Random Walk Metropolis Algorithm Research Articles

Bayesian Inference for the Gamma Zero-Truncated Poisson Distribution with an Application to Real Data

This article presents Bayesian estimation methods applied to the gamma zero-truncated Poisson (GZTP) and the complementary gamma zero-truncated Poisson (CGZTP) distributions, encompassing both one-parameter and two-parameter models. These distributions are notably flexible and useful for modeling lifetime data. In the one-parameter model case, the Jeffreys prior is mathematically derived. The use of informative and noninformative priors, combined with the random walk Metropolis algorithm within a Bayesian framework, generates samples from the posterior distributions. Bayesian estimators’ effectiveness is examined through extensive simulation studies, in comparison with the maximum likelihood method. Results indicate that Bayesian estimators provide more precise parameter estimates, even with smaller sample sizes. Furthermore, the study and comparison of the coverage probabilities (CPs) and average lengths (ALs) of the credible intervals with those from Wald intervals suggest that Bayesian credible intervals typically yield shorter ALs and higher CPs, thereby demonstrating the effectiveness of Bayesian inference in the context of GZTP and CGZTP distributions. Lastly, Bayesian inference is applied to real data.

Bayesian estimation for median discrete Weibull regression model

<abstract><p>The discrete Weibull model can be adapted to capture different levels of dispersion in the count data. This paper takes into account the direct relationship between explanatory variables and the median of discrete Weibull response variable. Additionally, it provides the Bayesian estimate of the discrete Weibull regression model using the random walk Metropolis algorithm. The prior distributions of the coefficient predictors were carried out based on the uniform non-informative, normal and Laplace distributions. The performance of the Bayes estimators was also compared with the maximum likelihood estimator in terms of the mean square error and the coverage probability through the Monte Carlo simulation study. Meanwhile, a real data set was analyzed to show how the proposed model and the methods work in practice.</p></abstract>

Variance reduction for Metropolis–Hastings samplers

We introduce a general framework that constructs estimators with reduced variance for random walk Metropolis and Metropolis-adjusted Langevin algorithms. The resulting estimators require negligible computational cost and are derived in a post-process manner utilising all proposal values of the Metropolis algorithms. Variance reduction is achieved by producing control variates through the approximate solution of the Poisson equation associated with the target density of the Markov chain. The proposed method is based on approximating the target density with a Gaussian and then utilising accurate solutions of the Poisson equation for the Gaussian case. This leads to an estimator that uses two key elements: (1) a control variate from the Poisson equation that contains an intractable expectation under the proposal distribution, (2) a second control variate to reduce the variance of a Monte Carlo estimate of this latter intractable expectation. Simulated data examples are used to illustrate the impressive variance reduction achieved in the Gaussian target case and the corresponding effect when target Gaussianity assumption is violated. Real data examples on Bayesian logistic regression and stochastic volatility models verify that considerable variance reduction is achieved with negligible extra computational cost.

ALTERNATIVE ROBUST ESTIMATORS FOR PARAMETERS OF THE LINEAR REGRESSION MODEL

This paper considers parameter estimation of the linear regression model with Ramsay-Novick (RN) distributed errors, focusing on its use as an aid to robustness. Positioning within the class of heavy tailed distributions, RN distribution can be defined as the modification of unbounded influence function of a non-robust density so that it has more resistance to outliers. Potential use of this robust density have so far been assessed in Bayesian settings on real data examples and there is a lack of performance assessment for finite samples in classical approach. This study therefore explores its robustness properties when used as error distribution in comparison to normal as well as other alternating heavy-tailed distributions like Laplace and Student-t. An extensive simulation study was conducted for this purpose under different settings of sample size, model parameters and outlier percantages. An efficient data generation of this distribution through random-walk Metropolis algorithm is here also suggested. The results were supported by a real world application on famously known as Brownlee’s stack loss plant data.

Optimal scaling of random walk Metropolis algorithms using Bayesian large-sample asymptotics

High-dimensional limit theorems have been shown useful to derive tuning rules for finding the optimal scaling in random walk Metropolis algorithms. The assumptions under which weak convergence results are proved are, however, restrictive: the target density is typically assumed to be of a product form. Users may thus doubt the validity of such tuning rules in practical applications. In this paper, we shed some light on optimal scaling problems from a different perspective, namely a large-sample one. This allows to prove weak convergence results under realistic assumptions and to propose novel parameter-dimension-dependent tuning guidelines. The proposed guidelines are consistent with the previous ones when the target density is close to having a product form, and the results highlight that the correlation structure has to be accounted for to avoid performance deterioration if that is not the case, while justifying the use of a natural (asymptotically exact) approximation to the correlation matrix that can be employed for the very first algorithm run.

