A central theme in the field of survey statistics is estimating population-level quantities through data coming from potentially non-representative samples of the population. Multilevel regression and poststratification (MRP), a model-based approach, is gaining traction against the traditional weighted approach for survey estimates. MRP estimates are susceptible to bias if there is an underlying structure that the methodology does not capture. This work aims to provide a new framework for specifying structured prior distributions that lead to bias reduction in MRP estimates. We use simulation studies to explore the benefit of these prior distributions and demonstrate their efficacy on non-representative US survey data. We show that structured prior distributions offer absolute bias reduction and variance reduction for posterior MRP estimates in a large variety of data regimes.

Sequential Monte Carlo (SMC) samplers are an alternative to MCMC for Bayesian computation. However, their performance depends strongly on the Markov kernels used to rejuvenate particles. We discuss how to calibrate automatically (using the current particles) Hamiltonian Monte Carlo kernels within SMC. To do so, we build upon the adaptive SMC approach of Fearnhead and Taylor (2013), and we also suggest alternative methods. We illustrate the advantages of using HMC kernels within an SMC sampler via an extensive numerical study.

Bayesian experimental design (BED) is a framework that uses statistical models and decision making under uncertainty to optimise the cost and performance of a scientific experiment. Sequential BED, as opposed to static BED, considers the scenario where we can sequentially update our beliefs about the model parameters through data gathered in the experiment. A class of models of particular interest for the natural and medical sciences are implicit models, where the data generating distribution is intractable, but sampling from it is possible. Even though there has been a lot of work on static BED for implicit models in the past few years, the notoriously difficult problem of sequential BED for implicit models has barely been touched upon. We address this gap in the literature by devising a novel sequential design framework for parameter estimation that uses the Mutual Information (MI) between model parameters and simulated data as a utility function to find optimal experimental designs, which has not been done before for implicit models. Our approach uses likelihood-free inference by ratio estimation to simultaneously estimate posterior distributions and the MI. During the sequential BED procedure we utilise Bayesian optimisation to help us optimise the MI utility. We find that our framework is efficient for the various implicit models tested, yielding accurate parameter estimates after only a few iterations.

Network meta-analysis has gained popularity in the last decade as a method for comparing the efficacy/safety of multiple medical interventions by synthesizing data across clinical studies. Bayesian methods for network meta-analysis have undergone further development than frequentist methods and are more convenient to use. Most of the current literature pertains to connected networks but disconnected networks commonly arise. There is not at the moment a trusted gold-standard approach to analyze disconnected networks. Intuitively, the standard method for analyzing connected networks, which is contrast-based, does not seem useful in disconnected networks, but this has not been explained rigorously. Our work is the first to provide the theoretical groundwork for understanding how evidence flows within Bayesian contrast-based models of disconnected networks. We achieve this by quantifying the ratio of posterior to prior variance of disconnected treatment contrasts. We show that when using an uninformative prior on the treatment contrasts, the standard approach is not useful to analyze disconnected networks (even when the number of studies, treatments or patients is large); however, it can be useful under moderately informative priors, which can be informed from additional observational data when available. A simulation study provides a demonstration of the theoretical results and explores non-asymptotic cases. An illustration on a real-world dataset is provided.

This paper proposes randomized controlled clinical trial design to evaluate external cooling as a means to control fever and thereby reduce mortality in patients with septic shock. The trial will include concurrent external cooling and control arms while adaptively incorporating historical control arm data. Bayesian group sequential monitoring will be done using a posterior comparative test based on the 60-day survival distribution in each concurrent arm. Posterior inference will follow from a Bayesian discrete time survival model that facilitates adaptive incorporation of the historical control data through an innovative regression framework with a multivariate spike-and-slab prior distribution on the historical bias parameters. For each interim test, the amount of information borrowed from the historical control data will be determined adaptively in a manner that reflects the degree of agreement between historical and concurrent control arm data. Guidance is provided for selecting Bayesian posterior probability group-sequential monitoring boundaries. Simulation results elucidating how the proposed method borrows strength from the historical control data are reported. In the absence of historical control arm bias, the proposed design controls the type I error rate and provides substantially larger power than reasonable comparators, whereas in the presence bias of varying magnitude, type I error rate inflation is curbed.

We provide a nonparametric spectral approach to the modeling of correlation functions on spheres. The sequence of Schoenberg coefficients and their associated covariance functions are treated as random rather than assuming a parametric form. We propose a stick-breaking representation for the spectrum, and show that such a choice spans the support of the class of geodesically isotropic covariance functions under uniform convergence. Further, we examine the first order properties of such representation, from which geometric properties can be inferred, in terms of Hölder continuity, of the associated Gaussian random field. The properties of the posterior, in terms of existence, uniqueness, and Lipschitz continuity, are then inspected. Our findings are validated with MCMC simulations and illustrated using a global data set on surface temperatures.

We propose the use of a score based working likelihood function for quantile regression which can perform inference for multiple conditional quantiles of an arbitrary number. We show that the proposed likelihood can be used in a Bayesian framework leading to valid frequentist inference, whereas the commonly used asymmetric Laplace working likelihood leads to invalid interval estimations and requires further correction. For computation, we propose a novel adaptive importance sampling algorithm to compute important posterior summaries such as the posterior mean and the covariance matrix. Our proposed approach makes it feasible to perform valid inference for parameters such as the slope differences at different quantile levels, which is either not possible or cumbersome using existing Bayesian approaches. Empirical results demonstrate that the proposed likelihood has good estimation and inferential properties and that the proposed computational algorithm is more efficient than its competitors.

