Penalized model-based clustering with cluster-specific diagonal covariance matrices and grouped variables

Clustering analysis is one of the most widely used statistical tools in many emerging areas such as microarray data analysis. For microarray and other high-dimensional data, the presence of many noise variables may mask underlying clustering structures. Hence removing noise variables via variable selection is necessary. For simultaneous variable selection and parameter estimation, existing penalized likelihood approaches in model-based clustering analysis all assume a common diagonal covariance matrix across clusters, which however may not hold in practice. To analyze high-dimensional data, particularly those with relatively low sample sizes, this article introduces a novel approach that shrinks the variances together with means, in a more general situation with cluster-specific (diagonal) covariance matrices. Furthermore, selection of grouped variables via inclusion or exclusion of a group of variables altogether is permitted by a specific form of penalty, which facilitates incorporating subject-matter knowledge, such as gene functions in clustering microarray samples for disease subtype discovery. For implementation, EM algorithms are derived for parameter estimation, in which the M-steps clearly demonstrate the effects of shrinkage and thresholding. Numerical examples, including an application to acute leukemia subtype discovery with microarray gene expression data, are provided to demonstrate the utility and advantage of the proposed method.Comment: Published in at http://dx.doi.org/10.1214/08-EJS194 the Electronic Journal of Statistics (http://www.i-journals.org/ejs/) by the Institute of Mathematical Statistics (http://www.imstat.org

Discriminative variable selection for clustering with the sparse Fisher-EM algorithm

The interest in variable selection for clustering has increased recently due to the growing need in clustering high-dimensional data. Variable selection allows in particular to ease both the clustering and the interpretation of the results. Existing approaches have demonstrated the efficiency of variable selection for clustering but turn out to be either very time consuming or not sparse enough in high-dimensional spaces. This work proposes to perform a selection of the discriminative variables by introducing sparsity in the loading matrix of the Fisher-EM algorithm. This clustering method has been recently proposed for the simultaneous visualization and clustering of high-dimensional data. It is based on a latent mixture model which fits the data into a low-dimensional discriminative subspace. Three different approaches are proposed in this work to introduce sparsity in the orientation matrix of the discriminative subspace through $\ell_{1}$-type penalizations. Experimental comparisons with existing approaches on simulated and real-world data sets demonstrate the interest of the proposed methodology. An application to the segmentation of hyperspectral images of the planet Mars is also presented

Regularized Maximum Likelihood Estimation and Feature Selection in Mixtures-of-Experts Models

Mixture of Experts (MoE) are successful models for modeling heterogeneous data in many statistical learning problems including regression, clustering and classification. Generally fitted by maximum likelihood estimation via the well-known EM algorithm, their application to high-dimensional problems is still therefore challenging. We consider the problem of fitting and feature selection in MoE models, and propose a regularized maximum likelihood estimation approach that encourages sparse solutions for heterogeneous regression data models with potentially high-dimensional predictors. Unlike state-of-the art regularized MLE for MoE, the proposed modelings do not require an approximate of the penalty function. We develop two hybrid EM algorithms: an Expectation-Majorization-Maximization (EM/MM) algorithm, and an EM algorithm with coordinate ascent algorithm. The proposed algorithms allow to automatically obtaining sparse solutions without thresholding, and avoid matrix inversion by allowing univariate parameter updates. An experimental study shows the good performance of the algorithms in terms of recovering the actual sparse solutions, parameter estimation, and clustering of heterogeneous regression data

High dimensional Sparse Gaussian Graphical Mixture Model

This paper considers the problem of networks reconstruction from heterogeneous data using a Gaussian Graphical Mixture Model (GGMM). It is well known that parameter estimation in this context is challenging due to large numbers of variables coupled with the degeneracy of the likelihood. We propose as a solution a penalized maximum likelihood technique by imposing an $l_{1}$ penalty on the precision matrix. Our approach shrinks the parameters thereby resulting in better identifiability and variable selection. We use the Expectation Maximization (EM) algorithm which involves the graphical LASSO to estimate the mixing coefficients and the precision matrices. We show that under certain regularity conditions the Penalized Maximum Likelihood (PML) estimates are consistent. We demonstrate the performance of the PML estimator through simulations and we show the utility of our method for high dimensional data analysis in a genomic application

Sparse integrative clustering of multiple omics data sets

High resolution microarrays and second-generation sequencing platforms are powerful tools to investigate genome-wide alterations in DNA copy number, methylation and gene expression associated with a disease. An integrated genomic profiling approach measures multiple omics data types simultaneously in the same set of biological samples. Such approach renders an integrated data resolution that would not be available with any single data type. In this study, we use penalized latent variable regression methods for joint modeling of multiple omics data types to identify common latent variables that can be used to cluster patient samples into biologically and clinically relevant disease subtypes. We consider lasso [J. Roy. Statist. Soc. Ser. B 58 (1996) 267-288], elastic net [J. R. Stat. Soc. Ser. B Stat. Methodol. 67 (2005) 301-320] and fused lasso [J. R. Stat. Soc. Ser. B Stat. Methodol. 67 (2005) 91-108] methods to induce sparsity in the coefficient vectors, revealing important genomic features that have significant contributions to the latent variables. An iterative ridge regression is used to compute the sparse coefficient vectors. In model selection, a uniform design [Monographs on Statistics and Applied Probability (1994) Chapman & Hall] is used to seek "experimental" points that scattered uniformly across the search domain for efficient sampling of tuning parameter combinations. We compared our method to sparse singular value decomposition (SVD) and penalized Gaussian mixture model (GMM) using both real and simulated data sets. The proposed method is applied to integrate genomic, epigenomic and transcriptomic data for subtype analysis in breast and lung cancer data sets.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS578 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Sparse modeling of categorial explanatory variables

Shrinking methods in regression analysis are usually designed for metric predictors. In this article, however, shrinkage methods for categorial predictors are proposed. As an application we consider data from the Munich rent standard, where, for example, urban districts are treated as a categorial predictor. If independent variables are categorial, some modifications to usual shrinking procedures are necessary. Two $L_1$-penalty based methods for factor selection and clustering of categories are presented and investigated. The first approach is designed for nominal scale levels, the second one for ordinal predictors. Besides applying them to the Munich rent standard, methods are illustrated and compared in simulation studies.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS355 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org