Graphical models in Macaulay2

The Macaulay2 package GraphicalModels contains algorithms for the algebraic study of graphical models associated to undirected, directed and mixed graphs, and associated collections of conditional independence statements. Among the algorithms implemented are procedures for computing the vanishing ideal of graphical models, for generating conditional independence ideals of families of independence statements associated to graphs, and for checking for identifiable parameters in Gaussian mixed graph models. These procedures can be used to study fundamental problems about graphical models.Comment: Several changes to address referee comments and suggestions. We will eventually include this package in the standard distribution of Macaulay2. But until then, the associated Macaulay2 file can be found at http://www.shsu.edu/~ldg005/papers.htm

The Geometry of Statistical Models for Two-Way Contingency Tables with Fixed Odds Ratios

We study the geometric structure of the statistical models for two-by-two contingency tables. One or two odds ratios are fixed and the corresponding models are shown to be a portion of a ruled quadratic surface or a segment. Some pointers to the general case of two-way contingency tables are also given and an application to case-control studies is presented.Comment: References were not displaying properly in the previous versio

Algebraic geometry of Gaussian Bayesian networks

Conditional independence models in the Gaussian case are algebraic varieties in the cone of positive definite covariance matrices. We study these varieties in the case of Bayesian networks, with a view towards generalizing the recursive factorization theorem to situations with hidden variables. In the case when the underlying graph is a tree, we show that the vanishing ideal of the model is generated by the conditional independence statements implied by graph. We also show that the ideal of any Bayesian network is homogeneous with respect to a multigrading induced by a collection of upstream random variables. This has a number of important consequences for hidden variable models. Finally, we relate the ideals of Bayesian networks to a number of classical constructions in algebraic geometry including toric degenerations of the Grassmannian, matrix Schubert varieties, and secant varieties.Comment: 30 page, 4 figure