Related papers: Classifying Tree Topologies along Tropical Line Se…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
A grove is a spanning forest of a planar graph in which every component tree contains at least one of a special subset of vertices on the outer face called nodes. For the natural probability measure on groves, we compute various connection…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
We examine the incidence geometry of lines in the tropical plane. We prove tropical analogs of the Sylvester-Gallai and Motzkin-Rabin theorems in classical incidence geometry. This study leads naturally to a discussion of the realizability…
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…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
Trophic coherence, a measure of the extent to which the nodes of a directed network are organised in levels, has recently been shown to be closely related to many structural and dynamical aspects of complex systems, including graph…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
We introduce tropical dual numbers as an extension of tropical semiring. By this innovation, one can work with honest ideals, instead of congruences, and recover the Euclidean topology on affine tropical spaces similar to Zariski's approach…
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…
In a deterministic or random tree, a notion of ancestral diversity can be defined as follows. Sample independently $n$ groups of $k$ leaves and count the number $N_n(k)$ of distinct most recent common ancestors of each of the groups. As $n$…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Temporal sequences of terrains arise in various application areas. To analyze them efficiently, one generally needs a suitable abstraction of the data as well as a method to compare and match them over time. In this paper we consider merge…
An acyclic mapping from an $n$ element set into itself is a mapping $\phi$ such that if $\phi^k(x) = x$ for some $k$ and $x$, then $\phi(x) = x$. Equivalently, $\phi^\ell = \phi^{\ell+1} = ...$ for $\ell$ sufficiently large. We investigate…
General graphs are difficult for learning due to their irregular structures. Existing works employ message passing along graph edges to extract local patterns using customized graph kernels, but few of them are effective for the integration…
Cayley's formula states that the number of labelled trees on $n$ vertices is $n^{n-2}$, and many of the current proofs involve complex structures or rigorous computation. We present a bijective proof of the formula by providing an…
We show how to equip the cone complexes of toroidal embeddings with additional structure that allows to define a balancing condition for weighted subcomplexes. We then proceed to develop the foundations of an intersection theory on cone…
We study the Tree Builder Random Walk: a randomly growing tree, built by a walker as she is walking around the tree. Namely, at each time $n$, she adds a leaf to her current vertex with probability $p_n \asymp n^{-\gamma}$, $\gamma\in…
Scaffolds are the one-dimensional skeleta of high-dimensional flag simplicial complexes of nonpositive curvature. They generalize the phylogenetic trees of Trop G(2,n) to arbitrary $k$, drawing together SL(k)-web bases, affine buildings,…