相关论文: Toric ideals of phylogenetic invariants for the ge…

We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…

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.…

This work concerns the study of properties of a group of Koszul algebras coming from the toric ideals of a chordal bipartite infinite family of graphs (alternately, these rings may be interpreted as coming from determinants of certain…

Characteristic imsets are 0-1 vectors which correspond to Markov equivalence classes of directed acyclic graphs. The study of their convex hull, named the characteristic imset polytope, has led to new and interesting geometric perspectives…

Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining…

In this paper we present geometric features of group based models. We focus on the 3-Kimura model. We present a precise geometric description of the variety associated to any tree on a Zariski open set. In particular this set contains all…

In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary…

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 code can be constructed as a gauge theory of finite groups on oriented two dimensional lattices. Here we construct analogous models with the gauge fields belonging to groupoids, which are categories where every morphism has an…

We study the combinatorics of Gr\"obner degenerations of Grassmannians and the Schubert varieties inside them. We provide a family of binomial ideals whose combinatorics is governed by tableaux induced by matching fields in the sense of…

We show that the number of rational points of a subgroup inside a toric variety over a finite field defined by a homogeneous lattice ideal can be computed via Smith normal form of the matrix whose columns constitute a basis of the lattice.…

In this article we consider the problem of finding generators of the toric ideal associated to a combinatorial object called a staged tree. Our main theorem states that toric ideals of staged trees that are balanced and stratified are…

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…

Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…

Let $X$ be a complete simplicial toric variety over a finite field $\mathbb{F}_q$ with homogeneous coordinate ring $S=\mathbb{F}_q[x_1,\dots,x_r]$ and split torus $T_X\cong (\mathbb{F}^*_q)^n$. We prove that vanishing ideal of a subset $Y$…

We study the algebraic combinatorics of monomial degenerations of Pl\"ucker forms which is governed by matching fields in the sense of Sturmfels and Zelevinsky. We provide a necessary condition for a matching field to yield a Khovanskii…

We give a combinatorial description of the toric ideal of invariants of the Cavender-Farris-Neyman model with a molecular clock (CFN-MC) on a rooted binary phylogenetic tree and prove results about the polytope associated to this toric…

A cut ideal of a graph records the relations among the cuts of the graph. These toric ideals have been introduced by Sturmfels and Sullivant who also posed the problem of relating their properties to the combinatorial structure of the…

We introduce a family of toric algebras defined by maximal chains of a finite distributive lattice. Applying results on stable set polytopes we conclude that every such algebra is normal and Cohen-Macaulay, and give an interpretation of its…

Let $G$ be a simply connected semi-simple complex algebraic group. Fix a maximal torus $T$ and a Borel subgroup $B$ such that $T\subset B\subset G$. Let $W$ the Weyl group of $G$ relative to $T$. For any $w$ in $W$, let $X_w=\bar {BwB/B}$…