Related papers: Halfspace Representations of Path Polytopes of Tre…
The notions of convexity and convex polytopes are introduced in the setting of tropical geometry. Combinatorial types of tropical polytopes are shown to be in bijection with regular triangulations of products of two simplices. Applications…
Abstractly, tropical hyperelliptic curves are metric graphs that admit a two-to-one harmonic morphism to a tree. They also appear as embedded tropical curves in the plane arising from triangulations of polygons with all interior lattice…
Let $G=(V, E)$ be an undirected graph. The spanning trees polytope $P(G)$ is the convex hull of the characteristic vectors of all spanning trees of $G$. In this paper, we describe all facets of $P(G)$ as a consequence of the facets of the…
As a new concept tropical halfspaces are introduced to the (linear algebraic) geometry of the tropical semiring (R,min,+). This yields exterior descriptions of the tropical polytopes that were recently studied by Develin and Sturmfels in a…
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…
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…
We study lattice polytopes which arise as the convex hull of chip vectors for \textit{self-reachable} chip configurations on a tree $T$. We show that these polytopes always have the integer decomposition property and characterize the vertex…
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…
A biconvex polytope is a classical and tropical convex hull of finitely many points. Given a biconvex polytope, for each vertex of it we construct a directed bigraph and a gammoid so that the collection of base polytopes of those gammoids…
Lattice polytope representation of natural numbers is introduced based on the fundamental theorem of arithmetic. The combinatorial and geometric properties of the polytopes are studied using Polymake and Qhull software. The volume of the…
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…
In this article, we give two extended space formulations, respectively, for the induced tree and path polytopes of chordal graphs with vertex and edge variables. These formulations are obtained by proving that the induced tree and path…
Starting from the data of an arbor, which is a rooted tree with vertices decorated by disjoint sets, we introduce a lattice polytope and a partial order on its lattice points. We give recursive algorithms for various classical invariants of…
Every generic linear functional $f$ on a convex polytope $P$ induces an orientation on the graph of $P$. From the resulting directed graph one can define a notion of $f$-arborescence and $f$-monotone path on $P$, as well as a natural graph…
We define and study a new family of polytopes which are formed as convex hulls of partial alternating sign matrices. We determine the inequality descriptions, number of facets, and face lattices of these polytopes. We also study partial…
A transportation polytope consists of all multidimensional arrays or tables of non-negative real numbers that satisfy certain sum conditions on subsets of the entries. They arise naturally in optimization and statistics, and also have…
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…
It is known that any tropical polytope is the image under the valuation map of ordinary polytopes over the Puiseux series field. The latter polytopes are called lifts of the tropical polytope. We prove that any pure tropical polytope is the…
The type A_n full root polytope is the convex hull in R^{n+1} of the origin and the points e_i-e_j for 1<= i<j <= n+1. Given a tree T on the vertex set [n+1], the associated root polytope P(T) is the intersection of the full root polytope…
Given a tree and a set P of non-trivial simple paths on it, VPT(P) is the VPT graph (i.e. the vertex intersection graph) of the paths P, and EPT(P) is the EPT graph (i.e. the edge intersection graph) of P. These graphs have been extensively…