Sequential Design for Computer Experiments with a Flexible Bayesian Additive Model

In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex phenomena. Simulators can be thought of as complex functions that take many inputs and provide an output. Often these simulators are themselves expensive to compute, and may be approximated by "surrogate models" such as statistical regression models. In this paper we consider a new kind of surrogate model, a Bayesian ensemble of trees (Chipman et al. 2010), with the specific goal of learning enough about the simulator that a particular feature of the simulator can be estimated. We focus on identifying the simulator's global minimum. Utilizing the Bayesian version of the Expected Improvement criterion (Jones et al. 1998), we show that this ensemble is particularly effective when the simulator is ill-behaved, exhibiting nonstationarity or abrupt changes in the response. A number of illustrations of the approach are given, including a tidal power application.Comment: 21 page

GPfit: An R package for Gaussian Process Model Fitting using a New Optimization Algorithm

Gaussian process (GP) models are commonly used statistical metamodels for emulating expensive computer simulators. Fitting a GP model can be numerically unstable if any pair of design points in the input space are close together. Ranjan, Haynes, and Karsten (2011) proposed a computationally stable approach for fitting GP models to deterministic computer simulators. They used a genetic algorithm based approach that is robust but computationally intensive for maximizing the likelihood. This paper implements a slightly modified version of the model proposed by Ranjan et al. (2011), as the new R package GPfit. A novel parameterization of the spatial correlation function and a new multi-start gradient based optimization algorithm yield optimization that is robust and typically faster than the genetic algorithm based approach. We present two examples with R codes to illustrate the usage of the main functions in GPfit. Several test functions are used for performance comparison with a popular R package mlegp. GPfit is a free software and distributed under the general public license, as part of the R software project (R Development Core Team 2012).Comment: 20 pages, 17 image

Bayesian Variable Selection with Related Predictors

In data sets with many predictors, algorithms for identifying a good subset of predictors are often used. Most such algorithms do not account for any relationships between predictors. For example, stepwise regression might select a model containing an interaction AB but neither main effect A or B. This paper develops mathematical representations of this and other relations between predictors, which may then be incorporated in a model selection procedure. A Bayesian approach that goes beyond the standard independence prior for variable selection is adopted, and preference for certain models is interpreted as prior information. Priors relevant to arbitrary interactions and polynomials, dummy variables for categorical factors, competing predictors, and restrictions on the size of the models are developed. Since the relations developed are for priors, they may be incorporated in any Bayesian variable selection algorithm for any type of linear model. The application of the methods here is illustrated via the Stochastic Search Variable Selection algorithm of George and McCulloch (1993), which is modified to utilize the new priors. The performance of the approach is illustrated with two constructed examples and a computer performance dataset. Keywords: Model Selection, Prior Distributions, Interaction, Dummy VariableComment: uuencoded, gzipped postscript file, 24 pages including graphics and tables. Revised version includes new example and improved plot. Paper also available at http://gsbhac.uchicago.edu/techreports/ Author has web page at http://www-gsb.uchicago.edu