arXiv subjects

Seth Sullivant

Publications and source records attributed to Seth Sullivant.

78 records · Page 5Linked to original sources

arXiv2004

Polyhedral conditions for the nonexistence of the MLE for hierarchical log-linear models

We provide a polyhedral description of the conditions for the existence of the maximum likelihood estimate (MLE) for a hierarchical log-linear model. The MLE exists if and only if the observed margins lie in the relative interior of the marginal cone. Using this description, we give an algorithm for determining if the MLE exists. If the tree width is bounded, the algorithm runs in polynomial time. We also perform a computational study of the case of three random variables under the no three-factor effect model.

math.CO↗

arXiv2004

The space of compatible full conditionals is a unimodular toric variety

The set of all m-tuples of compatible full conditional distributions on discrete random variables is an algebraic set whose defining ideal is a unimodular toric ideal. We identify the defining polynomials of these ideals with closed walks on a bipartite graph. Our algebraic characterization provides a natural generalization of the requirement that compatible conditionals have identical odds ratios and holds regardless of the patterns of zeros in the conditional arrays.

math.AG↗

arXiv2004

Small contingency tables with large gaps

We construct examples of contingency tables on $n$ binary random variables where the gap between the linear programming lower/upper bound and the true integer lower/upper bounds on cell entries is exponentially large. These examples provide evidence that linear programming may not be an effective heuristic for detecting disclosures when releasing margins of multi-way tables.

math.OC↗

arXiv2004

Toric ideals of phylogenetic invariants

Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an abelian group. Their phylogenetic invariants form a toric ideal in the Fourier coordinates. We determine generators and Gröbner bases for these toric ideals. For the Jukes-Cantor and Kimura models on a binary tree, our Gröbner bases consist of certain explicitly constructed polynomials of degree at most four.

q-bio.PE↗

arXiv2003

Markov bases of binary graph models

This paper is concerned with the topological invariant of a graph given by the maximum degree of a Markov basis element for the corresponding graph model for binary contingency tables. We describe a degree four Markov basis for the model when the underlying graph is a cycle and generalize this result to the complete bipartite graph $K_{2,n}$. We also give a combinatorial classification of degree two and three Markov basis moves as well as a Buchberger-free algorithm to compute moves of arbitrary given degree. Finally, we compute the algebraic degree of the model when the underlying graph is a forest.

math.CO↗

arXiv2003

Ideals of Adjacent Minors

We give a description of the minimal primes of the ideal generated by the 2 x 2 adjacent minors of a generic matrix. We also compute the complete prime decomposition of the ideal of adjacent m x m minors of an m x n generic matrix when the characteristic of the ground field is zero. A key intermediate result is the proof that the ideals which appear as minimal primes are, in fact, prime ideals. This introduces a large new class of mixed determinantal ideals that are prime.

math.AC↗