相关论文: Toric ideals of phylogenetic invariants

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…

We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…

The general Markov model of the evolution of biological sequences along a tree leads to a parameterization of an algebraic variety. Understanding this variety and the polynomials, called phylogenetic invariants, which vanish on it, is a…

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…

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…

A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…

Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be…

We define phylogenetic projective toric model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. Generators of the pro- jective coordinate ring of the models of graphs with one cycle are…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

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…

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…

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…

We introduce and study the toric fiber product of two ideals in polynomial rings that are homogeneous with respect to the same multigrading. Under the assumption that the set of degrees of the variables form a linearly independent set, we…

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…

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…

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 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…

For an arbitrary field K, let I be an ideal in the ring K[[x,y]] expressible as a polynomial in either the pair of ideals (x, y^4) and (x,y) or the pair (x,y^3) and (x^2, y). Let G be the group of automorphisms of K[[x,y]] sending the ideal…

In combinatorial commutative algebra and algebraic statistics many toric ideals are constructed from graphs. Keeping the categorical structure of graphs in mind we give previous results a more functorial context and generalize them by…

In this paper we show that the agglomeration of rows or columns of a contingency table with a hierarchical clustering algorithm yields statistical models defined through toric ideals. In particular, starting from the classical independence…