compute functional forms of prior distributions from statistical tables. Empirical likelihood functions are proposed to replace parametric likelihood functions within the structure of the posterior mean calculations to provide a Bayesian‐type procedure with a distribution‐free set of assumptions. We derive the asymptotic properties of the proposed nonparametric posterior means of quantiles process. Using the theoretical propositions, we calculate the minimum number of needed Monte Carlo resamples for desired level of accuracy on the basis of distances between actual data characteristics (e.g. sample sizes) and characteristics of data used to present corresponding critical values in a table. The proposed approach makes practical applications of exact tests simple and rapid. Implementations of the proposed technique are easily carried out via the recently developed STATA and R statistical packages.     

Local influence for generalized linear mixed models

The authors describe a method for assessing model inadequacy in maximum likelihood estimation of a generalized linear mixed model. They treat the latent random effects in the model as missing data and develop the influence analysis on the basis of a Q‐function which is associated with the conditional expectation of the complete‐data log‐likelihood function in the EM algorithm. They propose a procedure to detect influential observations in six model perturbation schemes. They also illustrate their methodology in a hypothetical situation and in two real cases.     

A unified empirical likelihood approach for testing MCAR and subsequent estimation

For an estimation with missing data, a crucial step is to determine if the data are missing completely at random (MCAR), in which case a complete‐case analysis would suffice. Most existing tests for MCAR do not provide a method for a subsequent estimation once the MCAR is rejected. In the setting of estimating means, we propose a unified approach for testing MCAR and the subsequent estimation. Upon rejecting MCAR, the same set of weights used for testing can then be used for estimation. The resulting estimators are consistent if the missingness of each response variable depends only on a set of fully observed auxiliary variables and the true outcome regression model is among the user‐specified functions for deriving the weights. The proposed method is based on the calibration idea from survey sampling literature and the empirical likelihood theory.     

Smooth Plug‐in Inverse Estimators in the Current Status Continuous Mark Model

Abstract. We consider the problem of estimating the joint distribution function of the event time and a continuous mark variable when the event time is subject to interval censoring case 1 and the continuous mark variable is only observed in case the event occurred before the time of inspection. The non‐parametric maximum likelihood estimator in this model is known to be inconsistent. We study two alternative smooth estimators, based on the explicit (inverse) expression of the distribution function of interest in terms of the density of the observable vector. We derive the pointwise asymptotic distribution of both estimators.     

Estimation of parameters for trend-renewal processes

Methods of estimating unknown parameters of a trend function for trend-renewal processes are investigated in the case when the renewal distribution function is unknown. If the renewal distribution is unknown, then the likelihood function of the trend-renewal process is unknown and consequently the maximum likelihood method cannot be used. In such a situation we propose three other methods of estimating the trend parameters. The methods proposed can also be used to predict future occurrence times. The performance of the estimators based on these methods is illustrated numerically for some trend-renewal processes for which the statistical inference is analytically intractable.     

An additive–multiplicative mean model for panel count data with dependent observation and dropout processes

This paper discusses regression analysis of panel count data with dependent observation and dropout processes. For the problem, a general mean model is presented that can allow both additive and multiplicative effects of covariates on the underlying point process. In addition, the proportional rates model and the accelerated failure time model are employed to describe possible covariate effects on the observation process and the dropout or follow‐up process, respectively. For estimation of regression parameters, some estimating equation‐based procedures are developed and the asymptotic properties of the proposed estimators are established. In addition, a resampling approach is proposed for estimating a covariance matrix of the proposed estimator and a model checking procedure is also provided. Results from an extensive simulation study indicate that the proposed methodology works well for practical situations, and it is applied to a motivating set of real data.     

Variable Selection for Panel Count Data via Non-Concave Penalized Estimating Function

Abstract.  Variable selection is an important issue in all regression analyses, and in this paper we discuss this in the context of regression analysis of panel count data. Panel count data often occur in long-term studies that concern occurrence rate of a recurrent event, and their analysis has recently attracted a great deal of attention. However, there does not seem to exist any established approach for variable selection with respect to panel count data. For the problem, we adopt the idea behind the non-concave penalized likelihood approach and develop a non-concave penalized estimating function approach. The proposed methodology selects variables and estimates regression coefficients simultaneously, and an algorithm is presented for this process. We show that the proposed procedure performs as well as the oracle procedure in that it yields the estimates as if the correct submodel were known. Simulation studies are conducted for assessing the performance of the proposed approach and suggest that it works well for practical situations. An illustrative example from a cancer study is provided.     

Semi-parametric modelling and likelihood estimation with estimating equations

This paper proposes a semi-parametric modelling and estimating method for analysing censored survival data. The proposed method uses the empirical likelihood function to describe the information in data, and formulates estimating equations to incorporate knowledge of the underlying distribution and regression structure. The method is more flexible than the traditional methods such as the parametric maximum likelihood estimation (MLE), Cox's (1972) proportional hazards model, accelerated life test model, quasi-likelihood (Wedderburn, 1974) and generalized estimating equations (Liang & Zeger, 1986). This paper shows the existence and uniqueness of the proposed semi-parametric maximum likelihood estimates (SMLE) with estimating equations. The method is validated with known cases studied in the literature. Several finite sample simulation and large sample efficiency studies indicate that when the sample size is larger than 100 the SMLE is compatible with the parametric MLE; and in all case studies, the SMLE is about 15% better than the parametric MLE with a mis-specified underlying distribution.     

Adjusted empirical likelihood models with estimating equations for accelerated life tests

This article proposes an adjusted empirical likelihood estimation (AMELE) method to model and analyze accelerated life testing data. This approach flexibly and rigorously incorporates distribution assumptions and regression structures by estimating equations within a semiparametric estimation framework. An efficient method is provided to compute the empirical likelihood estimates, and asymptotic properties are studied. Real-life examples and numerical studies demonstrate the advantage of the proposed methodology.