Related papers: Polyhedral Combinatorics of UPGMA Cones
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this…
The purpose of this thesis is to study classical combinatorial objects, such as polytopes, polytopal complexes, and subspace arrangements, using tools that have been developed in combinatorial topology, especially those tools developed in…
We construct the ordinary irreducible representations of the group of automorphisms of a finite rooted tree and we get a natural parametrization of them. To achieve this goals, we introduce and study the combinatorics of tree compositions,…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
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…
Combinatorial samplers are algorithmic schemes devised for the approximate- and exact-size generation of large random combinatorial structures, such as context-free words, various tree-like data structures, maps, tilings, RNA molecules.…
Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…
We provide a naturally isomorphic description of the persistence map from merge trees to barcodes in terms of a monotone map from the partition lattice to the subset lattice. Our description is local, which offers the potential to speed up…
Orthogonal polynomials are of fundamental importance in many fields of mathematics and science, therefore the study of a particular family is always relevant. In this manuscript, we present a survey of some general results of the Hermite…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of…
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
A notion of "radially monotone" cut paths is introduced as an effective choice for finding a non-overlapping edge-unfolding of a convex polyhedron. These paths have the property that the two sides of the cut avoid overlap locally as the cut…
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…
The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…
We compute averages of products and ratios of characteristic polynomials associated with Orthogonal, Unitary, and Symplectic Ensembles of Random Matrix Theory. The pfaffian/determinantal formulas for these averages are obtained, and the…
We provide two new characterizations of bounded orthogonally additive polynomials from a uniformly complete vector lattice into a convex bornological space using harmonic means and completely partitioned weighted geometric means. Our result…
Taking a Feynman categorical perspective, several key aspects of the geometry of surfaces are deduced from combinatorial constructions with graphs. This provides a direct route from combinatorics of graphs to string topology operations via…