The Macaulay2 package PHCpack.m2 provides an interface to some of the
functionality of PHCpack, a general-purpose solver for polynomial systems by
homotopy continuation. The main function of the package interfaces PHCpack's
numerical solver phc, published as Algorithm 795 in ACM Trans. Math. Softw.
(TOMS). The blackbox solver computes mixed volumes using mixedvol, ACM TOMS
Algorithm 846, and then applies polyhedral homotopy methods to solve a
polynomial system.
Associated to any toric ideal are two special generating sets: the universal
Gr\"obner basis and the Graver basis. While the former is a subset of the
typically much larger Graver basis, there are cases for which the two sets
coincide. The most prominent examples among them are toric ideals of unimodular
matrices. Yet, a general classification of all matrices for which both sets
agree is far from known.
There are two seemingly unrelated classical objects associated to a
simplicial complex: a hierarchical model and a Stanley-Reisner ring. A
hierarchical model gives rise to a toric ideal, a relationship that is a staple
of algebraic statistics. In this note, we explore the connection between
degrees of Markov bases elements of the model and the rows of the Betti diagram
of the Stanley-Reisner ideal. We propose a precise conjecture, which we
establish in several cases, most notably for decomposable and
vertex-decomposable complexes.
There are two seemingly unrelated classical objects associated to a
simplicial complex: a hierarchical model and a Stanley-Reisner ring. A
hierarchical model gives rise to a toric ideal, a relationship that is a staple
of algebraic statistics. In this note, we explore the connection between
degrees of Markov bases elements of the model and the rows of the Betti diagram
of the Stanley-Reisner ideal. We propose a precise conjecture, which we
establish in several cases, most notably for decomposable and
vertex-decomposable complexes.
The p_1 model is a directed random graph model used to describe dyadic
interactions in a social network in terms of effects due to differential
attraction (popularity) and expansiveness, as well as an additional effect due
to reciprocation. In this article we carry out an algebraic statistics analysis
of this model. We show that the p_1 model is a toric model specified by a
multi-homogeneous ideal. We conduct an extensive study of the Markov bases for
p_1 models that incorporate explicitly the constraint arising from
multi-homogeneity.