Toric algebra of hypergraphs

The edges of any hypergraph parametrize a monomial algebra called the edge subring of the hypergraph. We study presentation ideals of these edge subrings, and describe their generators in terms of balanced walks on hypergraphs. Our results generalize those for the defining ideals of edge subrings of graphs, which are well-known in the commutative algebra community, and popular in the algebraic statistics community. One of the motivations for studying toric ideals of hypergraphs comes from algebraic statistics, where generators of the toric ideal give a basis for random walks on fibers of the statistical model specified by the hypergraph. Further, understanding the structure of the generators gives insight into the model geometry.Comment: Section 3 is new: it explains connections to log-linear models in algebraic statistics and to combinatorial discrepancy. Section 6 (open problems) has been moderately revise

Random Sampling in Computational Algebra: Helly Numbers and Violator Spaces

This paper transfers a randomized algorithm, originally used in geometric optimization, to computational problems in commutative algebra. We show that Clarkson's sampling algorithm can be applied to two problems in computational algebra: solving large-scale polynomial systems and finding small generating sets of graded ideals. The cornerstone of our work is showing that the theory of violator spaces of G\"artner et al.\ applies to polynomial ideal problems. To show this, one utilizes a Helly-type result for algebraic varieties. The resulting algorithms have expected runtime linear in the number of input polynomials, making the ideas interesting for handling systems with very large numbers of polynomials, but whose rank in the vector space of polynomials is small (e.g., when the number of variables and degree is constant).Comment: Minor edits, added two references; results unchange

Goodness of fit for log-linear ERGMs

Many popular models from the networks literature can be viewed through a common lens of contingency tables on network dyads, resulting in \emph{log-linear ERGMs}: exponential family models for random graphs whose sufficient statistics are linear on the dyads. We propose a new model in this family, the \emph{$p_1$-SBM}, which combines node and group effects common in network formation mechanisms. In particular, it is a generalization of several well-known ERGMs including the stochastic blockmodel for undirected graphs, the degree-corrected version of it, and the directed $p_1$ model without group structure. We frame the problem of testing model fit for the log-linear ERGM class through an exact conditional test whose $p$-value can be approximated efficiently in networks of both small and moderately large sizes. The sampling methods we build rely on a dynamic adaptation of Markov bases. We use quick estimation algorithms adapted from the contingency table literature and effective sampling methods rooted in graph theory and algebraic statistics. The performance and scalability of the method is demonstrated on two data sets from biology: the connectome of \emph{C. elegans} and the interactome of \emph{Arabidopsis thaliana}. These two networks -- a neuronal network and a protein-protein interaction network -- have been popular examples in the network science literature. Our work provides a model-based approach to studying them

Strong Hanani-Tutte on the Projective Plane

If a graph can be drawn in the projective plane so that every two non-adjacent edges cross an even number of times, then the graph can be embedded in the projective plane

Gr\"obner Bases and Nullstellens\"atze for Graph-Coloring Ideals

We revisit a well-known family of polynomial ideals encoding the problem of graph-$k$-colorability. Our paper describes how the inherent combinatorial structure of the ideals implies several interesting algebraic properties. Specifically, we provide lower bounds on the difficulty of computing Gr\"obner bases and Nullstellensatz certificates for the coloring ideals of general graphs. For chordal graphs, however, we explicitly describe a Gr\"obner basis for the coloring ideal, and provide a polynomial-time algorithm.Comment: 16 page

Statistical models for cores decomposition of an undirected random graph

The $k$-core decomposition is a widely studied summary statistic that describes a graph's global connectivity structure. In this paper, we move beyond using $k$-core decomposition as a tool to summarize a graph and propose using $k$-core decomposition as a tool to model random graphs. We propose using the shell distribution vector, a way of summarizing the decomposition, as a sufficient statistic for a family of exponential random graph models. We study the properties and behavior of the model family, implement a Markov chain Monte Carlo algorithm for simulating graphs from the model, implement a direct sampler from the set of graphs with a given shell distribution, and explore the sampling distributions of some of the commonly used complementary statistics as good candidates for heuristic model fitting. These algorithms provide first fundamental steps necessary for solving the following problems: parameter estimation in this ERGM, extending the model to its Bayesian relative, and developing a rigorous methodology for testing goodness of fit of the model and model selection. The methods are applied to a synthetic network as well as the well-known Sampson monks dataset.Comment: Subsection 3.1 is new: `Sample space restriction and degeneracy of real-world networks'. Several clarifying comments have been added. Discussion now mentions 2 additional specific open problems. Bibliography updated. 25 pages (including appendix), ~10 figure