Related papers: Phylogenetic degrees for Jukes-Cantor model
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…
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…
We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
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…
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…
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…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
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…
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…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the…
We study the ChorHendySnir2006 evolutionary model, which consists of a rooted phylogenetic tree with three leaves, subject to the Jukes--Cantor (JC69) molecular evolutionary model and molecular clock. We show that the likelihood function…
We study the maximum likelihood degree (ML degree) of toric varieties, known as discrete exponential models in statistics. By introducing scaling coefficients to the monomial parameterization of the toric variety, one can change the ML…
Toric geometry provides a bridge between the theory of polytopes and algebraic geometry: one can associate to each lattice polytope a polarized toric variety. In this thesis we explore this correspondence to classify smooth lattice…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
Toric geometry provides a bridge between the theory of polytopes and algebraic geometry: one can associate to each lattice polytope a polarized toric variety. In this paper we explore this correspondence to classify smooth lattice polytopes…
The univariate Ehrhart and $h^*$-polynomials of lattice polytopes have been widely studied. We describe methods from toric geometry for computing multivariate versions of volume, Ehrhart and $h^*$-polynomials of lattice polytropes, which…