11,645 research outputs found
Binary Models for Marginal Independence
Log-linear models are a classical tool for the analysis of contingency
tables. In particular, the subclass of graphical log-linear models provides a
general framework for modelling conditional independences. However, with the
exception of special structures, marginal independence hypotheses cannot be
accommodated by these traditional models. Focusing on binary variables, we
present a model class that provides a framework for modelling marginal
independences in contingency tables. The approach taken is graphical and draws
on analogies to multivariate Gaussian models for marginal independence. For the
graphical model representation we use bi-directed graphs, which are in the
tradition of path diagrams. We show how the models can be parameterized in a
simple fashion, and how maximum likelihood estimation can be performed using a
version of the Iterated Conditional Fitting algorithm. Finally we consider
combining these models with symmetry restrictions
Penalized EM algorithm and copula skeptic graphical models for inferring networks for mixed variables
In this article, we consider the problem of reconstructing networks for
continuous, binary, count and discrete ordinal variables by estimating sparse
precision matrix in Gaussian copula graphical models. We propose two
approaches: penalized extended rank likelihood with Monte Carlo
Expectation-Maximization algorithm (copula EM glasso) and copula skeptic with
pair-wise copula estimation for copula Gaussian graphical models. The proposed
approaches help to infer networks arising from nonnormal and mixed variables.
We demonstrate the performance of our methods through simulation studies and
analysis of breast cancer genomic and clinical data and maize genetics data
Estimation of a Covariance Matrix with Zeros
We consider estimation of the covariance matrix of a multivariate random
vector under the constraint that certain covariances are zero. We first present
an algorithm, which we call Iterative Conditional Fitting, for computing the
maximum likelihood estimator of the constrained covariance matrix, under the
assumption of multivariate normality. In contrast to previous approaches, this
algorithm has guaranteed convergence properties. Dropping the assumption of
multivariate normality, we show how to estimate the covariance matrix in an
empirical likelihood approach. These approaches are then compared via
simulation and on an example of gene expression.Comment: 25 page
An empirical Bayes procedure for the selection of Gaussian graphical models
A new methodology for model determination in decomposable graphical Gaussian
models is developed. The Bayesian paradigm is used and, for each given graph, a
hyper inverse Wishart prior distribution on the covariance matrix is
considered. This prior distribution depends on hyper-parameters. It is
well-known that the models's posterior distribution is sensitive to the
specification of these hyper-parameters and no completely satisfactory method
is registered. In order to avoid this problem, we suggest adopting an empirical
Bayes strategy, that is a strategy for which the values of the hyper-parameters
are determined using the data. Typically, the hyper-parameters are fixed to
their maximum likelihood estimations. In order to calculate these maximum
likelihood estimations, we suggest a Markov chain Monte Carlo version of the
Stochastic Approximation EM algorithm. Moreover, we introduce a new sampling
scheme in the space of graphs that improves the add and delete proposal of
Armstrong et al. (2009). We illustrate the efficiency of this new scheme on
simulated and real datasets
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