Related papers: Order-Dependent Dissimilarity Measures on Phylogen…
The Horton-Strahler (HS) index $r=\max{(i,j)}+\delta_{i,j}$ has been shown to be relevant to a number of physical (such at diffusion limited aggregation) geological (river networks), biological (pulmonary arteries, blood vessels, various…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
We give an algorithm that, given an $n$-vertex graph $G$ and an integer $k$, in time $2^{O(k)} n$ either outputs a tree decomposition of $G$ of width at most $2k + 1$ or determines that the treewidth of $G$ is larger than $k$. This is the…
Given a finite set $X$, a collection $\mathcal{T}$ of rooted phylogenetic trees on $X$ and an integer $k$, the Hybridization Number problem asks if there exists a phylogenetic network on $X$ that displays all trees from $\mathcal{T}$ and…
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…
We study two computational problems, parameterised by a fixed tree H. #HomsTo(H) is the problem of counting homomorphisms from an input graph G to H. #WHomsTo(H) is the problem of counting weighted homomorphisms to H, given an input graph G…
The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…
We obtain a representation of Feller's branching diffusion with logistic growth in terms of the local times of a reflected Brownian motion $H$ with a drift that is affine linear in the local time accumulated by $H$ at its current level. As…
The relaxation in the calculus of variation motivates the numerical analysis of a class of degenerate convex minimization problems with non-strictly convex energy densities with some convexity control and two-sided $p$-growth. The…
Tree shape statistics are important for investigating evolutionary mechanisms mediating phylogenetic trees. As a step towards bridging shape statistics between rooted and unrooted trees, we present a comparison study on two subtree…
We consider drawings of graphs in the plane in which vertices are assigned distinct points in the plane and edges are drawn as simple curves connecting the vertices and such that the edges intersect only at their common endpoints. There is…
The hop-constrained Steiner tree problem (HSTP) is a generalization of the classical Steiner tree problem. It asks for a minimum cost subtree that spans some specified nodes of a given graph, such that the number of edges between each node…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…
Consider any locally checkable labeling problem $\Pi$ in rooted regular trees: there is a finite set of labels $\Sigma$, and for each label $x \in \Sigma$ we specify what are permitted label combinations of the children for an internal node…
For a fixed digraph $\mathbb H$, the $\mathbb H$-coloring problem is the problem of deciding whether a given input digraph $\mathbb G$ admits a homomorphism to $\mathbb H$. The CSP dichotomy conjecture of Feder and Vardi is equivalent to…
Geolocated time series, i.e., time series associated with certain locations, abound in many modern applications. In this paper, we consider hybrid queries for retrieving geolocated time series based on filters that combine spatial distance…
We investigate the computation of minimum-cost spanning trees satisfying prescribed vertex degree constraints: Given a graph $G$ and a constraint function $D$, we ask for a (minimum-cost) spanning tree $T$ such that for each vertex $v$, $T$…