Adaptive Bayesian variable clustering via structural learning of breast cancer data.

The clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce the clustering through prior modeling using angle-based unconstrained reparameterization of correlations and assume a truncated Poisson distribution (to penalize a large number of clusters) as prior on the number of clusters. The posterior distributions of the parameters are not in explicit form and we use a reversible jump Markov chain Monte Carlo based technique is used to simulate the parameters from the posteriors. The end products of the proposed method are estimated cluster configuration of the proteins (variables) along with the number of clusters. The Bayesian method is flexible enough to cluster the proteins as well as estimate the number of clusters. The performance of the proposed method has been substantiated with extensive simulation studies and one protein expression data with a hereditary disposition in breast cancer where the proteins are coming from different pathways.

Reducing Brain Signal Noise in the Prediction of Economic Choices: A Case Study in Neuroeconomics.

In order to reduce the noise of brain signals, neuroeconomic experiments typically aggregate data from hundreds of trials collected from a few individuals. This contrasts with the principle of simple and controlled designs in experimental and behavioral economics. We use a frequency domain variant of the stationary subspace analysis (SSA) technique, denoted as DSSA, to filter out the noise (nonstationary sources) in EEG brain signals. The nonstationary sources in the brain signal are associated with variations in the mental state that are unrelated to the experimental task. DSSA is a powerful tool for reducing the number of trials needed from each participant in neuroeconomic experiments and also for improving the prediction performance of an economic choice task. For a single trial, when DSSA is used as a noise reduction technique, the prediction model in a food snack choice experiment has an increase in overall accuracy by around 10% and in sensitivity and specificity by around 20% and in AUC by around 30%, respectively.

Multivariate time series analysis of neuroscience data: some challenges and opportunities.

Neuroimaging data may be viewed as high-dimensional multivariate time series, and analyzed using techniques from regression analysis, time series analysis and spatiotemporal analysis. We discuss issues related to data quality, model specification, estimation, interpretation, dimensionality and causality. Some recent research areas addressing aspects of some recurring challenges are introduced.

Modeling the Cholesky factors of covariance matrices of multivariate longitudinal data.

Modeling the covariance matrix of multivariate longitudinal data is more challenging as compared to its univariate counterpart due to the presence of correlations among multiple responses. The modified Cholesky block decomposition reduces the task of covariance modeling into parsimonious modeling of its two matrix factors: the regression coefficient matrices and the innovation covariance matrices. These parameters are statistically interpretable, however ensuring positive-definiteness of several (innovation) covariance matrices presents itself as a new challenge. We address this problem using a subclass of Anderson's (1973) linear covariance models and model several covariance matrices using linear combinations of known positive-definite basis matrices with unknown non-negative scalar coefficients. A novelty of this approach is that positive-definiteness is guaranteed by construction; it removes a drawback of Anderson's model and hence makes linear covariance models more realistic and viable in practice. Maximum likelihood estimates are computed using a simple iterative majorization-minimization algorithm. The estimators are shown to be asymptotically normal and consistent. Simulation and a data example illustrate the applicability of the proposed method in providing good models for the covariance structure of a multivariate longitudinal data.

Gaussian estimation and joint modeling of dispersions and correlations in longitudinal data.

Analysis of longitudinal, spatial and epidemiological data often requires modelling dispersions and dependence among the measurements. Moreover, data involving counts or proportions usually exhibit greater variation than would be predicted by the Poisson and binomial models. We propose a strategy for the joint modelling of mean, dispersion and correlation matrix of nonnormal multivariate correlated data. The parameter estimation for dispersions and correlations is based on the Whittle's [P. Whittle, Gaussian estimation in stationary time series, Bull Inst. Statist. Inst. 39 (1962) 105-129.] Gaussian likelihood of the partially standardized data which eliminates the mean parameters. The model formulation for the dispersions and correlations relies on a recent unconstrained parameterization of covariance matrices and a graphical method [M. Pourahmadi, Joint mean-covariance models with applications to longitudinal data: unconstrained parameterization, Biometrika 86 (1999) 677-690] similar to the correlogram in time series analysis. We show that the estimating equations for the regression and dependence parameters derived from a modified Gaussian likelihood (involving two distinct covariance matrices) are broad enough to include generalized estimating equations and its many recent extensions and improvements. The results are illustrated using two datasets.