On Graphical Models via Univariate Exponential Family Distributions

Undirected graphical models, or Markov networks, are a popular class of statistical models, used in a wide variety of applications. Popular instances of this class include Gaussian graphical models and Ising models. In many settings, however, it might not be clear which subclass of graphical models to use, particularly for non-Gaussian and non-categorical data. In this paper, we consider a general sub-class of graphical models where the node-wise conditional distributions arise from exponential families. This allows us to derive multivariate graphical model distributions from univariate exponential family distributions, such as the Poisson, negative binomial, and exponential distributions. Our key contributions include a class of M-estimators to fit these graphical model distributions; and rigorous statistical analysis showing that these M-estimators recover the true graphical model structure exactly, with high probability. We provide examples of genomic and proteomic networks learned via instances of our class of graphical models derived from Poisson and exponential distributions.Comment: Journal of Machine Learning Researc

Multivariate Bernoulli distribution

In this paper, we consider the multivariate Bernoulli distribution as a model to estimate the structure of graphs with binary nodes. This distribution is discussed in the framework of the exponential family, and its statistical properties regarding independence of the nodes are demonstrated. Importantly the model can estimate not only the main effects and pairwise interactions among the nodes but also is capable of modeling higher order interactions, allowing for the existence of complex clique effects. We compare the multivariate Bernoulli model with existing graphical inference models - the Ising model and the multivariate Gaussian model, where only the pairwise interactions are considered. On the other hand, the multivariate Bernoulli distribution has an interesting property in that independence and uncorrelatedness of the component random variables are equivalent. Both the marginal and conditional distributions of a subset of variables in the multivariate Bernoulli distribution still follow the multivariate Bernoulli distribution. Furthermore, the multivariate Bernoulli logistic model is developed under generalized linear model theory by utilizing the canonical link function in order to include covariate information on the nodes, edges and cliques. We also consider variable selection techniques such as LASSO in the logistic model to impose sparsity structure on the graph. Finally, we discuss extending the smoothing spline ANOVA approach to the multivariate Bernoulli logistic model to enable estimation of non-linear effects of the predictor variables.Comment: Published in at http://dx.doi.org/10.3150/12-BEJSP10 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

mgm: Estimating Time-Varying Mixed Graphical Models in High-Dimensional Data

We present the R-package mgm for the estimation of k-order Mixed Graphical Models (MGMs) and mixed Vector Autoregressive (mVAR) models in high-dimensional data. These are a useful extensions of graphical models for only one variable type, since data sets consisting of mixed types of variables (continuous, count, categorical) are ubiquitous. In addition, we allow to relax the stationarity assumption of both models by introducing time-varying versions MGMs and mVAR models based on a kernel weighting approach. Time-varying models offer a rich description of temporally evolving systems and allow to identify external influences on the model structure such as the impact of interventions. We provide the background of all implemented methods and provide fully reproducible examples that illustrate how to use the package