A Metropolis-class sampler for targets with non-convex support

We aim to improve upon the exploration of the general-purpose random walk Metropolis algorithm when the target has non-convex support Asubset {mathbb {R}}^d, by reusing proposals in A^c which would otherwise be rejected. The algorithm is Metropolis-class and under standard conditions the chain satisfies a strong law of large numbers and central limit theorem. Theoretical and numerical evidence of improved performance relative to random walk Metropolis are provided. Issues of implementation are discussed and numerical examples, including applications to global optimisation and rare event sampling, are presented.

Efficiency of delayed-acceptance random walk Metropolis algorithms

Delayed-acceptance Metropolis–Hastings and delayed-acceptance pseudo-marginal Metropolis–Hastings algorithms can be applied when it is computationally expensive to calculate the true posterior or an unbiased stochastic approximation thereof, but a computationally cheap deterministic approximation is available. An initial accept–reject stage uses the cheap approximation for computing the Metropolis–Hastings ratio; proposals which are accepted at this stage are subjected to a further accept–reject step, which corrects for the error in the approximation. Since the expensive posterior, or the approximation thereof, is only evaluated for proposals which are accepted at the first stage, the cost of the algorithm is reduced and larger scalings may be used. We focus on the random walk Metropolis (RWM) and consider the delayed-acceptance RWM and the delayed-acceptance pseudo-marginal RWM. We provide a framework for incorporating relatively general deterministic approximations into the theoretical analysis of high-dimensional targets. Justified by diffusion-approximation arguments, we derive expressions for the limiting efficiency and acceptance rates in high-dimensional settings. Finally, these theoretical insights are leveraged to formulate practical guidelines for the efficient tuning of the algorithms. The robustness of these guidelines and predicted properties are verified against simulation studies, all of which are strictly outside of the domain of validity of our limit results.

Applying kriging proxies for Markov chain Monte Carlo in reservoir simulation

One way to quantify the uncertainty in Bayesian inverse problems arising in the engineering domain is to generate samples from the posterior distribution using Markov chain Monte Carlo (MCMC) algorithms. The basic MCMC methods tend to explore the parameter space slowly, which makes them inefficient for practical problems. On the other hand, enhanced MCMC approaches, like Hamiltonian Monte Carlo (HMC), require the gradients from the physical problem simulator, which are often not available. In this case, a feasible option is to use the gradient approximations provided by the surrogate (proxy) models built on the simulator output. In this paper, we consider proxy-aided HMC employing the Gaussian process (kriging) emulator. We overview in detail the different aspects of kriging proxies, the underlying principles of the HMC sampler and its interaction with the proxy model. The proxy-aided HMC algorithm is thoroughly tested in different settings, and applied to three case studies—one toy problem, and two synthetic reservoir simulation models. We address the question of how the sampler performance is affected by the increase of the problem dimension, the use of the gradients in proxy training, the use of proxy-for-the-data and the different approaches to the design points selection. It turns out that applying the proxy model with HMC sampler may be beneficial for relatively small physical models, with around 20 unknown parameters. Such a sampler is shown to outperform both the basic Random Walk Metropolis algorithm, and the HMC algorithm fed by the exact simulator gradients.

Optimal scaling of random-walk metropolis algorithms on general target distributions

One main limitation of the existing optimal scaling results for Metropolis–Hastings algorithms is that the assumptions on the target distribution are unrealistic. In this paper, we consider optimal scaling of random-walk Metropolis algorithms on general target distributions in high dimensions arising from practical MCMC models from Bayesian statistics. For optimal scaling by maximizing expected squared jumping distance (ESJD), we show the asymptotically optimal acceptance rate 0.234 can be obtained under general realistic sufficient conditions on the target distribution. The new sufficient conditions are easy to be verified and may hold for some general classes of MCMC models arising from Bayesian statistics applications, which substantially generalize the product i.i.d. condition required in most existing literature of optimal scaling. Furthermore, we show one-dimensional diffusion limits can be obtained under slightly stronger conditions, which still allow dependent coordinates of the target distribution. We also connect the new diffusion limit results to complexity bounds of Metropolis algorithms in high dimensions.

Hierarchical Models and Tuning of Random Walk Metropolis Algorithms

We obtain weak convergence and optimal scaling results for the random walk Metropolis algorithm with a Gaussian proposal distribution. The sampler is applied to hierarchical target distributions, which form the building block of many Bayesian analyses. The global asymptotically optimal proposal variance derived may be computed as a function of the specific target distribution considered. We also introduce the concept of locally optimal tunings, i.e., tunings that depend on the current position of the Markov chain. The theorems are proved by studying the generator of the first and second components of the algorithm and verifying their convergence to the generator of a modified RWM algorithm and a diffusion process, respectively. The rate at which the algorithm explores its state space is optimized by studying the speed measure of the limiting diffusion process. We illustrate the theory with two examples. Applications of these results on simulated and real data are also presented.

