Related papers: Polyhedral Covers of Tree Space
We define and study a simplicial complex which is a homogeneous space for the group $PGL(2, K)$ over a two-dimensional local field $K$. The complex is a generalization of the tree studied by F. Bruhat, J. Tits, J.-P. Serre and P. Cartier in…
The orientable cover of the moduli space of real genus zero algebraic curves with marked points is a compact aspherical manifold tiled by associahedra, which resolves the singularities of the space of phylogenetic trees. The resolution maps…
In the early 1990s, a family of combinatorial CW-complexes named permutoassociahedra was introduced by Kapranov, and it was realized by Reiner and Ziegler as a family of convex polytopes. The polytopes in this family are "hybrids" of…
We explicitly describe the tropicalization of a type C cluster variety by identifying it with the space of axially symmetric phylogenetic trees. We also study the signed tropicalizations of this cluster variety, realizing them as subfans of…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
Recently, the existence of an Amplituhedron for tree level amplitudes in the bi-adjoint scalar field theory has been proved by Arkhani-Hamed et al. We argue that hyperbolic geometry constitutes a natural framework to address the study of…
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…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
For each poset $P$, we construct a polytope $A(P)$ called the $P$-associahedron. Similarly to the case of graph associahedra, the faces of $A(P)$ correspond to certain nested collections of subsets of $P$. The Stasheff associahedron is a…
Polyfold theory was developed by Hofer-Wysocki-Zehnder by finding commonalities in the analytic framework for a variety of geometric elliptic PDEs, in particular moduli spaces of pseudoholomorphic curves. It aims to systematically address…
In this article, we construct a cofibrantly generated model structure on the category of spaces stratified over a fixed poset, and show that it is Quillen-equivalent to a category of diagrams of simplicial sets. Then, considering all those…
In this paper we establish a connection between the loop space homology of the generalization of wedge defined by a simplicial complex K (so called polyhedral product) and the homology of certain diagonal arrangements associated with K. We…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Motivated by the theory of cluster algebras, F. Chapoton, S. Fomin and A. Zelevinsky associated to each finite type root system a simple convex polytope called \emph{generalized associahedron}. They provided an explicit realization of this…
In this article we consider the homotopy theory of stratified spaces through a simplicial point of view. We first consider a model category of filtered simplicial sets over some fixed poset $P$, and show that it is a simplicial…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
We are introducing a general framework for the construction of polyhedra and simplicial comlexes that are {\em bifoldable}, i.e. foldable into two two different planes. This vastly generalizes Origami folds known as the Miura pattern, the…
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…
The associahedron is a convex polytope whose face poset is based on nonintersecting diagonals of a convex polygon. In this paper, given an arbitrary simple polygon P, we construct a polytopal complex analogous to the associahedron based on…
The type A cluster configuration space, commonly known as $\mathcal M_{0,n}$, is the very affine part of the binary geometry associated with the associahedron. The tropicalization of $\mathcal M_{0,n}$ can be realized as the space of…