Related papers: Phylogenetic degrees for Jukes-Cantor model
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Toric geometry provides a bridge between algebraic geometry and combinatorics of fans and polytopes. For each polarized toric variety (X,L) we have associated a polytope P. In this thesis we use this correspondence to study birational…
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…
The lectures are devoted to a remarkable class of $3$-dimensional polytopes, which are mathematical models of the important object of quantum physics, quantum chemistry and nanotechnology -- fullerenes. The main goal is to show how results…
In this thesis we study toric degenerations of projective varieties. We compare different constructions to understand how and why they are related as s first step towards developing a global framework. In focus are toric degenerations…
Subspace varieties are algebraic varieties whose elements are tensors with bounded multilinear rank. In this paper, we compute their degrees by computing their volumes.
We study the problem of maximum likelihood (ML) estimation for statistical models defined by reflexive polytopes. Our focus is on the maximum likelihood degree of these models as an algebraic measure of complexity of the corresponding…
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…
This paper studies affine algebraic varieties parametrized by sine and cosine functions, generalizing algebraic Lissajous figures in the plane. We show that, up to a combinatorial factor, the degree of these varieties equals the volume of a…
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…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
We discuss an experimental approach to open problems in toric geometry: are smooth projective toric varieties (i) projectively normal and (ii) defined by degree 2 equations? We discuss the creation of lattice polytopes defining smooth toric…
The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic…
In this paper we give a combinatorial view on the adjunction theory of toric varieties. Inspired by classical adjunction theory of polarized algebraic varieties we define two convex-geometric notions: the Q-codegree and the nef value of a…
The purpose of this thesis is to study classical combinatorial objects, such as polytopes, polytopal complexes, and subspace arrangements, using tools that have been developed in combinatorial topology, especially those tools developed in…
We compute all dynamical degrees of monomial maps by interpreting them as mixed volumes of polytopes. By exploiting further the isomorphism between the polytope algebra of P. McMullen and the universal cohomology of complete toric…
We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
Maximum likelihood estimation in statistics leads to the problem of maximizing a product of powers of polynomials. We study the algebraic degree of the critical equations of this optimization problem. This degree is related to the number of…