The null hypothesis test (NHT) is widely used for validating scientific hypotheses but is actually highly criticized. Although Bayesian tests overcome several criticisms, some limits remain. We propose a Bayesian two-interval test (2IT) in which two hypotheses on an effect being present or absent are expressed as prespecified joint or disjoint intervals and their posterior probabilities are computed. The same formalism can be applied for superiority, non-inferiority, or equivalence tests. The 2IT was studied for three real examples and three sets of simulations (comparison of a proportion and a mean to a reference and comparison of two proportions). Several scenarios were created (with different sample sizes), and simulations were conducted to compute the probabilities of the parameter of interest being in the interval corresponding to either hypothesis given the data generated under one of the hypotheses. Posterior estimates were obtained using conjugacy with a low-informative prior. Bias was also estimated. The probability of accepting a hypothesis when that hypothesis is true progressively increases the sample size, tending towards 1, while the probability of accepting the other hypothesis is always very low (less than 5%) and tends towards 0. The speed of convergence varies with the gap between the hypotheses and with their width. In the case of a mean, the bias is low and rapidly becomes negligible. We propose a Bayesian test that follows a scientifically sound process, in which two interval hypotheses are explicitly used and tested. The proposed test has almost none of the limitations of the NHT and suggests new features, such as a rationale for serendipity or a justification for a "trend in data". The conceptual framework of the 2-IT also allows the calculation of a sample size and the use of sequential methods in numerous contexts.
We develop a Bayesian highest-density interval (HDI) for use in within-subject designs. This credible interval is based on a standard noninformative prior and a modified posterior distribution that conditions on both the data and point estimates of the subject-specific random effects. Conditioning on the estimated random effects removes between-subject variance and produces intervals that are the Bayesian analogue of the within-subject confidence interval proposed in Loftus and Masson (1994). We show that the latter interval can also be derived as a Bayesian within-subject HDI under a certain …
The prediction interval has been increasingly used in meta-analyses as a useful measure for assessing the magnitude of treatment effect and between-studies heterogeneity. In calculations of the prediction interval, although the Higgins-Thompson-Spiegelhalter method is used most often in practice, it might not have adequate coverage probability for the true treatment effect of a future study under realistic situations. An effective alternative candidate is the Bayesian prediction interval, which has also been widely used in general prediction problems. However, these prediction intervals are co…
There has been an increasing interest in using interval-based Bayesian designs for dose finding, one of which is the modified toxicity probability interval (mTPI) method. We show that the decision rules in mTPI correspond to an optimal rule under a formal Bayesian decision theoretic framework. However, the probability models in mTPI are overly sharpened by the Ockham's razor, which, while in general helps with parsimonious statistical inference, leads to suboptimal decisions in small-sample inference such as dose finding. We propose a new framework that blunts the Ockham's razor, and demonstra…
Calibrating hierarchical Bayesian domain inference for a proportion
Continuing Academic Specialist Center for Statistical Training and Consulting, Michigan State University（密歇根州立大学统计培训与咨询中心继续教育学术专员）；Institute for Social Research, University of Michigan（密歇根大学社会研究所）
Data and Statistical Sciences, AbbVie（AbbVie 数据与统计科学）；Department of Statistics, Brigham Young University（杨百翰大学统计系）；Department of Statistics, University of California, Santa Cruz（加州大学圣克鲁兹分校统计系）
Our approach to Mendelian Randomization (MR) analysis is designed to increase reproducibility of causal effect "discoveries" by: (i) using a Bayesian approach to inference; (ii) replacing the point null hypothesis with a region of practical equivalence consisting of values of negligible magnitude for the effect of interest, while exploiting the ability of Bayesian analysis to quantify the evidence of the effect falling inside/outside the region; (iii) rejecting the usual binary decision logic in favour of a ternary logic where the hypothesis test may result in either an acceptance or a rejecti…
Penalized B-splines are routinely used in additive models to describe smooth changes in a response with quantitative covariates. It is typically done through the conditional mean in the exponential family using generalized additive models with an indirect impact on other conditional moments. Another common strategy consists in focussing on several low-order conditional moments, leaving the complete conditional distribution unspecified. Alternatively, a multi-parameter distribution could be assumed for the response with several of its parameters jointly regressed on covariates using additive ex…
This book chapter introduces regression approaches and regression adjustment for Approximate Bayesian Computation (ABC). Regression adjustment adjusts parameter values after rejection sampling in order to account for the imperfect match between simulations and observations. Imperfect match between simulations and observations can be more pronounced when there are many summary statistics, a phenomenon coined as the curse of dimensionality. Because of this imperfect match, credibility intervals obtained with regression approaches can be inflated compared to true credibility intervals. The chapte…