Bayesian inference for models with intractable likelihood functions represents a challenging suite of problems in modern statistics. In this work we analyse the Conway-Maxwell-Poisson (COM-Poisson) distribution, a two parameter generalisation of the Poisson distribution. COM-Poisson regression modelling allows the flexibility to model dispersed count data as part of a generalised linear model (GLM) with a COM-Poisson response, where exogenous covariates control the mean and dispersion level of the response. The major difficulty with COM-Poisson regression is that the likelihood function contains multiple intractable normalising constants and is not amenable to standard inference and Markov Chain Monte Carlo (MCMC) techniques. Recent work by Chanialidis et al. (2018) has seen the development of a sampler to draw random variates from the COM-Poisson likelihood using a rejection sampling algorithm. We provide a new rejection sampler for the COM-Poisson distribution which significantly reduces the central processing unit (CPU) time required to perform inference for COM-Poisson regression models. An extension of this work shows that for any intractable likelihood function with an associated rejection sampler it is possible to construct unbiased estimators of the intractable likelihood which proves useful for model selection or for use within pseudo-marginal MCMC algorithms (Andrieu and Roberts, 2009). We demonstrate all of these methods on a real-world dataset of takeover bids.

We consider exact algorithms for Bayesian inference with model selection priors (including spike-and-slab priors) in the sparse normal sequence model. Because the best existing exact algorithm becomes numerically unstable for sample sizes over $n=500$, there has been much attention for alternative approaches like approximate algorithms (Gibbs sampling, variational Bayes, etc.), shrinkage priors (e.g. the Horseshoe prior and the Spike-and-Slab LASSO) or empirical Bayesian methods. However, by introducing algorithmic ideas from online sequential prediction, we show that exact calculations are feasible for much larger sample sizes: for general model selection priors we reach $n=25000$, and for certain spike-and-slab priors we can easily reach $n=100000$. We further prove a de Finetti-like result for finite sample sizes that characterizes exactly which model selection priors can be expressed as spike-and-slab priors. The computational speed and numerical accuracy of the proposed methods are demonstrated in experiments on simulated data, on a differential gene expression data set, and to compare the effect of multiple hyper-parameter settings in the beta-binomial prior. In our experimental evaluation we compute guaranteed bounds on the numerical accuracy of all new algorithms, which shows that the proposed methods are numerically reliable whereas an alternative based on long division is not.

It is often claimed that Bayesian methods, in particular Bayes factor methods for hypothesis testing, can deal with optional stopping. We first give an overview, using elementary probability theory, of three different mathematical meanings that various authors give to this claim: (1) stopping rule independence, (2) posterior calibration and (3) (semi-) frequentist robustness to optional stopping. We then prove theorems to the effect that these claims do indeed hold in a general measure-theoretic setting. For claims of type (2) and (3), such results are new. By allowing for non-integrable measures based on improper priors, we obtain particularly strong results for the practically important case of models with nuisance parameters satisfying a group invariance (such as location or scale). We also discuss the practical relevance of (1)–(3), and conclude that whether Bayes factor methods actually perform well under optional stopping crucially depends on details of models, priors and the goal of the analysis.

Fitted probabilities from widely used Bayesian multinomial probit models can depend strongly on the choice of a base category, which is used to uniquely identify the parameters of the model. This paper proposes a novel identification strategy, and associated prior distribution for the model parameters, that renders the prior symmetric with respect to relabeling the outcome categories. The new prior permits an efficient Gibbs algorithm that samples rank-deficient covariance matrices without resorting to Metropolis-Hastings updates.

In this paper we describe Bayesian inferential methods for data modeled by controlled branching processes that account for model robustness via the use of disparities. Under regularity conditions, we establish that estimators obtained using disparity-based posterior, such as expected and maximum a posteriori estimates, are consistent and efficient under the posited model. Additionally, we establish that the estimates are robust to model misspecification and presence of outliers. To this end, we develop several fundamental ideas relating minimum disparity estimators to Bayesian estimators obtained using the disparity-based posterior, for dependent tree-structured data. We illustrate the methodology through a simulated example and apply our methods to a real data set from cell kinetics.

Estimation of correlation matrices is a challenging problem due to the notorious positive-definiteness constraint and high-dimensionality. Reparameterizing Cholesky factors of correlation matrices in terms of angles or hyperspherical coordinates where the angles vary freely in the range $[0,\mathrm{\pi })$ has become popular in the last two decades. However, it has not been used in Bayesian estimation of correlation matrices perhaps due to lack of clear statistical relevance and suitable priors for the angles. In this paper, we show for the first time that for longitudinal data these angles are the inverse cosine of the semi-partial correlations (SPCs). This simple connection makes it possible to introduce physically meaningful selection and shrinkage priors on the angles or correlation matrices with emphasis on selection (sparsity) and shrinking towards longitudinal structure. Our method deals effectively with the positive-definiteness constraint in posterior computation. We compare the performance of our Bayesian estimation based on angles with some recent methods based on partial autocorrelations through simulation and apply the method to a data related to clinical trial on smoking.