Bayesian predictive power: choice of prior and some recommendations for its use as probability of success in drug development

Bayesian predictive power, the expectation of the power function with respect to a prior distribution for the true underlying effect size, is routinely used in drug development to quantify the probability of success of a clinical trial. Choosing the prior is crucial for the properties and interpretability of Bayesian predictive power. We review recommendations on the choice of prior for Bayesian predictive power and explore its features as a function of the prior. The density of power values induced by a given prior is derived analytically and its shape characterized. We find that for a typical clinical trial scenario, this density has a u‐shape very similar, but not equal, to a β‐distribution. Alternative priors are discussed, and practical recommendations to assess the sensitivity of Bayesian predictive power to its input parameters are provided. Copyright © 2016 John Wiley & Sons, Ltd.     

Bias Reduction in Logistic Regression with Missing Responses When the Missing Data Mechanism is Nonignorable

ABSTRACT

In logistic regression with nonignorable missing responses, Ibrahim and Lipsitz proposed a method for estimating regression parameters. It is known that the regression estimates obtained by using this method are biased when the sample size is small. Also, another complexity arises when the iterative estimation process encounters separation in estimating regression coefficients. In this article, we propose a method to improve the estimation of regression coefficients. In our likelihood-based method, we penalize the likelihood by multiplying it by a noninformative Jeffreys prior as a penalty term. The proposed method reduces bias and is able to handle the issue of separation. Simulation results show substantial bias reduction for the proposed method as compared to the existing method. Analyses using real world data also support the simulation findings. An R package called brlrmr is developed implementing the proposed method and the Ibrahim and Lipsitz method.     

Generating random variates from D-distributions via substitution sampling

Laud et al. (1993) describe a method for random variate generation from D-distributions. In this paper an alternative method using substitution sampling is given. An algorithm for the random variate generation from SD-distributions is also given.     

Random variate generation from D-distributions

Within the context of non-parametric Bayesian inference, Dykstra and Laud (1981) define an extended gamma (EG) process and use it as a prior on increasing hazard rates. The attractive features of the extended gamma (EG) process, among them its capability to index distribution functions that are absolutely continuous, are offset by the intractable nature of the computation that needs to be performed. Sampling based approaches such as the Gibbs Sampler can alleviate these difficulties but the EG processes then give rise to the problem of efficient random variate generation from a class of distributions called D-distributions. In this paper, we describe a novel technique for sampling from such distributions, thereby providing an efficient computation procedure for non-parametric Bayesian inference with a rich class of priors for hazard rates.     

On forecasting with univariate autoregressive processes: a bayesian approach

Using a normal-gamma prior density for the parameters of a p-th order autoregressive process, the Bayesian predictive density of k future observations is derived and it is shown that it is the product of k univariate t densities. Our results are illustrated with one step ahead forecasts employing AR(1) and AR(2) models with a vague prior density for the parameters.     

Some properties of the dirichlet-multinomial distribution and its use in prior elicitation

Two results on the unimodality of the Dirichlet-multinomial distribution are proved, and a further result is alos proved on the identifiability of mixtures of multinomial distributions. These properties are used in developing a method for eliciting a Dirchlet prior distribution. The elicitation method is based on the mode, and region around the mode, of the Dirichlet-multinomial predictive distribution.     

Estimation of random coefficient regression models

Linear regression models with coefficients across individual units regarded as random samples from some population are studied in this article from a Bayesian viewpoint. A prior distribution of the secondary parameters is derived following the Jeffreys rule. Posterior distribution of the primary and secondary parameters, and the predictive distribution of the future value are then examined. Computations of the parameter estimates are found to be rather straightforward. Data from a performance test on pigs is analysed and discussed. We also discuss the difficulties involved in using a Lindley and Smith (1972) prior in this problem.     

Bayesian Estimation for Deformed Modified Power Series Distribution

In this article, posterior distribution, posterior moments, and predictive distribution for the modified power series distributions deformed at any of a support point under linex and generalized entropy loss function are derived. It is assumed that the prior information can be summarized by a uniform, Beta, two-sided power, Gamma, or generalized Pareto distributions. The obtained results are demonstrated on the generalized Poisson and the generalized negative binomial distribution deformed at a given point.     

Using the EM-algorithm for survival data with incomplete categorical covariates

Incomplete covariate data is a common occurrence in many studies in which the outcome is survival time. With generalized linear models, when the missing covariates are categorical, a useful technique for obtaining parameter estimates is the EM by the method of weights proposed in Ibrahim (1990). In this article, we extend the EM by the method of weights to survival outcomes whose distributions may not fall in the class of generalized linear models. This method requires the estimation of the parameters of the distribution of the covariates. We present a clinical trials example with five covariates, four of which have some missing values.     

A Generalized Bayes Rule for Prediction

In the case of prior knowledge about the unknown parameter, the Bayesian predictive density coincides with the Bayes estimator for the true density in the sense of the Kullback-Leibler divergence, but this is no longer true if we consider another loss function. In this paper we present a generalized Bayes rule to obtain Bayes density estimators with respect to any α-divergence, including the Kullback-Leibler divergence and the Hellinger distance. For curved exponential models, we study the asymptotic behaviour of these predictive densities. We show that, whatever prior we use, the generalized Bayes rule improves (in a non-Bayesian sense) the estimative density corresponding to a bias modification of the maximum likelihood estimator. It gives rise to a correspondence between choosing a prior density for the generalized Bayes rule and fixing a bias for the maximum likelihood estimator in the classical setting. A criterion for comparing and selecting prior densities is also given.     

