Revisiting the Gelman-Rubin Diagnostic

Gelman and Rubin's (1992) convergence diagnostic is one of the most popular methods for terminating a Markov chain Monte Carlo (MCMC) sampler. Since the seminal paper, researchers have developed sophisticated methods for estimating variance of Monte Carlo averages. We show that these estimators find immediate use in the Gelman-Rubin statistic, a connection not previously established in the literature. We incorporate these estimators to upgrade both the univariate and multivariate Gelman-Rubin statistics, leading to improved stability in MCMC termination time. An immediate advantage is that our new Gelman-Rubin statistic can be calculated for a single chain. In addition, we establish a one-to-one relationship between the Gelman-Rubin statistic and effective sample size. Leveraging this relationship, we develop a principled termination criterion for the Gelman-Rubin statistic. Finally, we demonstrate the utility of our improved diagnostic via examples

Deep unsupervised clustering with Gaussian mixture variational autoencoders

We study a variant of the variational autoencoder model with a Gaussian mixture as a prior distribution, with the goal of performing unsupervised clustering through deep generative models. We observe that the standard variational approach in these models is unsuited for unsupervised clustering, and mitigate this problem by leveraging a principled information-theoretic regularisation term known as consistency violation. Adding this term to the standard variational optimisation objective yields networks with both meaningful internal representations and well-defined clusters. We demonstrate the performance of this scheme on synthetic data, MNIST and SVHN, showing that the obtained clusters are distinct, interpretable and result in achieving higher performance on unsupervised clustering classification than previous approaches

Kernel estimators of asymptotic variance for adaptive Markov chain Monte Carlo

We study the asymptotic behavior of kernel estimators of asymptotic variances (or long-run variances) for a class of adaptive Markov chains. The convergence is studied both in $L^p$ and almost surely. The results also apply to Markov chains and improve on the existing literature by imposing weaker conditions. We illustrate the results with applications to the $\operatorname {GARCH}(1,1)$ Markov model and to an adaptive MCMC algorithm for Bayesian logistic regression.Comment: Published in at http://dx.doi.org/10.1214/10-AOS828 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Multiorder neurons for evolutionary higher-order clustering and growth

This letter proposes to use multiorder neurons for clustering irregularly shaped data arrangements. Multiorder neurons are an evolutionary extension of the use of higher-order neurons in clustering. Higher-order neurons parametrically model complex neuron shapes by replacing the classic synaptic weight by higher-order tensors. The multiorder neuron goes one step further and eliminates two problems associated with higher-order neurons. First, it uses evolutionary algorithms to select the best neuron order for a given problem. Second, it obtains more information about the underlying data distribution by identifying the correct order for a given cluster of patterns. Empirically we observed that when the correlation of clusters found with ground truth information is used in measuring clustering accuracy, the proposed evolutionary multiorder neurons method can be shown to outperform other related clustering methods. The simulation results from the Iris, Wine, and Glass data sets show significant improvement when compared to the results obtained using self-organizing maps and higher-order neurons. The letter also proposes an intuitive model by which multiorder neurons can be grown, thereby determining the number of clusters in data

Application of Volcano Plots in Analyses of mRNA Differential Expressions with Microarrays

Volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log10(p-value) from the t test). We review the basic and an interactive use of the volcano plot, and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide an unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility to apply volcano plots to other fields beyond microarray.Comment: 8 figure

Bounding Optimality Gap in Stochastic Optimization via Bagging: Statistical Efficiency and Stability

We study a statistical method to estimate the optimal value, and the optimality gap of a given solution for stochastic optimization as an assessment of the solution quality. Our approach is based on bootstrap aggregating, or bagging, resampled sample average approximation (SAA). We show how this approach leads to valid statistical confidence bounds for non-smooth optimization. We also demonstrate its statistical efficiency and stability that are especially desirable in limited-data situations, and compare these properties with some existing methods. We present our theory that views SAA as a kernel in an infinite-order symmetric statistic, which can be approximated via bagging. We substantiate our theoretical findings with numerical results