It is known that a Markov basis of the binary graph model of a graph $G$ corresponds to a set of binomial generators of cut ideals $I_{widehat{G}}$ of the suspension $widehat{G}$ of $G$. In this paper, we give another application of cut ideals to statistics. We show that a set of binomial generators of cut ideals is a Markov basis of some regular two-level fractional factorial design. As application, we give a Markov basis of degree 2 for designs defined by at most two relations.
We consider Markov chain Monte Carlo methods for calculating conditional p values of statistical models for count data arising in Box-Behnken designs. The statistical model we consider is a discrete version of the first-order model in the response surface methodology. For our models, the Markov basis, a key notion to construct a connected Markov chain on a given sample space, is characterized as generators of the toric ideals for the centrally symmetric configurations of root system D_n. We show the structure of the Groebner bases for these cases. A numerical example for an imaginary data set is given.
Markov chain Monte Carlo (MCMC) produces a correlated sample for estimating expectations with respect to a target distribution. A fundamental question is when should sampling stop so that we have good estimates of the desired quantities? The key to answering this question lies in assessing the Monte Carlo error through a multivariate Markov chain central limit theorem (CLT). The multivariate nature of this Monte Carlo error largely has been ignored in the MCMC literature. We present a multivariate framework for terminating simulation in MCMC. We define a multivariate effective sample size, estimating which requires strongly consistent estimators of the covariance matrix in the Markov chain CLT; a property we show for the multivariate batch means estimator. We then provide a lower bound on the number of minimum effective samples required for a desired level of precision. This lower bound depends on the problem only in the dimension of the expectation being estimated, and not on the underlying stochastic process. This result is obtained by drawing a connection between terminating simulation via effective sample size and terminating simulation using a relative standard deviation fixed-volume sequential stopping rule; which we demonstrate is an asymptotically valid procedure. The finite sample properties of the proposed method are demonstrated in a variety of examples.
The minimum aberration criterion has been frequently used in the selection of fractional factorial designs with nominal factors. For designs with quantitative factors, however, level permutation of factors could alter their geometrical structures and statistical properties. In this paper uniformity is used to further distinguish fractional factorial designs, besides the minimum aberration criterion. We show that minimum aberration designs have low discrepancies on average. An efficient method for constructing uniform minimum aberration designs is proposed and optimal designs with 27 and 81 runs are obtained for practical use. These designs have good uniformity and are effective for studying quantitative factors.
This paper proposes a family of weighted batch means variance estimators, which are computationally efficient and can be conveniently applied in practice. The focus is on Markov chain Monte Carlo simulations and estimation of the asymptotic covariance matrix in the Markov chain central limit theorem, where conditions ensuring strong consistency are provided. Finite sample performance is evaluated through auto-regressive, Bayesian spatial-temporal, and Bayesian logistic regression examples, where the new estimators show significant computational gains with a minor sacrifice in variance compared with existing methods.
We present some optimal criteria to evaluate model-robustness of non-regular two-level fractional factorial designs. Our method is based on minimizing the sum of squares of all the off-diagonal elements in the information matrix, and considering expectation under appropriate distribution functions for unknown contamination of the interaction effects. By considering uniform distributions on symmetric support, our criteria can be expressed as linear combinations of $B_s(d)$ characteristic, which is used to characterize the generalized minimum aberration. We give some empirical studies for 12-run non-regular designs to evaluate our method.