We review recent work concerning optimal proposal scalings for Metropolis-Hastings MCMC algorithms, and adaptive MCMC algorithms for trying to improve the algorithm on the y.

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Optimal Proposal Distributions and Adaptive MCMC

Bayesian inference has found widespread application and use in science and engineering to reconcile Earth system models with data, including prediction in space (interpolation), prediction in time (forecasting), assimilation of observations and deterministic/stochastic model output, and inference of the model parameters. Bayes theorem states that the posterior probability, p ( H | Y ˜ ) of a hypothesis, H is proportional to the product of the prior probability, p(H) of this hypothesis and the likelihood, L ( H | Y ˜ ) of the same hypothesis given the new observations, Y ˜ , or p ( H | Y ˜ ) ∝ p ( H ) L ( H | Y ˜ ) . In science and engineering, H often constitutes some numerical model, ℱ(x) which summarizes, in algebraic and differential equations, state variables and fluxes, all knowledge of the system of interest, and the unknown parameter values, x are subject to inference using the data Y ˜ . Unfortunately, for complex system models the posterior distribution is often high dimensional and analytically intractable, and sampling methods are required to approximate the target. In this paper I review the basic theory of Markov chain Monte Carlo (MCMC) simulation and introduce a MATLAB toolbox of the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm developed by Vrugt et al. (2008a, 2009a) and used for Bayesian inference in fields ranging from physics, chemistry and engineering, to ecology, hydrology, and geophysics. This MATLAB toolbox provides scientists and engineers with an arsenal of options and utilities to solve posterior sampling problems involving (among others) bimodality, high-dimensionality, summary statistics, bounded parameter spaces, dynamic simulation models, formal/informal likelihood functions (GLUE), diagnostic model evaluation, data assimilation, Bayesian model averaging, distributed computation, and informative/noninformative prior distributions. The DREAM toolbox supports parallel computing and includes tools for convergence analysis of the sampled chain trajectories and post-processing of the results. Seven different case studies illustrate the main capabilities and functionalities of the MATLAB toolbox.

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Markov chain Monte Carlo simulation using the DREAM software package: Theory, concepts, and MATLAB implementation

[1] Spatially distributed hydrologic models are increasingly being used to study and predict soil moisture flow, groundwater recharge, surface runoff, and river discharge. The usefulness and applicability of such complex models is increasingly held back by the potentially many hundreds (thousands) of parameters that require calibration against some historical record of data. The current generation of search and optimization algorithms is typically not powerful enough to deal with a very large number of variables and summarize parameter and predictive uncertainty. We have previously presented a general-purpose Markov chain Monte Carlo (MCMC) algorithm for Bayesian inference of the posterior probability density function of hydrologic model parameters. This method, entitled differential evolution adaptive Metropolis (DREAM), runs multiple different Markov chains in parallel and uses a discrete proposal distribution to evolve the sampler to the posterior distribution. The DREAM approach maintains detailed balance and shows excellent performance on complex, multimodal search problems. Here we present our latest algorithmic developments and introduce MT-DREAM(ZS), which combines the strengths of multiple-try sampling, snooker updating, and sampling from an archive of past states. This new code is especially designed to solve high-dimensional search problems and receives particularly spectacular performance improvement over other adaptive MCMC approaches when using distributed computing. Four different case studies with increasing dimensionality up to 241 parameters are used to illustrate the advantages of MT-DREAM(ZS).

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2011WR010608

High-dimensional posterior exploration of hydrologic models using multiple-try DREAM (ZS) and high-performance computing

https://www.csm.ornl.gov/workshops/applmath11/documents/Marzouk_uncertainty_oralpresentation.pdf

Bayesian inference with optimal maps

S U M M A R Y Non-linear inverse problems in the geosciences often involve probabilistic sampling of multimodal density functions or global optimization and sometimes both. Efficient algorithmic tools for carrying out sampling or optimization in challenging cases are of major interest. Here results are presented of some numerical experiments with a technique, known as Parallel Tempering, which originated in the field of computational statistics but is finding increasing numbers of applications in fields ranging from Chemical Physics to Astronomy. To date, experience in use of Parallel Tempering within earth sciences problems is very limited. In this paper, we describe Parallel Tempering and compare it to related methods of Simulated Annealing and Simulated Tempering for optimization and sampling, respectively. A key feature of Parallel Tempering is that it satisfies the detailed balance condition required for convergence of Markov chain Monte Carlo (McMC) algorithms while improving the efficiency of probabilistic sampling. Numerical results are presented on use of Parallel Tempering for trans-dimensional inversion of synthetic seismic receiver functions and also the simultaneous fitting of multiple receiver functions using global optimization. These suggest that its use can significantly accelerate sampling algorithms and improve exploration of parameter space in optimization. Parallel Tempering is a meta-algorithm which may be used together with many existing McMC sampling and direct search optimization techniques. It’s generality and demonstrated performance suggests that there is significant potential for applications to both sampling and optimization problems in the geosciences.

/pdf/a-parallel-tempering-algorithm-for-probabilistic-sampling-2zoldbezbz.pdf

A Parallel Tempering algorithm for probabilistic sampling and multimodal optimization

Starting with the seminal paper of Haario, Saksman and Tamminen (Haario et al. (2001)), a substantial amount of work has been done to validate adaptive Markov chain Monte Carlo algorithms. In this paper we focus on two practical aspects of adaptive Metropolis samplers. First, we draw attention to the deficient performance of standard adaptation when the target distribution is multi-modal. We propose a parallel chain adaptation strategy that incorporates multiple Markov chains which are run in parallel. Second, we note that

/pdf/learn-from-thy-neighbor-parallel-chain-and-regional-adaptive-2itq8jhyid.pdf

Learn From Thy Neighbor: Parallel-Chain and Regional Adaptive MCMC

Starting with the seminal paper of Haario, Saksman and Tamminen (Haario et al. (2001)), a substantial amount of work has been done to validate adaptive Markov chain Monte Carlo algorithms. In this paper we focus on two practical aspects of adaptive Metropolis samplers. First, we draw attention to the deficient performance of standard adaptation when the target distribution is multi-modal. We propose a parallel chain adaptation strategy that incorporates multiple Markov chains which are run in parallel. Second, the current adaptive MCMC paradigm implicitly assumes that

Chao Yang

Papers

Learn From Thy Neighbor: Parallel-Chain and Regional Adaptive MCMC

Learn From Thy Neighbor: Parallel-Chain Adaptive MCMC