We develop scalable methods for producing conformal Bayesian predictive intervals with finite sample calibration guarantees. Bayesian posterior predictive distributions, $p(y \mid x)$, characterize subjective beliefs on outcomes of interest, $y$, conditional on predictors, $x$. Bayesian prediction is well-calibrated when the model is true, but the predictive intervals may exhibit poor empirical coverage when the model is misspecified, under the so called ${\cal{M}}$-open perspective. In contrast, conformal inference provides finite sample frequentist guarantees on predictive confidence interva…
In this paper, we investigate the classical and Bayesian estimation of unknown parameters of the Gumbel type-II distribution based on adaptive type-II progressive hybrid censored sample (AT-II PHCS). The maximum likelihood estimates (MLEs) and maximum product spacing estimates (MPSEs) are developed and computed numerically using Newton-Raphson method. Bayesian approaches are employed to estimate parameters under symmetric and asymmetric loss functions. Bayesian estimates are not in explicit forms. Thus, Bayesian estimates are obtained by using Markov chain Monte Carlo (MCMC) method along with …
Population attributable risk (PAR) is used in epidemiology to predict the impact of removing a risk factor from the population. Until recently, no standard approach for calculating confidence intervals or the variance for PAR was available in the literature. Pirikahu et al. (2016) outlined a fully Bayesian approach to provide credible intervals for the PAR from a cross-sectional study, where the data was presented in the form of a 2 x 2 table. However, extensions to cater for other frequently used study designs were not provided. In this paper we provide methodology to calculate credible inter…
We consider a Bayesian method for simultaneous quantile regression on a real variable. By monotone transformation, we can make both the response variable and the predictor variable take values in the unit interval. A representation of quantile function is given by a convex combination of two monotone increasing functions $ξ_1$ and $ξ_2$ not depending on the prediction variables. In a Bayesian approach, a prior is put on quantile functions by putting prior distributions on $ξ_1$ and $ξ_2$. The monotonicity constraint on the curves $ξ_1$ and $ξ_2$ are obtained through a spline basis expansion wi…
Building on recent research for prediction of hurricane trajectories using recurrent neural networks (RNNs), we have developed improved methods and generalized the approach to predict Bayesian intervals in addition to simple point estimates. Tropical storms are capable of causing severe damage, so accurately predicting their trajectories can bring significant benefits to cities and lives, especially as they grow more intense due to climate change effects. By implementing the Bayesian interval using dropout in an RNN, we improve the actionability of the predictions, for example by estimating th…
We review and contrast frequentist and Bayesian definitions of tolerance regions. We give conditions under which for large samples a Bayesian region also has frequentist validity, and study the latter for smaller samples in a simulation study. We discuss a computational strategy for computing a Bayesian two-sided tolerance interval for a Gaussian future variable, and apply this to the case of possibly unbalanced linear mixed models. We illustrate the method on a quality control experiment from the pharmaceutical industry.
Assume we observe a finite number of inspection times together with information on whether a specific event has occurred before each of these times. Suppose replicated measurements are available on multiple event times. The set of inspection times, including the number of inspections, may be different for each event. This is known as mixed case interval censored data. We consider Bayesian estimation of the distribution function of the event time while assuming it is concave. We provide sufficient conditions on the prior such that the resulting procedure is consistent from the Bayesian point of…
We propose a quasi-Bayesian method to conduct inference for the production frontier. This approach combines multiple first-stage extreme quantile estimates by the quasi-Bayesian method to produce the point estimate and confidence interval for the production frontier. We show the asymptotic properties of the proposed estimator and the validity of the inference procedure. The finite sample performance of our method is illustrated through simulations and an empirical application.
There has been strong recent interest in testing interval null hypothesis for improved scientific inference. For example, Lakens et al (2018) and Lakens and Harms (2017) use this approach to study if there is a pre-specified meaningful treatment effect in gerontology and clinical trials, which is different from the more traditional point null hypothesis that tests for any treatment effect. Two popular Bayesian approaches are available for interval null hypothesis testing. One is the standard Bayes factor and the other is the Region of Practical Equivalence (ROPE) procedure championed by Krusch…
Let $X$ have a Generalized Poisson distribution with mean $kb$, where $b$ is a known constant in the unit interval and $k$ is a discrete, non-negative parameter. We show that if an uninformative uniform prior for $k$ is assumed, then the posterior distribution of $k$ can be approximated using the gamma distribution when $b$ is small.
