The ensemble Kalman filter is an ABC algorithm

The ensemble Kalman filter is the method of choice for many difficult high-dimensional filtering problems in meteorology, oceanography, hydrology and other fields. In this note we show that a common variant of the ensemble Kalman filter is an approximate Bayesian computation (ABC) algorithm. This is of interest for a number of reasons. First, the ensemble Kalman filter is an example of an ABC algorithm that predates the development of ABC algorithms. Second, the ensemble Kalman filter is used for very high-dimensional problems, whereas ABC methods are normally applied only in very low-dimensional problems. Third, recent state of the art extensions of the ensemble Kalman filter can also be understood within the ABC framework.     

Bayesian Estimation of Survival Functions under Stochastic Precedence

When estimating the distributions of two random variables, X and Y, investigators often have prior information that Y tends to be bigger than X. To formalize this prior belief, one could potentially assume stochastic ordering between X and Y, which implies Pr(X < or = z) > or = Pr(Y < or = z) for all z in the domain of X and Y. Stochastic ordering is quite restrictive, though, and this article focuses instead on Bayesian estimation of the distribution functions of X and Y under the weaker stochastic precedence constraint, Pr(X < or = Y) > or = 0.5. We consider the case where both X and Y are categorical variables with common support and develop a Gibbs sampling algorithm for posterior computation. The method is then generalized to the case where X and Y are survival times. The proposed approach is illustrated using data on survival after tumor removal for patients with malignant melanoma.     

Marginal Means/Rates Models for Multiple Type Recurrent Event Data

Recurrent events are frequently observed in biomedical studies, and often more than one type of event is of interest. Follow-up time may be censored due to loss to follow-up or administrative censoring. We propose a class of semi-parametric marginal means/rates models, with a general relative risk form, for assessing the effect of covariates on the censored event processes of interest. We formulate estimating equations for the model parameters, and examine asymptotic properties of the parameter estimators. Finite sample properties of the regression coefficients are examined through simulations. The proposed methods are applied to a retrospective cohort study of risk factors for preschool asthma.     

Tests for a difference in timing of physiological response between two brain regions measured by using functional magnetic resonance imaging

Summary.  Functional magnetic resonance imaging (FMRI) measures the physiological response of the human brain to experimentally controlled stimulation. In a periodically designed experiment it is of interest to test for a difference in the timing (phase shift) of the response between two anatomically distinct brain regions. We suggest two tests for an interregional difference in phase shift: one based on asymptotic theory and one based on bootstrapping. Whilst the two procedures differ in some of their assumptions, both tests rely on employing the large number of voxels (three-dimensional pixels) in non-activated brain regions to take account of spatial autocorrelation between voxelwise phase shift observations within the activated regions of interest. As an example we apply both tests, and their counterparts assuming spatial independence, to FMRI phase shift data that were acquired from a normal young woman during performance of a periodically designed covert verbal fluency task. We conclude that it is necessary to take account of spatial autocovariance between voxelwise FMRI time series parameter estimates such as the phase shift, and that the most promising way of achieving this is by modelling the spatial autocorrelation structure from a suitably defined base region of the image slice.     

Bayesian analysis of discrete time warranty data

Summary.  The analysis of warranty claim data, and their use for prediction, has been a topic of active research in recent years. Field data comprising numbers of units returned under guarantee are examined, covering both situations in which the ages of the failed units are known and in which they are not. The latter case poses particular computational problems for likelihood-based methods because of the large number of feasible failure patterns that must be included as contributions to the likelihood function. For prediction of future warranty exposure, which is of central concern to the manufacturer, the Bayesian approach is adopted. For this, Markov chain Monte Carlo methodology is developed.     

Recurrence relations for moments of progressively censored order statistics from logistic distribution with applications to inference

In this paper, we establish several recurrence relations for the single and product moments of progressively Type-II right censored order statistics from a logistic distribution. The use of these relations in a systematic manner allows us to compute all the means, variances and covariances of progressively Type-II right censored order statistics from the logistic distribution for all sample sizes n, effective sample sizes m, and all progressive censoring schemes (R₁,…,R_m). The results established here generalize the corresponding results for the usual order statistics due to [Shah, 1966] and [Shah, 1970]. These moments are then utilized to derive best linear unbiased estimators of the location and scale parameters of the logistic distribution. A comparison of these estimators with the maximum likelihood estimations is then made. The best linear unbiased predictors of censored failure times are briefly discussed. Finally, an illustrative example is presented.     

Reliability analysis of consecutive k-out-of-n systems with non-identical components lifetimes

In recent years, the study of reliability properties of consecutive k-out-of-n systems has attracted a great deal of attention from both theoretical and practical perspectives. In this paper we consider linear and circular consecutive k-out-of-n systems. It is assumed that lifetimes of components of the systems are independent but their probability distributions are non-identical. We study the reliability properties of the residual lifetimes of such systems under the condition that at least (n−r+1), r≤n, components of the system are operating. We also investigate the probability that a specific number of components of the above-mentioned system operate at time t, t>0, under the condition that the system is alive at time t.     

Why a Bayesian approach to safety analysis in pharmacovigilance is important

Large databases of routinely collected data are a valuable source of information for detecting potential associations between drugs and adverse events (AE). A pharmacovigilance system starts with a scan of these databases for potential signals of drug-AE associations that will subsequently be examined by experts to aid in regulatory decision-making. The signal generation process faces some key challenges: (1) an enormous volume of drug-AE combinations need to be tested (i.e. the problem of multiple testing); (2) the results are not in a format that allows the incorporation of accumulated experience and knowledge for future signal generation; and (3) the signal generation process ignores information captured from other processes in the pharmacovigilance system and does not allow feedback. Bayesian methods have been developed for signal generation in pharmacovigilance, although the full potential of these methods has not been realised. For instance, Bayesian hierarchical models will allow the incorporation of established medical and epidemiological knowledge into the priors for each drug-AE combination. Moreover, the outputs from this analysis can be incorporated into decision-making tools to help in signal validation and posterior actions to be taken by the regulators and companies. We discuss in this paper the apparent advantage of the Bayesian methods used in safety signal generation and the similarities and differences between the two widely used Bayesian methods. We will also propose the use of Bayesian hierarchical models to address the three key challenges and discuss the reasons why Bayesian methodology still have not been fully utilised in pharmacovigilance activities.     

A course for clinical trial personnel in clinical study designs, randomization, allocation schedules, and interactive response systems

This continuing education course for professionals involved in all areas of clinical trials integrates concepts related to the role of randomization in the scientific process. The course includes two interactive lecture and discussion sections and a workshop practicum. The first interactive lecture introduces basic clinical trial issues and statistical principles such as bias, blinding, randomization, control groups, and the importance of formulating clear and discriminating clinical and statistical hypotheses. It then focuses on the most commonly used clinical study designs and the corresponding patient randomization schemes. The second interactive lecture focuses on the implementation of randomization of patients and drug supply through allocation and component ID schedules. The workshop practicum, conducted in small groups, enables students to apply the lecture concepts to real clinical studies. Flexibility was built into the workshop practicum materials to allow the course content to be customized to specific audiences, and the interactive lecture sessions can be stretched to cover more advanced topics according to class interest and time availability.