Related papers: Regular networks are determined by their trees
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been…
Transport networks are crucial to the functioning of natural systems and technological infrastructures. For flow networks in many scenarios, such as rivers or blood vessels, acyclic networks (i.e., trees) are optimal structures when…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…
The structure of networks that provide optimal transport properties has been investigated in a variety of contexts. While many different formulations of this problem have been considered, it is recurrently found that optimal networks are…
A theory is developed which uses "networks" (directed acyclic graphs with some extra structure) as a formalism for expressions in multilinear algebra. It is shown that this formalism is valid for arbitrary PROPs (short for 'PROducts and…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Network models with latent geometry have been used successfully in many applications in network science and other disciplines, yet it is usually impossible to tell if a given real network is geometric, meaning if it is a typical element in…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Highly dynamic networks are characterized by frequent changes in the availability of communication links. These networks are often partitioned into several components, which split and merge unpredictably. We present a distributed algorithm…
We call a tree $T$ is \emph{even} if every pair of its leaves is joined by a path of even length. Jackson and Yoshimoto~[J. Graph Theory, 2024] conjectured that every $r$-regular nonbipartite connected graph $G$ has a spanning even tree.…
From the perspective of network analysis, the ubiquitous networks are comprised of regular and irregular components, which makes uncovering the complexity of network structures to be a fundamental challenge. Exploring the regular…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…