Given a sample of size $n$ from a population of individuals belonging to different species with unknown proportions, a popular problem of practical interest consists in making inference on the probability $D_{n}(l)$ that the $(n+1)$-th draw coincides with a species with frequency $l$ in the sample, for any $l=0,1,\ldots,n$. This paper contributes to the methodology of Bayesian nonparametric inference for $D_{n}(l)$. Specifically, under the general framework of Gibbs-type priors we show how to derive credible intervals for a Bayesian nonparametric estimation of $D_{n}(l)$, and we investigate th…
Many recently developed Bayesian methods have focused on sparse signal detection. However, much less work has been done addressing the natural follow-up question: how to make valid inferences for the magnitude of those signals after selection. Ordinary Bayesian credible intervals suffer from selection bias, owing to the fact that the target of inference is chosen adaptively. Existing Bayesian approaches for correcting this bias produce credible intervals with poor frequentist properties, while existing frequentist approaches require sacrificing the benefits of shrinkage typical in Bayesian met…
Robust Survival Estimation under Interval Censoring: Expectation-Maximization and Bayesian Accelerated Failure Time Assessment via Simulation and Application
Estimating the difference between two binomial proportions will be investigated, where Bayesian, frequentist and fiducial (BFF) methods will be considered. Three vague priors will be used, the Jeffreys prior, a divergence prior and the probability matching prior. A probability matching prior is a prior distribution under which the posterior probabilities of certain regions coincide with their coverage probabilities. Fiducial inference can be viewed as a procedure that obtains a measure on a parameter space while assuming less than what Bayesian inference does, i.e. no prior. Fisher introduced …
The Net Promoter Score is a simple measure used by several companies as indicator of customer loyalty. Studies that address the statistical properties of this measure are still scarce and none of them considered the sample size determination problem. We adopt a Bayesian approach to provide point and interval estimators for the Net Promoter Score and discuss the determination of the sample size. Computational tools were implemented to use this methodology in practice. An illustrative example with data from financial services is also presented.
Model-assisted estimation with complex survey data is an important practical problem in survey sampling. When there are many auxiliary variables, selecting significant variables associated with the study variable would be necessary to achieve efficient estimation of population parameters of interest. In this paper, we formulate a regularized regression estimator in the framework of Bayesian inference using the penalty function as the shrinkage prior for model selection. The proposed Bayesian approach enables us to get not only efficient point estimates but also reasonable credible intervals. R…
Hypothesis testing is an essential statistical method in psychology and the cognitive sciences. The problems of traditional null hypothesis significance testing (NHST) have been discussed widely, and among the proposed solutions to the replication problems caused by the inappropriate use of significance tests and $p$-values is a shift towards Bayesian data analysis. However, Bayesian hypothesis testing is concerned with various posterior indices for significance and the size of an effect. This complicates Bayesian hypothesis testing in practice, as the availability of multiple Bayesian alterna…
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms is an important field of neuroscience. In the absence of high quality data on humans, mouse vocalization experiments in laboratory settings have been proven to be useful in providing valuable insights into mammalian vocal development and evolution, including especially the impact of certain genetic mutations. Data sets from mouse vocalization experiments usually consist of categorical syllable sequences along with continuous inter-syllable interval times for mice of different genotypes vocalizing …
The study of animal movement is challenging because it is a process modulated by many factors acting at different spatial and temporal scales. Several models have been proposed which differ primarily in the temporal conceptualization, namely continuous and discrete time formulations. Naturally, animal movement occurs in continuous time but we tend to observe it at fixed time intervals. To account for the temporal mismatch between observations and movement decisions, we used a state-space model where movement decisions (steps and turns) are made in continuous time. The movement process is then …
Popular parametric and semiparametric hazards regression models for clustered survival data are inappropriate and inadequate when the unknown effects of different covariates and clustering are complex. This calls for a flexible modeling framework to yield efficient survival prediction. Moreover, for some survival studies involving time to occurrence of some asymptomatic events, survival times are typically interval censored between consecutive clinical inspections. In this article, we propose a robust semiparametric model for clustered interval-censored survival data under a paradigm of Bayesi…
We consider the nonparametric multivariate isotonic regression problem, where the regression function is assumed to be nondecreasing with respect to each predictor. Our goal is to construct a Bayesian credible interval for the function value at a given interior point with assured limiting frequentist coverage. We put a prior on unrestricted step-functions, but make inference using the induced posterior measure by an "immersion map" from the space of unrestricted functions to that of multivariate monotone functions. This allows maintaining the natural conjugacy for posterior sampling. A natural…
This paper considers the problem of making statistical inferences about a parameter when a narrow interval centred at a given value of the parameter is considered special, which is interpreted as meaning that there is a substantial degree of prior belief that the true value of the parameter lies in this interval. A clear justification of the practical importance of this problem is provided. The main difficulty with the standard Bayesian solution to this problem is discussed and, as a result, a pseudo-Bayesian solution is put forward based on determining lower limits for the posterior probabili…
Chongqing University（重庆大学）；National University of Singapore（新加坡国立大学）；Bioinformatics Institute, A*STAR（A*STAR生物信息研究所）；Lanzhou University of Technology（兰州理工大学）；Lanzhou University（兰州大学）
Complex activity recognition is challenging due to the inherent uncertainty and diversity of performing a complex activity. Normally, each instance of a complex activity has its own configuration of atomic actions and their temporal dependencies. We propose in this paper an atomic action-based Bayesian model that constructs Allen's interval relation networks to characterize complex activities with structural varieties in a probabilistic generative way: By introducing latent variables from the Chinese restaurant process, our approach is able to capture all possible styles of a particular comple…
