Related papers: Phylogenetic toric varieties on graphs
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
This paper announces results on the behavior of some important algebraic and topological invariants --- Euler characteristic, arithmetic genus, and their intersection homology analogues; the signature, etc. --- and their associated…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
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…
We introduce an algebraic method for describing the Hodge filtration of degenerating hypersurfaces in projective toric varieties. For this purpose, we show some fundamental properties of logarithmic differential forms on proper equivariant…
By analogy with algebraic geometry, we define a category of non-linear sheaves (quasi-coherent homotopy-sheaves of topological spaces) on projective toric varieties and prove a splitting result for its algebraic K-theory, generalising…
I. Panin proved in the nineties that the algebraic K-theory of twisted projective homogeneous varieties can be expressed in terms of central simple algebras. Later, Merkurjev and Panin described the algebraic K-theory of toric varieties as…
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…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
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…
Let $G$ be a complex classical group, and let $V$ be its defining representation (possibly plus a copy of the dual). A foundational problem in classical invariant theory is to write down generators and relations for the ring of…
In this paper we construct a tilting sheaf for Severi-Brauer Varieties and Involution Varieties. This sheaf relates the derived category of each variety to the derived category of modules over a ring whose semisimple component consists of…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
We study semigroups of labellings associated to a graph. These generalize the Jukes-Cantor model and phylogenetic toric varieties defined by Buczy\'nska. Our main theorem bounds the degree of the generators of the semigroup by g+1 when the…
In this paper, we introduce new combinatorial invariants of any finite simple graph, which arise in toric topology. We compute the $i$-th (rational) Betti number and Euler characteristic of the real toric variety associated to a graph…
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…
Toric orbifolds are a topological generalization of projective toric varieties associated to simplicial fans. We introduce some sufficient conditions on the combinatorial data associated to a toric orbifold to ensure the existence of an…
This note presents a formula for the enumerative invariants of arbitrary genus in toric surfaces. The formula computes the number of curves of a given genus through a collection of generic points in the surface. The answer is given in terms…
A toric degeneration in algebraic geometry is a process where a given projective variety is being degenerated into a toric one. Then one can obtain information about the original variety via analyzing the toric one, which is a much easier…
We give various examples of Q-factorial projective toric varieties such that the sum of the squared torus invariant prime divisors is positive. We also determine the generators for the cone of effective $2$-cycles on a toric variety of…