Unbiased and Consistent Nested Sampling via Sequential Monte Carlo

We introduce a new class of sequential Monte Carlo methods called Nested Sampling via Sequential Monte Carlo (NS-SMC), which reframes the Nested Sampling method of Skilling (2006) in terms of sequential Monte Carlo techniques. This new framework allows convergence results to be obtained in the setting when Markov chain Monte Carlo (MCMC) is used to produce new samples. An additional benefit is that marginal likelihood estimates are unbiased. In contrast to NS, the analysis of NS-SMC does not require the (unrealistic) assumption that the simulated samples be independent. As the original NS algorithm is a special case of NS-SMC, this provides insights as to why NS seems to produce accurate estimates despite a typical violation of its assumptions. For applications of NS-SMC, we give advice on tuning MCMC kernels in an automated manner via a preliminary pilot run, and present a new method for appropriately choosing the number of MCMC repeats at each iteration. Finally, a numerical study is conducted where the performance of NS-SMC and temperature-annealed SMC is compared on several challenging and realistic problems. MATLAB code for our experiments is made available at https://github.com/LeahPrice/SMC-NS .Comment: 45 pages, some minor typographical errors fixed since last versio

BSL: An R Package for Efficient Parameter Estimation for Simulation-Based Models via Bayesian Synthetic Likelihood

Bayesian synthetic likelihood (BSL; Price, Drovandi, Lee, and Nott 2018) is a popular method for estimating the parameter posterior distribution for complex statistical models and stochastic processes that possess a computationally intractable likelihood function. Instead of evaluating the likelihood, BSL approximates the likelihood of a judiciously chosen summary statistic of the data via model simulation and density estimation. Compared to alternative methods such as approximate Bayesian computation (ABC), BSL requires little tuning and requires less model simulations than ABC when the chosen summary statistic is high-dimensional. The original synthetic likelihood relies on a multivariate normal approximation of the intractable likelihood, where the mean and covariance are estimated by simulation. An extension of BSL considers replacing the sample covariance with a penalized covariance estimator to reduce the number of required model simulations. Further, a semi-parametric approach has been developed to relax the normality assumption. Finally, another extension of BSL aims to develop a more robust synthetic likelihood estimator while acknowledging there might be model misspecification. In this paper, we present the R package BSL that amalgamates the aforementioned methods and more into a single, easy-to-use and coherent piece of software. The package also includes several examples to illustrate use of the package and the utility of the methods

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Discussion of: A Bayesian information criterion for singular models

The BIC can be viewed as an easily computable proxy to fully Bayesian model choice, which is conducted by comparing the marginal likelihood (or evidence) for each of the models. However, the derivation for BIC relies on informative data and a noninformative prior and that the models under consideration are non-singular. Thus the development of associated information criteria that are suitable when the models are singular is an important research problem. Hence, the authors should be congratulated for their contribution..

Postprocessing of MCMC

Markov chain Monte Carlo is the engine of modern Bayesian statistics, being used to approximate the posterior and derived quantities of interest. Despite this, the issue of how the output from a Markov chain is post-processed and reported is often overlooked. Convergence diagnostics can be used to control bias via burn-in removal, but these do not account for (common) situations where a limited computational budget engenders a bias-variance trade-off. The aim of this article is to review state-of-the-art techniques for post-processing Markov chain output. Our review covers methods based on discrepancy minimisation, which directly address the bias-variance trade-off, as well as general-purpose control variate methods for approximating expected quantities of interest

Discussion of: A Bayesian information criterion for\ud singular models

The BIC can be viewed as an easily computable proxy to fully Bayesian model choice, which is conducted by comparing the marginal likelihood (or evidence) for each of the models. However, the derivation for BIC relies on informative data and a noninformative prior and that the models under consideration are non-singular. Thus the development of associated information criteria that are suitable when the models are singular is an important research problem. Hence, the authors should be congratulated for their contribution..

Sequential Monte Carlo samplers with independent Markov chain Monte Carlo proposals

<I>Sequential Monte Carlo</I> (SMC) methods for sampling from the posterior of static Bayesian models are flexible, parallelisable and capable of handling complex targets. However, it is common practice to adopt a Markov chain Monte Carlo (MCMC) kernel with a multivariate normal random walk (RW) proposal in the move step, which can be both inefficient and detrimental to the ability to explore challenging posterior distributions. We propose a flexible copula-type independent proposal which uses the population of particles to adapt the kernel in a more sophisticated way than the RW. The result is fewer likelihood evaluations, improved exploration of challenging posterior distributions and an improved ability to perform likelihood evaluations in parallel. Another consequence of using independent proposals is that all candidates generated in the SMC process can be used to estimate the marginal likelihood and posterior expectations. We consider various importance sampling (IS) estimators that use all candidates and devise a novel IS marginal likelihood estimator. We demonstrate through several examples that more precise estimates of posterior expectations and the marginal likelihood can be obtained using fewer likelihood evaluations than the more standard RW approach