Related papers: Tropical $k$-means clustering for phylogenetic tre…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
For time series comparisons, it has often been observed that z-score normalized Euclidean distances far outperform the unnormalized variant. In this paper we show that a z-score normalized, squared Euclidean Distance is, in fact, equal to a…
k-medoids algorithm is a partitional, centroid-based clustering algorithm which uses pairwise distances of data points and tries to directly decompose the dataset with $n$ points into a set of $k$ disjoint clusters. However, k-medoids…
We establish a limit formula for the median of the distance between two leaves in a fully resolved unrooted phylogenetic tree with n leaves. More precisely, we prove that this median is equal, in the limit, to the square root of 4*ln(2)*n.
This paper explores hierarchical clustering in the case where pairs of points have dissimilarity scores (e.g. distances) as a part of the input. The recently introduced objective for points with dissimilarity scores results in every tree…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
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…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Metric graphs are important models for capturing the structure of complex data across various domains. While much effort has been devoted to extracting geometric and topological features from graph data, computational aspects of metric…
Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
The notion of geometric construction is introduced. This notion allows to compare incidence configurations in the algebraic and tropical plane. We provide an algorithm such that, given a tropical instance of a geometric construction, it…
The goal of this paper is to make a connection between tropical geometry, representations of quantum affine algebras, and scattering amplitudes in physics. The connection allows us to study important and difficult questions in these areas:…
In this paper we focus on the tropical convex hull of convex sets and polyhedral complexes. We give a vertex description of the tropical convex hull of a line segment and a ray. %in \RR^{n+1}/\RR\mathbf{1}. Next we show that tropical convex…
We consider the rooted trees which not have isomorphic representation and introduce a conception of complexity a natural number also. The connection between quantity such trees with $n$ edges and a complexity of natural number $n$ is…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
The aim of applied topology is to use and develop topological methods for applied mathematics, science and engineering. One of the main tools is persistent homology, an adaptation of classical homology, which assigns a barcode, i.e. a…
In this paper, we present a linear-time approximation scheme for $k$-means clustering of \emph{incomplete} data points in $d$-dimensional Euclidean space. An \emph{incomplete} data point with $\Delta>0$ unspecified entries is represented as…
We investigate the Voronoi diagrams with respect to an asymmetric tropical distance function, also for infinite point sets. These turn out to be much better behaved than the tropical Voronoi diagrams arising from the standard tropical…