Related papers: Tropical $k$-means clustering for phylogenetic tre…
The diameter $k$-clustering problem is the problem of partitioning a finite subset of $\mathbb{R}^d$ into $k$ subsets called clusters such that the maximum diameter of the clusters is minimized. One early clustering algorithm that computes…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…
We develop combinatorial methods for computing the rotation distance between binary trees, i.e., equivalently, the flip distance between triangulations of a polygon. As an application, we prove that, for each n, there exist size n trees at…
We present an algorithm for computing zero-dimensional tropical varieties based on triangular decomposition and Newton polygon methods. From it, we derive algorithms for computing points on and links of higher-dimensional tropical…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
We investigate location problems whose optimum lies in the tropical convex hull of the input points. Firstly, we study geodesically star-convex sets under the asymmetric tropical distance and introduce the class of tropically quasiconvex…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
Polytropes are both ordinary and tropical polytopes. We show that tropical types of polytropes in $\mathbb{TP}^{n-1}$ are in bijection with cones of a certain Gr\"{o}bner fan $\mathcal{GF}_n$ in $\mathbb{R}^{n^2 - n}$ restricted to a small…
We study the geometry of tropical Fermat--Weber points, that is, optimal solutions to a location problem over a projective space using a dissimilarity measure derived from the tropical metric. It is well-known that for a given sample, such…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
We compute a number of distance-dependent universal scaling functions characterizing the distance statistics of large maps of genus one. In particular, we obtain explicitly the probability distribution for the length of the shortest…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
Using a trimming approach, we investigate a k-means type method based on Bregman divergences for clustering data possibly corrupted with clutter noise. The main interest of Bregman divergences is that the standard Lloyd algorithm adapts to…
k-means is a widely used clustering algorithm, but for $k$ clusters and a dataset size of $N$, each iteration of Lloyd's algorithm costs $O(kN)$ time. Although there are existing techniques to accelerate single Lloyd iterations, none of…
The Fr\'{e}chet mean is a fundamental notion of central tendency defined as a minimizer of a sum of squared distances in a general metric space. In this paper, we study Fr\'{e}chet means in tropical geometry -- a piecewise linear,…
In this paper, we study the interplay between tropical and analytic geometry for closed subschemes of toric varieties. Let $K$ be a complete non-Archimedean field, and let $X$ be a closed subscheme of a toric variety over $K$. We define the…
While the positive Grassmannian is deeply understood through the rich combinatorics of plabic graphs and positroid cells, its tropical counterpart, the positive tropical Grassmannian Trop$_{>0}G(k,n)$, has lacked a comparable structural…
We provide a cluster-algebraic approach to the computation of the recently introduced generalised biadjoint scalar amplitudes related to Grassmannians ${\rm Gr}(k,n)$. A finite cluster algebra provides a natural triangulation for the…
Tropical algebraic geometry is the geometry of the tropical semiring (R, min, +). The theory of total positivity is a natural generalization of the study of matrices with all minors positive. In this paper we introduce the totally positive…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…