Related papers: Point configurations, phylogenetic trees, and diss…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
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…
Tropical rainforests exhibit a rich repertoire of spatial patterns emerging from the intricate relationship between the microscopic interaction between species. In particular, the distribution of vegetation clusters can shed much light on…
We find a relation between mixed volumes of several polytopes and the convex hull of their union, deducing it from the following fact: the mixed volume of a collection of polytopes only depends on the product of their support functions…
Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor…
We consider the dimer model on piecewise Temperleyan, simply connected domains, on families of graphs which include the square lattice as well as superposition graphs. We focus on the spanning tree $\mathcal{T}_\delta$ associated to this…
We study tree metrics that can be realized as a mixture of two star tree metrics. We prove that the only trees admitting such a decomposition are the ones coming from a tree with at most one internal edge, and whose weight satisfies certain…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…
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…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
We introduce bijections between families of rooted maps with unfixed genus and families of so-called blossoming trees endowed with an arbitrary forward matching of their leaves. We first focus on Eulerian maps with controlled vertex…
The paper introduces a Poisson-type problem on a mixed-dimensional structure combining a Euclidean domain and a lower-dimensional self-similar component touching a compact surface (interface). The lower-dimensional piece is a so-called…
In the open map approach to bisimilarity, the paths and their runs in a given state-based system are the first-class citizens, and bisimilarity becomes a derived notion. While open maps were successfully used to model bisimilarity in…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
We provide a complete description of possible covariance matrices consistent with a Gaussian latent tree model for any tree. We then present techniques for utilising these constraints to assess whether observed data is compatible with that…
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…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Hex-trees are identified as a particular instance of weighted unary-binary trees. The Horton-Strahler numbers of these objects are revisited, and, thanks to a substitution that is not immediately intuitive, explicit results are possible.…