Random walk Metropolis algorithm in high dimension with non-Gaussian target distributions

High-dimensional asymptotics of the random walk Metropolis–Hastings algorithm are well understood for a class of light-tailed target distributions. Although this idealistic assumption is instructive, it may not always be appropriate, especially for complicated target distributions. We here study heavy-tailed target distributions for the random walk Metropolis algorithms. When the number of dimensions is d, the rate of consistency is d2 and the calculation cost is O(d3), which might be too expensive in high dimension.

Comparison of hit-and-run, slice sampler and random walk Metropolis

Abstract Different Markov chains can be used for approximate sampling of a distribution given by an unnormalized density function with respect to the Lebesgue measure. The hit-and-run, (hybrid) slice sampler, and random walk Metropolis algorithm are popular tools to simulate such Markov chains. We develop a general approach to compare the efficiency of these sampling procedures by the use of a partial ordering of their Markov operators, the covariance ordering. In particular, we show that the hit-and-run and the simple slice sampler are more efficient than a hybrid slice sampler based on hit-and-run, which, itself, is more efficient than a (lazy) random walk Metropolis algorithm.

MCMC for Imbalanced Categorical Data

ABSTRACTMany modern applications collect highly imbalanced categorical data, with some categories relatively rare. Bayesian hierarchical models combat data sparsity by borrowing information, while also quantifying uncertainty. However, posterior computation presents a fundamental barrier to routine use; a single class of algorithms does not work well in all settings and practitioners waste time trying different types of Markov chain Monte Carlo (MCMC) approaches. This article was motivated by an application to quantitative advertising in which we encountered extremely poor computational performance for data augmentation MCMC algorithms but obtained excellent performance for adaptive Metropolis. To obtain a deeper understanding of this behavior, we derive theoretical results on the computational complexity of commonly used data augmentation algorithms and the Random Walk Metropolis algorithm for highly imbalanced binary data. In this regime, our results show computational complexity of Metropolis is logarithmic in sample size, while data augmentation is polynomial in sample size. The root cause of this poor performance of data augmentation is a discrepancy between the rates at which the target density and MCMC step sizes concentrate. Our methods also show that MCMC algorithms that exhibit a similar discrepancy will fail in large samples—a result with substantial practical impact. Supplementary materials for this article are available online.

Efficient strategy for the Markov chain Monte Carlo in high-dimension with heavy-tailed target probability distribution

The purpose of this paper is to introduce a new Markov chain Monte Carlo method and to express its effectiveness by simulation and high-dimensional asymptotic theory. The key fact is that our algorithm has a reversible proposal kernel, which is designed to have a heavy-tailed invariant probability distribution. A high-dimensional asymptotic theory is studied for a class of heavy-tailed target probability distributions. When the number of dimensions of the state space passes to infinity, we will show that our algorithm has a much higher convergence rate than the pre-conditioned Crank–Nicolson (pCN) algorithm and the random-walk Metropolis algorithm.

Effluent trading planning and its application in water quality management: A factor-interaction perspective

In this study, a Bayesian risk-induced interval stochastic modeling framework (BRISF) is proposed for planning effluent trading program among point and nonpoint sources as well as identifying interactions of important trading factors under system risk. BRISF incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian inference with random walk Metropolis algorithm (RWM), and constraint-violation risk-based two-stage stochastic programming (CRTSP) within a general framework. Bayesian inference is employed for uncertainty analysis of SWAT model parameters and uncertain prediction of nutrient loadings; this process provides the random inputs for optimization process. CRTSP is capable of dealing with multiple uncertainties in modeling effluent trading program as well as system risk of environmental allowance violation. BRISF is applied to a real case of Xiangxihe watershed in China for water quality management. Solutions for optimal trading scheme corresponding to different risk levels are generated. Thousands of scenarios are examined to analyze the individual and interactive effects of trading ratios and treatment rates on trading system. Comparison between cross-industry and intra-industry effluent trading scheme is also conducted. It is proved that cross-industry trading would bring about higher benefit with reduced pollution loading; cross-industry effluent trading scheme would be recommended to achieve optimal water quality management and system benefit.

Asymptotic analysis of the random walk Metropolis algorithm on ridged densities

We study the asymptotic behaviour of the Random Walk Metropolis algorithm on “ridged” probability densities where most of the probability mass is distributed along some key directions. Such class of probability measures arise in various applied contexts including for instance Bayesian inverse problems where the posterior measure concentrates on a manifold when the noise variance goes to zero. When the target measure concentrates on a linear manifold, we derive analytically a diffusion limit for the Random Walk Metropolis Markov chain as the scale parameter goes to zero. In contrast to the existing works on scaling limits, our limiting stochastic differential equation does not in general have a constant diffusion coefficient. Our results show that in some cases, the usual practice of adapting the step-size to control the acceptance probability might be sub-optimal as the optimal acceptance probability is zero (in the limit).

