Bani K. Mallick

Automatic Bayesian curve fitting

A method of estimating a variety of curves by a sequence of piecewise polynomials is proposed, motivated by a Bayesian model and an appropriate summary of the resulting posterior distribution. A joint distribution is set up over both the number and the position of the knots defining the piecewise polynomials. Throughout we use reversible jump Markov chain Monte Carlo methods to compute the posteriors. The methodology has been successful in giving good estimates for ‘smooth’ functions (i.e. continuous and differentiable) as well as functions which are not differentiable, and perhaps not even continuous, at a finite number of points. The methodology is extended to deal with generalized additive models.

Gene selection: a Bayesian variable selection approach

UNLABELLED Selection of significant genes via expression patterns is an important problem in microarray experiments. Owing to small sample size and the large number of variables (genes), the selection process can be unstable. This paper proposes a hierarchical Bayesian model for gene (variable) selection. We employ latent variables to specialize the model to a regression setting and uses a Bayesian mixture prior to perform the variable selection. We control the size of the model by assigning a prior distribution over the dimension (number of significant genes) of the model. The posterior distributions of the parameters are not in explicit form and we need to use a combination of truncated sampling and Markov Chain Monte Carlo (MCMC) based computation techniques to simulate the parameters from the posteriors. The Bayesian model is flexible enough to identify significant genes as well as to perform future predictions. The method is applied to cancer classification via cDNA microarrays where the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify a set of significant genes. The method is also applied successfully to the leukemia data. SUPPLEMENTARY INFORMATION http://stat.tamu.edu/people/faculty/bmallick.html.

Nonlinear estimation and classification

Nonlinear Classification * Approximation Theory and Signal Processing * Modeling of Complex Objects * Splines Gaussian Processes and Support Vector Machines * Case Studies * Theory * Machine Learning and Optimization * Future Directions

Generalized linear models : a Bayesian perspective

Part 1 Extending the GLMs. Part 2 Categorical and longitudinal data. Part 3 Semiparametric approaches. Part 4 Model diagnositics and value selection in GLMs. Part 5 Challenging problems in GLMs.

Gene selection using a two-level hierarchical Bayesian model

SUMMARY The fundamental problem of gene selection via cDNA data is to identify which genes are differentially expressed across different kinds of tissue samples (e.g. normal and cancer). cDNA data contain large number of variables (genes) and usually the sample size is relatively small so the selection process can be unstable. Therefore, models which incorporate sparsity in terms of variables (genes) are desirable for this kind of problem. This paper proposes a two-level hierarchical Bayesian model for variable selection which assumes a prior that favors sparseness. We adopt a Markov chain Monte Carlo (MCMC) based computation technique to simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer. SUPPLEMENTARY INFORMATION http://stat.tamu.edu/people/faculty/bmallick.html.

Analyzing Nonstationary Spatial Data Using Piecewise Gaussian Processes

In many problems in geostatistics the response variable of interest is strongly related to the underlying geology of the spatial location. In these situations there is often little correlation in the responses found in different rock strata, so the underlying covariance structure shows sharp changes at the boundaries of the rock types. Conventional stationary and nonstationary spatial methods are inappropriate, because they typically assume that the covariance between points is a smooth function of distance. In this article we propose a generic method for the analysis of spatial data with sharp changes in the underlying covariance structure. Our method works by automatically decomposing the spatial domain into disjoint regions within which the process is assumed to be stationary, but the data are assumed independent across regions. Uncertainty in the number of disjoint regions, their shapes, and the model within regions is dealt with in a fully Bayesian fashion. We illustrate our approach on a previously unpublished dataset relating to soil permeability of the Schneider Buda oil field in Wood County, Texas.

Bayesian radial basis functions of variable dimension

A Bayesian framework for the analysis of radial basis functions (RBF) is proposed that accommodates uncertainty in the dimension of the model. A distribution is defined over the space of all RBF models of a given basis function, and posterior densities are computed using reversible jump Markov chain Monte Carlo samplers (Green, 1995). This alleviates the need to select the architecture during the modeling process. The resulting networks are shown to adjust their size to the complexity of the data.

Bayesian semiparametric inference for the accelerated failure-time model

Bayesian semiparametric inference is considered for a loglinear model. This model consists of a parametric component for the regression coefficients and a nonparametric component for the unknown error distribution. Bayesian analysis is studied for the case of a parametric prior on the regression coefficients and a mixture-of-Dirichlet-processes prior on the unknown error distribution. A Markov-chain Monte Carlo (MCMC) method is developed to compute the features of the posterior distribution. A model selection method for obtaining a more parsimonious set of predictors is studied. The method adds indicator variables to the regression equation. The set of indicator variables represents all the possible subsets to be considered. A MCMC method is developed to search stochastically for the best subset. These procedures are applied to two examples, one with censored data.

BAYESIAN ANALYSIS OF PROPORTIONAL HAZARDS MODELS BUILT FROM MONOTONE FUNCTIONS

We consider the usual proportional hazards model in the case where the baseline hazard, the covariate link, and the covariate coefficients are all unknown. Both the baseline hazard and the covariate link are monotone functions and thus are characterized using a dense class of such functions which arises, upon transformation, as a mixture of Beta distribution functions. We take a Bayesian approach for fitting such a model. Since interest focuses more upon the likelihood, we consider vague prior specifications including Jeffreyss prior. Computations are carried out using sampling-based methods. Model criticism is also discussed. Finally, a data set studying survival of a sample of lung cancer patients is analyzed.

Bayesian MARS

A Bayesian approach to multivariate adaptive regression spline (MARS) fitting (Friedman, 1991) is proposed. This takes the form of a probability distribution over the space of possible MARS models which is explored using reversible jump Markov chain Monte Carlo methods (Green, 1995). The generated sample of MARS models produced is shown to have good predictive power when averaged and allows easy interpretation of the relative importance of predictors to the overall fit.