Factorial graphical lasso for dynamic networks

Dynamic networks models describe a growing number of important scientific processes, from cell biology and epidemiology to sociology and finance. There are many aspects of dynamical networks that require statistical considerations. In this paper we focus on determining network structure. Estimating dynamic networks is a difficult task since the number of components involved in the system is very large. As a result, the number of parameters to be estimated is bigger than the number of observations. However, a characteristic of many networks is that they are sparse. For example, the molecular structure of genes make interactions with other components a highly-structured and therefore sparse process. Penalized Gaussian graphical models have been used to estimate sparse networks. However, the literature has focussed on static networks, which lack specific temporal constraints. We propose a structured Gaussian dynamical graphical model, where structures can consist of specific time dynamics, known presence or absence of links and block equality constraints on the parameters. Thus, the number of parameters to be estimated is reduced and accuracy of the estimates, including the identification of the network, can be tuned up. Here, we show that the constrained optimization problem can be solved by taking advantage of an efficient solver, logdetPPA, developed in convex optimization. Moreover, model selection methods for checking the sensitivity of the inferred networks are described. Finally, synthetic and real data illustrate the proposed methodologies.Comment: 30 pp, 5 figure

MaxSkew and MultiSkew: Two R Packages for Detecting, Measuring and Removing Multivariate Skewness

Skewness plays a relevant role in several multivariate statistical techniques. Sometimes it is used to recover data features, as in cluster analysis. In other circumstances, skewness impairs the performances of statistical methods, as in the Hotelling's one-sample test. In both cases, there is the need to check the symmetry of the underlying distribution, either by visual inspection or by formal testing. The R packages MaxSkew and MultiSkew address these issues by measuring, testing and removing skewness from multivariate data. Skewness is assessed by the third multivariate cumulant and its functions. The hypothesis of symmetry is tested either nonparametrically, with the bootstrap, or parametrically, under the normality assumption. Skewness is removed or at least alleviated by projecting the data onto appropriate linear subspaces. Usages of MaxSkew and MultiSkew are illustrated with the Iris dataset

Algebraic Theory of Multi-Product Decisions, An

The typical firm produces for sale a plural number of distinct product lines. This paper characterizes the composition of a firm?s optimal production vector as a function of cost and revenue function attributes. The approach taken applies mathematical group theory and revealed preference arguments to exploit controlled asymmetries in the production environment. Assuming some symmetry on the cost function, our central result shows that all optimal production vectors must satisfy a dominance relation on permutations of the firm?s revenue function. When the revenue function is linear in outputs, then the set of admissible output vectors has linear bounds up to transformations. If these transformations are also linear, then convex analysis can be applied to characterize the set of admissible solutions. When the group of symmetries decomposes into a direct product group with index K in N, then the characterization problem separates into K problems of smaller dimension. The central result may be strengthened ; when the cost function is assumed to be quasiconvex.

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 Linear Identifiable Multivariate Modeling

In this paper we consider sparse and identifiable linear latent variable (factor) and linear Bayesian network models for parsimonious analysis of multivariate data. We propose a computationally efficient method for joint parameter and model inference, and model comparison. It consists of a fully Bayesian hierarchy for sparse models using slab and spike priors (two-component delta-function and continuous mixtures), non-Gaussian latent factors and a stochastic search over the ordering of the variables. The framework, which we call SLIM (Sparse Linear Identifiable Multivariate modeling), is validated and bench-marked on artificial and real biological data sets. SLIM is closest in spirit to LiNGAM (Shimizu et al., 2006), but differs substantially in inference, Bayesian network structure learning and model comparison. Experimentally, SLIM performs equally well or better than LiNGAM with comparable computational complexity. We attribute this mainly to the stochastic search strategy used, and to parsimony (sparsity and identifiability), which is an explicit part of the model. We propose two extensions to the basic i.i.d. linear framework: non-linear dependence on observed variables, called SNIM (Sparse Non-linear Identifiable Multivariate modeling) and allowing for correlations between latent variables, called CSLIM (Correlated SLIM), for the temporal and/or spatial data. The source code and scripts are available from http://cogsys.imm.dtu.dk/slim/.Comment: 45 pages, 17 figure

Inference in Graphical Gaussian Models with Edge and Vertex Symmetries with the gRc Package for R

In this paper we present the R package gRc for statistical inference in graphical Gaussian models in which symmetry restrictions have been imposed on the concentration or partial correlation matrix. The models are represented by coloured graphs where parameters associated with edges or vertices of same colour are restricted to being identical. We describe algorithms for maximum likelihood estimation and discuss model selection issues. The paper illustrates the practical use of the gRc package