Computational aspects of DNA mixture analysis

Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed locally involving only a few alleles at each step. In addition, we describe a general method for computing the expectation of a product of discrete random variables using auxiliary variables and probability propagation in a Bayesian network, which in combination with the genotype network allows efficient computation of the likelihood function and various other quantities relevant to the inference. Lastly, we introduce a set of diagnostic tools for assessing the adequacy of the model for describing a particular dataset

Unifying Markov Properties for Graphical Models

Several types of graphs with different conditional independence interpretations --- also known as Markov properties --- have been proposed and used in graphical models. In this paper we unify these Markov properties by introducing a class of graphs with four types of edges --- lines, arrows, arcs, and dotted lines --- and a single separation criterion. We show that independence structures defined by this class specialize to each of the previously defined cases, when suitable subclasses of graphs are considered. In addition, we define a pairwise Markov property for the subclass of chain mixed graphs which includes chain graphs with the LWF interpretation, as well as summary graphs (and consequently ancestral graphs). We prove the equivalence of this pairwise Markov property to the global Markov property for compositional graphoid independence models.Comment: 31 Pages, 6 figures, 1 tabl

Discussion: Latent variable graphical model selection via convex optimization

Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].Comment: Published in at http://dx.doi.org/10.1214/12-AOS980 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Markov properties for mixed graphs

In this paper, we unify the Markov theory of a variety of different types of graphs used in graphical Markov models by introducing the class of loopless mixed graphs, and show that all independence models induced by $m$-separation on such graphs are compositional graphoids. We focus in particular on the subclass of ribbonless graphs which as special cases include undirected graphs, bidirected graphs, and directed acyclic graphs, as well as ancestral graphs and summary graphs. We define maximality of such graphs as well as a pairwise and a global Markov property. We prove that the global and pairwise Markov properties of a maximal ribbonless graph are equivalent for any independence model that is a compositional graphoid.Comment: Published in at http://dx.doi.org/10.3150/12-BEJ502 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Estimation of means in graphical Gaussian models with symmetries

We study the problem of estimability of means in undirected graphical Gaussian models with symmetry restrictions represented by a colored graph. Following on from previous studies, we partition the variables into sets of vertices whose corresponding means are restricted to being identical. We find a necessary and sufficient condition on the partition to ensure equality between the maximum likelihood and least-squares estimators of the mean.Comment: Published in at http://dx.doi.org/10.1214/12-AOS991 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Total positivity in exponential families with application to binary variables

We study exponential families of distributions that are multivariate totally positive of order 2 (MTP2), show that these are convex exponential families, and derive conditions for existence of the MLE. Quadratic exponential familes of MTP2 distributions contain attractive Gaussian graphical models and ferromagnetic Ising models as special examples. We show that these are defined by intersecting the space of canonical parameters with a polyhedral cone whose faces correspond to conditional independence relations. Hence MTP2 serves as an implicit regularizer for quadratic exponential families and leads to sparsity in the estimated graphical model. We prove that the maximum likelihood estimator (MLE) in an MTP2 binary exponential family exists if and only if both of the sign patterns $(1,-1)$ and $(-1,1)$ are represented in the sample for every pair of variables; in particular, this implies that the MLE may exist with $n=d$ observations, in stark contrast to unrestricted binary exponential families where $2^d$ observations are required. Finally, we provide a novel and globally convergent algorithm for computing the MLE for MTP2 Ising models similar to iterative proportional scaling and apply it to the analysis of data from two psychological disorders

Harmonic analysis of symmetric random graphs

summary:This note attempts to understand graph limits as defined by Lovasz and Szegedy in terms of harmonic analysis on semigroups. This is done by representing probability distributions of random exchangeable graphs as mixtures of characters on the semigroup of unlabeled graphs with node-disjoint union, thereby providing an alternative derivation of de Finetti's theorem for random exchangeable graphs

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.

Linear Estimating Equations for Exponential Families with Application to Gaussian Linear Concentration Models

In many families of distributions, maximum likelihood estimation is intractable because the normalization constant for the density which enters into the likelihood function is not easily available. The score matching estimator of Hyv\"arinen (2005) provides an alternative where this normalization constant is not required. The corresponding estimating equations become linear for an exponential family. The score matching estimator is shown to be consistent and asymptotically normally distributed for such models, although not necessarily efficient. Gaussian linear concentration models are examples of such families. For linear concentration models that are also linear in the covariance we show that the score matching estimator is identical to the maximum likelihood estimator, hence in such cases it is also efficient. Gaussian graphical models and graphical models with symmetries form particularly interesting subclasses of linear concentration models and we investigate the potential use of the score matching estimator for this case