Related papers: H-Representation of the Kimura-3 Polytope
We introduce the M-representation of polytopes, which makes it possible to compute linear transformations, convex hulls, and Minkowski sums with linear complexity in the dimension of the polytopes. When the polytope is a convex hull of a…
Given a tree $T$, its path polytope is the convex hull of the edge indicator vectors for the paths between any two distinct leaves in $T$. These polytopes arise naturally in polyhedral geometry and applications, such as phylogenetics,…
We prove that each bounded polytope can be represented as a polynomial zonotope, which we refer to as the Z-representation of polytopes. Previous representations are the vertex representation (V-representation) and the halfspace…
A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching…
The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
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…
The purpose of this article is to describe the integral cohomology of the braid group B_3 and SL_2(Z) with local coefficients in a classical geometric representation given by symmetric powers of the natural symplectic representation. These…
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…
Many of the stochastic models used in inference of phylogenetic trees from biological sequence data have polynomial parameterization maps. The image of such a map --- the collection of joint distributions for a model --- forms the model…
We describe an approach to classify (meromorphic) representations of a given vertex operator algebra by calculating Zhu's algebra explicitly. We demonstrate this for FKS lattice theories and subtheories corresponding to the Z_2 reflection…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
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…
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…
The main purpose of this article is to give the integral cohomology of classical principal congruence subgroups in SL(2,Z) as well as their analogues in the third braid group with local coefficients in symmetric powers of the natural…
We apply the geometric quantization method with real polarizations to the quantization of a symplectic torus. By quantizing with half-densities we canonically associate to the symplectic torus a projective Hilbert space and prove that the…
Jukes-Cantor model is one of the most meaningful statistical models from a biological perspective. We are interested in computing the algebraic degrees for phylogenetic varieties, which we call phylogenetic degrees, associated to the…
Minkowski sums cover a wide range of applications in many different fields like algebra, morphing, robotics, mechanical CAD/CAM systems ... This paper deals with sums of polytopes in a n dimensional space provided that both H-representation…
We first describe the low energy dynamics of ten dimensional heterotic supergravity compactified on the smooth, flat 3-manifold ${\mathbb T^3}/{\mathbb Z_2}$, without supersymmetry, and explain how it arises from flat heterotic gauge…
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…