Chemical space is so large that brute force searches for new interesting molecules are infeasible. High-throughput virtual screening via computer cluster simulations can speed up the discovery process by collecting very large amounts of data in parallel, e.g., up to hundreds or thousands of parallel measurements. Bayesian optimization (BO) can produce additional acceleration by sequentially identifying the most useful simulations or experiments to be performed next. However, current BO methods cannot scale to the large numbers of parallel measurements and the massive libraries of molecules currently used in high-throughput screening. Here, we propose a scalable solution based on a parallel and distributed implementation of Thompson sampling (PDTS). We show that, in small scale problems, PDTS performs similarly as parallel expected improvement (EI), a batch version of the most widely used BO heuristic. Additionally, in settings where parallel EI does not scale, PDTS outperforms other scalable baselines such as a greedy search, @math -greedy approaches and a random search method. These results show that PDTS is a successful solution for large-scale parallel BO.
compute a Monte Carlo approximation of the expected acquisition function over potential fantasies sampled from the model's predictive distribution. Recent methods have been proposed to modify the parallel EI procedure to recommend points jointly @cite_8 @cite_16 @cite_29 .
@cite_29 @cite_16 @cite_8
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We introduce a new approach for amortizing inference in directed graphical models by learning heuristic approximations to stochastic inverses, designed specifically for use as proposal distributions in sequential Monte Carlo methods. We describe a procedure for constructing and learning a structured neural network which represents an inverse factorization of the graphical model, resulting in a conditional density estimator that takes as input particular values of the observed random variables, and returns an approximation to the distribution of the latent variables. This recognition model can be learned offline, independent from any particular dataset, prior to performing inference. The output of these networks can be used as automatically-learned high-quality proposal distributions to accelerate sequential Monte Carlo across a diverse range of problem settings. Monte Carlo importance sampling for evaluating numerical integration is discussed. We consider a parametric family of sampling distributions and propose the use of the sampling distribution estimated by maximum likelihood. The proposed method of importance sampling using the estimated sampling distribution is shown to improve the asymptotic variance of the ordinary method using the true sampling distribution. The argument is closely related to the discussion of the paradox in Henmi & Eguchi (2004). We focus on a condition under which the estimated integration value obtained by the proposed method has asymptotic zero variance. Copyright 2007, Oxford University Press. Researchers and analysts are increasingly using mixed logit models for estimating responses to forecast demand and to determine the factors that affect individual choices. However the numerical cost associated to their evaluation can be prohibitive, the inherent probability choices being represented by multidimensional integrals. This cost remains high even if Monte Carlo or quasi-Monte Carlo techniques are used to estimate those integrals. This paper describes a new algorithm that uses Monte Carlo approximations in the context of modern trust-region techniques, but also exploits accuracy and bias estimators to considerably increase its computational efficiency. Numerical experiments underline the importance of the choice of an appropriate optimisation technique and indicate that the proposed algorithm allows substantial gains in time while delivering more information to the practitioner. Copyright Springer-Verlag Berlin Heidelberg 2006 Monte Carlo methods have extensively been used and studied in the area of stochastic programming. Their convergence properties typically consider global minimizers or first-order critical points of the sample average approximation (SAA) problems and minimizers of the true problem, and show that the former converge to the latter for increasing sample size. However, the assumption of global minimization essentially restricts the scope of these results to convex problems. We review and extend these results in two directions: we allow for local SAA minimizers of possibly nonconvex problems and prove, under suitable conditions, almost sure convergence of local second-order solutions of the SAA problem to second-order critical points of the true problem. We also apply this new theory to the estimation of mixed logit models for discrete choice analysis. New useful convergence properties are derived in this context, both for the constrained and unconstrained cases, and associated estimates of the simulation bias and variance are proposed.