Related papers: Distinguished minimal toplogical lassos
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
It is known from the algebraic graph theory that if $L$ is the Laplacian matrix of some tree $G$ with a vertex degree sequence $\mathbf{d}=(d_1, ..., d_n)^\top$ and $D$ is its distance matrix, then…
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 problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
We consider the following graph reconstruction problem: given an unweighted connected graph $G = (V,E)$ with visible vertex set $V$ and an oracle which takes two vertices $u,v \in V$ and returns the shortest path distance between $u$ and…
The Tree Decomposition Conjecture by Bar\'at and Thomassen states that for every tree $T$ there exists a natural number $k(T)$ such that the following holds: If $G$ is a $k(T)$-edge-connected simple graph with size divisible by the size of…
The fused lasso, also known as (anisotropic) total variation denoising, is widely used for piecewise constant signal estimation with respect to a given undirected graph. The fused lasso estimate is highly nontrivial to compute when the…
Motivated by a question of Galby, Munaro, and Yang (SoCG 2023) asking whether every graph class of bounded layered tree-independence number admits clique-based separators of sublinear weight, we investigate relations between layered…
We consider locally checkable labeling LCL problems in the LOCAL model of distributed computing. Since 2016, there has been a substantial body of work examining the possible complexities of LCL problems. For example, it has been established…
We present a new and surprisingly simple analysis of random-shift decompositions -- originally proposed by Miller, Peng, and Xu [SPAA'13]: We show that decompositions for exponentially growing scales $D = 2^0, 2^1, \ldots,…
In this article, we present a novel approach to reconstruct the topology of networked linear dynamical systems with latent nodes. The network is allowed to have directed loops and bi-directed edges. The main approach relies on the unique…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
As an extension of a classical tree-partition problem, we consider decompositions of graphs into edge-disjoint (rooted-)trees with an additional matroid constraint. Specifically, suppose we are given a graph $G=(V,E)$, a multiset…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
We introduce the concept of a class of graphs, or more generally, relational structures, being locally tree-decomposable. There are numerous examples of locally tree-decomposable classes, among them the class of planar graphs and all…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…