相关论文: Geometry of the Kimura 3-parameter model

In algebraic statistics, the Kimura 3-parameter model is one of the most interesting and classical phylogenetic models. We prove that the ideals associated to this model are generated in degree four, confirming a conjecture by Sturmfels and…

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…

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…

Congruences, or $2$-parameter families of lines in $3$-space are of interest in many situations, in particular in geometric optics. In this paper we consider elements of their geometry which are invariant under affine changes of…

The Kimura 3-parameter model is one of the most fundamental phylogenetic models in algebraic statistics. We prove that all algebraic varieties associated to this model are projectively normal, confirming a conjecture of Michalek.

It is shown that, given any finite dimensional, split basic algebra $\Lambda = K\Gamma/I$ (where $\Gamma$ is a quiver and $I$ an admissible ideal in the path algebra $K \Gamma$), there is a finite list of affine algebraic varieties, the…

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…

Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…

Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover…

Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since…

We investigate projective varieties which are geometric models of binary symmetric phylogenetic 3-valent trees. We prove that these varieties have Gorenstein terminal singularities (with small resolution) and they are Fano varieties of…

Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based…

This article considers some affine algebraic varieties attached to finite trees and closely related to cluster algebras. Their definition involves a canonical coloring of vertices of trees into three colors. These varieties are proved to be…

To classify the classical field theories with W-symmetry one has to classify the symplectic leaves of the corresponding W-algebra, which are the intersection of the defining constraint and the coadjoint orbit of the affine Lie algebra if…

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.…

Using group actions and orbit-stabilizer methods, we study the geometry of isomorphism classes of finite-dimensional $\omega$-Lie algebras over a field $\mathbb{K}$ of characteristic $\neq 2$ and establish a one-to-one correspondence…

Consider a graphed holomorphic surface $u=F(x,y)$ in $\mathbb{C}^3_{x,y,u}$ under the action of the affine transformation group $A(3)$. In 1999, Eastwood and Ezhov obtained a list of homogeneous models by determining possible tangential…

A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…

Given a group-based Markov model on a tree, one can compute the vertex representation of a polytope which describes the associated toric variety. The half-space representation, however, is not easily computable. In the case of…

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…