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: $\ell_1$ 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

Analysis of Boolean Equation Systems through Structure Graphs

We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph

Generalized Permutohedra from Probabilistic Graphical Models

A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. There is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models and also for mixed graphical models containing undirected, directed and bidirected edges, we give a construction of this polytope, up to equivalence of normal fans, as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models.Comment: Appendix B is expanded. Final version to appear in SIAM J. Discrete Mat

Long-Range Correlation Underlying Childhood Language and Generative Models

Long-range correlation, a property of time series exhibiting long-term memory, is mainly studied in the statistical physics domain and has been reported to exist in natural language. Using a state-of-the-art method for such analysis, long-range correlation is first shown to occur in long CHILDES data sets. To understand why, Bayesian generative models of language, originally proposed in the cognitive scientific domain, are investigated. Among representative models, the Simon model was found to exhibit surprisingly good long-range correlation, but not the Pitman-Yor model. Since the Simon model is known not to correctly reflect the vocabulary growth of natural language, a simple new model is devised as a conjunct of the Simon and Pitman-Yor models, such that long-range correlation holds with a correct vocabulary growth rate. The investigation overall suggests that uniform sampling is one cause of long-range correlation and could thus have a relation with actual linguistic processes