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We introduce a powerful and flexible MCMC algorithm for stochastic simulation. The method builds on a pseudo-marginal method originally introduced in [Genetics 164 (2003) 1139-1160], showing how algorithms which are approximations to an idealized marginal algorithm, can share the same marginal stationary distribution as the idealized method. Theoretical results are given describing the convergence properties of the proposed method, and simple numerical examples are given to illustrate the promising empirical characteristics of the technique. Interesting comparisons with a more obvious, but inexact, Monte Carlo approximation to the marginal algorithm, are also given.

We adapt the expectation-maximization algorithm to incorporate unobserved heterogeneity into conditional choice probability (CCP) estimators of dynamic discrete choice problems. The unobserved heterogeneity can be time-invariant or follow a Markov chain. By developing a class of problems where the difference in future value terms depends on a few conditional choice probabilities, we extend the class of dynamic optimization problems where CCP estimators provide a computationally cheap alternative to full solution methods. Monte Carlo results confirm that our algorithms perform quite well, both in terms of computational time and in the precision of the parameter estimates.

We propose a methodology to sample sequentially from a sequence of probability distributions that are defined on a common space, each distribution being known up to a normalizing constant. These probability distributions are approximated by a cloud of weighted random samples which are propagated over time by using sequential Monte Carlo methods. This methodology allows us to derive simple algorithms to make parallel Markov chain Monte Carlo algorithms interact to perform global optimization and sequential Bayesian estimation and to compute ratios of normalizing constants. We illustrate these algorithms for various integration tasks arising in the context of Bayesian inference.

This paper concerns an acceleration method for fixed-point iterations that originated in work of D. G. Anderson [J. Assoc. Comput. Mach., 12 (1965), pp. 547–560], which we accordingly call Anderson acceleration here. This method has enjoyed considerable success and wide usage in electronic structure computations, where it is known as Anderson mixing; however, it seems to have been untried or underexploited in many other important applications. Moreover, while other acceleration methods have been extensively studied by the mathematics and numerical analysis communities, this method has received relatively little attention from these communities over the years. A recent paper by H. Fang and Y. Saad [Numer. Linear Algebra Appl., 16 (2009), pp. 197–221] has clarified a remarkable relationship of Anderson acceleration to quasi-Newton (secant updating) methods and extended it to define a broader Anderson family of acceleration methods. In this paper, our goals are to shed additional light on Anderson acceleration and to draw further attention to its usefulness as a general tool. We first show that, on linear problems, Anderson acceleration without truncation is \"essentially equivalent\" in a certain sense to the generalized minimal residual (GMRES) method. We also show that the Type 1 variant in the Fang—Saad Anderson family is similarly essentially equivalent to the Arnoldi (full orthogonalization) method. We then discuss practical considerations for implementing Anderson acceleration and illustrate its performance through numerical experiments involving a variety of applications.

Calculating a Monte Carlo standard error (MCSE) is an important step in the statistical analysis of the simulation output obtained from a Markov chain Monte Carlo experiment. An MCSE is usually based on an estimate of the variance of the asymptotic normal distribution. We consider spectral and batch means methods for estimating this variance. In particular, we establish conditions which guarantee that these estimators are strongly consistent as the simulation effort increases. In addition, for the batch means and overlapping batch means methods we establish conditions ensuring consistency in the mean-square sense which in turn allows us to calculate the optimal batch size up to a constant of proportionality. Finally, we examine the empirical finite-sample properties of spectral variance and batch means estimators and provide recommendations for practitioners.

Families, primarily female-headed minority households with children, living in high-poverty public housing projects in five U.S. cities were offered housing vouchers by lottery in the Moving to Opportunity program. Four to seven years after random assignment, families offered vouchers lived in safer neighborhoods that had lower poverty rates than those of the control group not offered vouchers. We find no significant overall effects of this intervention on adult economic self-sufficiency or physical health. Mental health benefits of the voucher offers for adults and for female youth were substantial. Beneficial effects for female youth on education, risky behavior, and physical health were offset by adverse effects for male youth. For outcomes that exhibit significant treatment effects, we find, using variation in treatment intensity across voucher types and cities, that the relationship between neighborhood poverty rate and outcomes is approximately linear.

Particle methods are popular computational tools for Bayesian inference in nonlinear non-Gaussian state space models. For this class of models, we present two particle algorithms to compute the score vector and observed information matrix recursively. The first algorithm is implemented with computational complexity 𝒪(N) and the second with complexity 𝒪(N²), where N is the number of particles. Although cheaper, the performance of the 𝒪(N) method degrades quickly, as it relies on the approximation of a sequence of probability distributions whose dimension increases linearly with time. In particular, even under strong mixing assumptions, the variance of the estimates computed with the 𝒪(N) method increases at least quadratically in time. The more expensive 𝒪(N²) method relies on a nonstandard particle implementation and does not suffer from this rapid degradation. It is shown how both methods can be used to perform batch and recursive parameter estimation.

We propose the elastic net, a new regularization and variable selection method. Real world data and a simulation study show that the elastic net often outperforms the lasso, while enjoying a similar sparsity of representation. In addition, the elastic net encourages a grouping effect, where strongly correlated predictors tend to be in or out of the model together. The elastic net is particularly useful when the number of predictors (p) is much bigger than the number of observations (n). By contrast, the lasso is not a very satisfactory variable selection method in the p ≫ n case. An algorithm called LARS-EN is proposed for computing elastic net regularization paths efficiently, much like algorithm LARS does for the lasso.

Geostatistics involves the fitting of spatially continuous models to spatially discrete data. Preferential sampling arises when the process that determines the data locations and the process being modelled are stochastically dependent. Conventional geostatistical methods assume, if only implicitly, that sampling is non-preferential. However, these methods are often used in situations where sampling is likely to be preferential. For example, in mineral exploration, samples may be concentrated in areas that are thought likely to yield high grade ore. We give a general expression for the likelihood function of preferentially sampled geostatistical data and describe how this can be evaluated approximately by using Monte Carlo methods. We present a model for preferential sampling and demonstrate through simulated examples that ignoring preferential sampling can lead to misleading inferences. We describe an application of the model to a set of biomonitoring data from Galicia, northern Spain, in which making allowance for preferential sampling materially changes the results of the analysis.

Model choice plays an increasingly important role in statistics. From a Bayesian perspective a crucial goal is to compute the marginal likelihood of the data for a given model. However, this is typically a difficult task since it amounts to integrating over all model parameters. The aim of the paper is to illustrate how this may be achieved by using ideas from thermodynamic integration or path sampling. We show how the marginal likelihood can be computed via Markov chain Monte Carlo methods on modified posterior distributions for each model. This then allows Bayes factors or posterior model probabilities to be calculated. We show that this approach requires very little tuning and is straightforward to implement. The new method is illustrated in a variety of challenging statistical settings.