相关论文: Toric ideals of homogeneous phylogenetic models

To any toric ideal $I_A$, encoded by an integer matrix $A$, we associate a matroid structure called {\em the bouquet graph} of $A$ and introduce another toric ideal called {\em the bouquet ideal} of $A$. We show how these objects capture…

We introduce the notion of Groebner S-basis of an ideal of the free associative algebra K<X> over a field K invariant under the action of a semigroup S of endomorphisms of the algebra. We calculate the Groebner S-bases of the ideal…

In this paper we introduce a new and large family of configurations whose toric ideals possess quadratic Groebner bases. As an application, a generalization of algebras of Segre-Veronese type will be studied.

We introduce a very natural topology on the set of total orderings of monomials of any algebra having a countable basis over a field. This topological space and some notable subspaces are compact. This topological framework allows us to…

In this article we present two new algorithms to compute the Groebner basis of an ideal that is invariant under certain permutations of the ring variables and which are both implemented in SINGULAR (cf. [DGPS12]). The first and major…

A homogeneous ideal is robust if its universal Gr\"obner basis is also a minimal generating set. For toric ideals, one has the stronger definition: A toric ideal is strongly robust if its Graver basis equals the set of indispensable…

In this paper, the tropical differential Gr\"obner basis is studied, which is a natural generalization of the tropical Gr\"obner basis to the recently introduced tropical differential algebra. Like the differential Gr\"obner basis, the…

Associated to any graph is a toric ideal whose generators record relations among the cuts of the graph. We study these ideals and the geometry of the corresponding toric varieties. Our theorems and conjectures relate the combinatorial…

The toric ring together with the toric ideal arising from a nested configuration is studied, with particular attention given to the algebraic study of normality of the toric ring as well as the Gr\"obner bases of the toric ideal. One of the…

We study the family of graphs whose number of primitive cycles equals its cycle rank. It is shown that this family is precisely the family of ring graphs. Then we study the complete intersection property of toric ideals of bipartite graphs…

In this paper we present a version of the general polynomial involutive algorithm for computing Janet bases specialized to toric ideals. The relevant data structures are Janet trees which provide a very fast search for a Janet divisor. We…

Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…

We investigate the structure of ideals generated by binomials (polynomials with at most two terms) and the schemes and varieties associated to them. The class of binomial ideals contains many classical examples from algebraic geometry, and…

It has been shown previously that a large class of monomial maps equivariant under the action of an infinite symmetric group have finitely generated kernels up to the symmetric action. We prove that these symmetric toric ideals also have…

Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how…

We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…

Let T(x) in k[x] be a monic non-constant polynomial and write R=k[x] / (T) the quotient ring. Consider two bivariate polynomials a(x, y), b(x, y) in R[y]. In a first part, T = p^e is assumed to be the power of an irreducible polynomial p. A…

We describe explicitly all multisets of weights whose defining projective toric varieties are self-dual. In addition, we describe a remarkable and unexpected combinatorial behaviour of the defining ideals of these varieties. The toric ideal…

A toric ideal is called robust if its universal Gr\"obner basis is a minimal set of generators, and is called generalized robust if its universal Gr\"obner basis equals its universal Markov basis (the union of all its minimal sets of…

A graph-theoretic method, simpler than existing ones, is used to characterize the minimal set of monomial generators for the integral closure of any algebra of polynomials generated by quadratic monomials. The toric ideal of relations…