相关论文: Tropical Grassmannian and Tropical Linear Varietie…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
We compare strongly recursive tropical linear series as defined by Farkas, Jensen, and Payne with combinatorial limit linear series as defined by Amini and Gierczak. We show that strongly recursive tropical linear series of rank $r$ are…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
This chapter provides a guide to our polymake extension cellularSheaves. We first define cellular sheaves on polyhedral complexes in Euclidean space, as well as cosheaves, and their (co)homologies. As motivation, we summarise some results…
This is an expository paper. The geometry of phylogenetic trees is used to present in an accessible and pleasant fashion the results of Deligne, Mumford, and Knudsen about the moduli space of n distinct points on the projective line and its…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
We explore several facets of tropical subrepresentations of a linear representation of a group over the tropical semifield $\mathbb{T}$. A key role in the study of tropical subrepresentations is played by two types of modules over a…
Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover…
The map which takes a square matrix to its tropical eigenvalue-eigenvector pair is piecewise linear. We determine the cones of linearity of this map. They are simplicial but they do not form a fan. Motivated by statistical ranking, we also…
Motivated by geometric origami and the straight skeleton construction, we outline a map between spaces of phylogenetic trees and spaces of planar polygons. The limitations of this map is studied through explicit examples, culminating in…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
We consider the enumeration of tropical curves in M\"obius strips for two different lattice structures and relate them to the enumeration of curves in two rational ruled surfaces over a complex elliptic curve. Using this correspondence, we…
We use tropical and nonarchimedean geometry to study the moduli space of genus $0$ stable maps to $\mathbb{P}^1$ relative to two points. This space is exhibited as a tropical compactification in a toric variety. Moreover, the fan of this…
We propose an algebraic geometric framework to study the expressivity of linear activation neural networks. A particular quantity of neural networks that has been actively studied is the number of linear regions, which gives a…
The map which takes a square matrix $A$ to its polytrope is piecewise linear. We show that cones of linearity of this map form a polytopal fan partition of $\{R}^{n \times n}$, whose face lattice is anti-isomorphic to the lattice of…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
In this paper we study the moduli space of the tropicalizations of Riemann surfaces. We first tropicalize a smooth pointed Riemann surface by a graph defined by its (hyperbolic) pair of pants decomposition. Then we can construct the moduli…
We introduce the notion of tropical curves of hyperelliptic type. These are tropical curves whose Jacobian is isomorphic to that of a hyperelliptic tropical curve, as polarized tropical abelian varieties. We show that this property depends…