Related papers: L-Infinity optimization to Bergman fans of matroid…
We investigate uniqueness issues that arise in $l^\infty$-optimization to linear spaces and Bergman fans of matroids. For linear spaces, we give a polyhedral decomposition of $\mathbb{R}^n$ based on the dimension of the set of…
Given a matroid M on the ground set E, the Bergman fan B(M), or space of M-ultrametrics, is a polyhedral complex in R^E which arises in several different areas, such as tropical algebraic geometry, dynamical systems, and phylogenetics.…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
The tropical variety defined by linear equations with constant coefficients is the Bergman fan of the corresponding matroid. Building on a self-contained introduction to matroid polytopes, we present a geometric construction of the Bergman…
Every tropical ideal in the sense of Maclagan-Rinc\'on has an associated tropical variety, a finite polyhedral complex equipped with positive integral weights on its maximal cells. This leads to the realisability question, ubiquitous in…
The set of ultrametrics on $[n]$ nodes that are $\ell^\infty$-nearest to a given dissimilarity map forms a $(\max,+)$ tropical polytope. Previous work of Bernstein has given a superset of the set containing all the phylogenetic trees that…
Motivated by applications to low-rank matrix completion, we give a combinatorial characterization of the independent sets in the algebraic matroid associated to the collection of $m\times n$ rank-2 matrices and $n\times n$ skew-symmetric…
We prove that the proper amalgam of matroids $M_1$ and $M_2$ along their common restriction $N$ exists if and only if the tropical fibre product of Bergman fans ${B(M_1) \times_{B(N)} B(M_2)}$ is positive. We introduce tropical…
We study a notion of tropical linear series on metric graphs that combines two essential properties of tropicalizations of linear series on algebraic curves: the Baker-Norine rank and the independence rank. Our main results relate the local…
We study the Bergman complex B(M) of a matroid M: a polyhedral complex which arises in algebraic geometry, but which we describe purely combinatorially. We prove that a natural subdivision of the Bergman complex of M is a geometric…
We prove that the number of tropical critical points of an affine matroid (M,e) is equal to the beta invariant of M. Motivated by the computation of maximum likelihood degrees, this number is defined to be the degree of the intersection of…
The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete…
An affine tropical fan is called regular if it supports a reduced 0-dimensional complete intersection. For some cases the classification of regular fans is already complete. It was proved by Fink that tropical varieties of degree 1 are…
We define and study the cyclic Bergman fan of a matroid M, which is a simplicial polyhedral fan supported on the tropical linear space T(M) of M and is amenable to computational purposes. It slightly refines the nested set structure on…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$.…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
We study a rational matroid invariant, obtained as the tropicalization of the Feynman period integral. It equals the volume of the polar of the matroid polytope and we give efficient formulas for its computation. This invariant is proven to…
To each prime ideal in a polynomial ring over a field we associate an algebraic matroid and show that it is preserved under tropicalization. This gives a necessary condition for a tropical variety to be set-theoretically realizable from a…