Optimal scaling of the independence sampler: Theory and practice

The independence sampler is one of the most commonly used MCMC algorithms usually as a component of a Metropolis-within-Gibbs algorithm. The common focus for the independence sampler is on the choice of proposal distribution to obtain an as high as possible acceptance rate. In this paper we have a somewhat different focus concentrating on the use of the independence sampler for updating augmented data in a Bayesian framework where a natural proposal distribution for the independence sampler exists. Thus we concentrate on the proportion of the augmented data to update to optimise the independence sampler. Generic guidelines for optimising the independence sampler are obtained for independent and identically distributed product densities mirroring findings for the random walk Metropolis algorithm. The generic guidelines are shown to be informative beyond the narrow confines of idealised product densities in two epidemic examples.

Diffusion limit for the random walk Metropolis algorithm out of stationarity

The Random Walk Metropolis (RWM) algorithm is a Metropolis–Hastings Markov Chain Monte Carlo algorithm designed to sample from a given target distribution π^N with Lebesgue density on R^N. Like any other Metropolis–Hastings algorithm, RWM constructs a Markov chain by randomly proposing a new position (the “proposal move”), which is then accepted or rejected according to a rule which makes the chain reversible with respect to π^N. When the dimension N is large, a key question is to determine the optimal scaling with N of the proposal variance: if the proposal variance is too large, the algorithm will reject the proposed moves too often; if it is too small, the algorithm will explore the state space too slowly. Determining the optimal scaling of the proposal variance gives a measure of the cost of the algorithm as well. One approach to tackle this issue, which we adopt here, is to derive diffusion limits for the algorithm. Such an approach has been proposed in the seminal papers (Ann. Appl. Probab. 7 (1) (1997) 110–120; J. R. Stat. Soc. Ser. B. Stat. Methodol. 60 (1) (1998) 255–268). In particular, in (Ann. Appl. Probab. 7 (1) (1997) 110–120) the authors derive a diffusion limit for the RWM algorithm under the two following assumptions: (i) the algorithm is started in stationarity; (ii) the target measure π^N is in product form. The present paper considers the situation of practical interest in which both assumptions (i) and (ii) are removed. That is (a) we study the case (which occurs in practice) in which the algorithm is started out of stationarity and (b) we consider target measures which are in non-product form. Roughly speaking, we consider target measures that admit a density with respect to Gaussian; such measures arise in Bayesian nonparametric statistics and in the study of conditioned diffusions. We prove that, out of stationarity, the optimal scaling for the proposal variance is O(N^(−1)), as it is in stationarity. In this optimal scaling, a diffusion limit is obtained and the cost of reaching and exploring the invariant measure scales as O(N). Notice that the optimal scaling in and out of stationatity need not be the same in general, and indeed they differ e.g. in the case of the MALA algorithm (Stoch. Partial Differ. Equ. Anal Comput. 6 (3) (2018) 446–499). More importantly, our diffusion limit is given by a stochastic PDE, coupled to a scalar ordinary differential equation; such an ODE gives a measure of how far from stationarity the process is and can therefore be taken as an indicator of convergence. In this sense, this paper contributes understanding to the old-standing problem of monitoring convergence of MCMC algorithms.

Quenched phantom distribution functions for Markov chains

It is known that random walk Metropolis algorithms with heavy-tailed target densities can model atypical (slow) growth of maxima, which in general is exhibited by processes with the extremal index zero. The asymptotics of maxima of such sequences can be analyzed in terms of continuous phantom distribution functions. We show that in a large class of positive Harris recurrent Markov chains (containing the above Metropolis chains) a phantom distribution function can be recovered by starting “at the point” rather than from the stationary distribution.

Optimal scaling of the random walk Metropolis algorithm under Lp mean differentiability

Abstract In this paper we consider the optimal scaling of high-dimensional random walk Metropolis algorithms for densities differentiable in the Lp mean but which may be irregular at some points (such as the Laplace density, for example) and/or supported on an interval. Our main result is the weak convergence of the Markov chain (appropriately rescaled in time and space) to a Langevin diffusion process as the dimension d goes to ∞. As the log-density might be nondifferentiable, the limiting diffusion could be singular. The scaling limit is established under assumptions which are much weaker than the one used in the original derivation of Roberts et al. (1997). This result has important practical implications for the use of random walk Metropolis algorithms in Bayesian frameworks based on sparsity inducing priors.