Skew Gaussian Process for Nonlinear Regression

In this article, we extend the Gaussian process for regression model by assuming a skew Gaussian process prior on the input function and a skew Gaussian white noise on the error term. Under these assumptions, the predictive density of the output function at a new fixed input is obtained in a closed form. Also, we study the Gaussian process predictor when the errors depart from the Gaussianity to the skew Gaussian white noise. The bias is derived in a closed form and is studied for some special cases. We conduct a simulation study to compare the empirical distribution function of the Gaussian process predictor under Gaussian white noise and skew Gaussian white noise.     

A note on predictive inference for multivariate elliptically contoured distributions

The prediction problem is considered for the multivariate regression model with an elliptically contoured error distribution. We show that the predictive distribution under elliptical errors assumption is the same as that obtained under normally distributed error in both the Bayesian approach using an im-proper prior and the classical approach. This gives inference robustness with respect to departures from the reference case of independent sampling from the normal distribution.     

Bayes prediction of number of failures in weibull samples

This work is concerned with the Bayesian prediction problem of the number of components which will fail in a future time interval, when the failure times are Weibull distributed. Both the 1-sample and the 2-sample prediction problems are dealed with, and some choices of the prior densities on the distribution parameters are discussed which are relatively easy to work with and allow different degrees of knowledge on the failure mechanism to be incorporated in the predictive procedure. Useful relations between the predictive distribution on the number of future failures and the predictive distribution on the future failure times are derived. Numerical examples are also given.     

A note on Bayesian estimation of traffic intensity in single-server Markovian queues

ABSTRACT

In queuing theory, a major interest of researchers is studying the behavior and formation process and analyzing the performance characteristics of queues, particularly the traffic intensity, which is defined as the ratio between the arrival rate and the service rate. How these parameters can be estimated using some statistical inferential method is the mathematical problem treated here. This article aims to obtain better Bayesian estimates for the traffic intensity of M/M/1 queues, which, in Kendall notation, stand for Markovian single-server infinity queues. The Jeffreys prior is proposed to obtain the posterior and predictive distributions of some parameters of interest. Samples are obtained through simulation and some performance characteristics are analyzed. It is observed from the Bayes factor that Jeffreys prior is competitive, among informative and non-informative prior distributions, and presents the best performance in many of the cases tested.     

Planning a Bayesian early-phase phase I/II study for human vaccines in HER2 carcinomas

Recent innovative statistical approaches for phase I/II clinical trials allow one to jointly model the toxicity and efficacy of a new treatment, taking into account the information gathered during the trial. Prior probabilities are then updated with interim data and thus predictive probabilities become more accurate as the trial progresses. In this study, prior distribution elicited from a physician's opinion on the available dose levels planned for a vaccination dose-finding trial, with human DNA in patients with HER2-positive tumours in terms of toxicity and therapeutic response is presented and discussed. A simulation study was conducted in order to quantify the impact of the choice of prior on study results, i.e. the recommended dose level at the end of the trial.     

A matching prior for extreme quantile estimation of the generalized Pareto distribution

Extreme quantile estimation plays an important role in risk management and environmental statistics among other applications. A popular method is the peaks-over-threshold (POT) model that approximate the distribution of excesses over a high threshold through generalized Pareto distribution (GPD). Motivated by a practical financial risk management problem, we look for an appropriate prior choice for Bayesian estimation of the GPD parameters that results in better quantile estimation. Specifically, we propose a noninformative matching prior for the parameters of a GPD so that a specific quantile of the Bayesian predictive distribution matches the true quantile in the sense of Datta et al. (2000).     

Default Bayesian goodness-of-fit tests for the skew-normal model

In this paper we propose a series of goodness-of-fit tests for the family of skew-normal models when all parameters are unknown. As the null distributions of the considered test statistics depend only on asymmetry parameter, we used a default and proper prior on skewness parameter leading to the prior predictive p-value advocated by G. Box. Goodness-of-fit tests, here proposed, depend only on sample size and exhibit full agreement between nominal and actual size. They also have good power against local alternative models which also account for asymmetry in the data.     

A note on fiducial model averaging as an alternative to checking Bayesian and frequentist models

Just as frequentist hypothesis tests have been developed to check model assumptions, prior predictive p-values and other Bayesian p-values check prior distributions as well as other model assumptions. These model checks not only suffer from the usual threshold dependence of p-values, but also from the suppression of model uncertainty in subsequent inference. One solution is to transform Bayesian and frequentist p-values for model assessment into a fiducial distribution across the models. Averaging the Bayesian or frequentist posterior distributions with respect to the fiducial distribution can reproduce results from Bayesian model averaging or classical fiducial inference.     

Predictive Inference from a Two-Parameter Rayleigh Life Model Given a Doubly Censored Sample

This article is concerned with making predictive inference on the basis of a doubly censored sample from a two-parameter Rayleigh life model. We derive the predictive distributions for a single future response, the ith future response, and several future responses. We use the Bayesian approach in conjunction with an improper flat prior for the location parameter and an independent proper conjugate prior for the scale parameter to derive the predictive distributions. We conclude with a numerical example in which the effect of the hyperparameters on the mean and standard deviation of the predictive density is assessed.