Related papers: A kernel for the maximum agreement forest problem …
The Minimum Spanning Tree Problem with Conflicts consists in finding the minimum conflict-free spanning tree of a graph, i.e., the spanning tree of minimum cost, including no pairs of edges that are in conflict. In this paper, we solve this…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
An out-tree $T$ of a directed graph $D$ is a rooted tree subgraph with all arcs directed outwards from the root. An out-branching is a spanning out-tree. By $l(D)$ and $l_s(D)$ we denote the maximum number of leaves over all out-trees and…
The basic goal of survivable network design is to build cheap networks that guarantee the connectivity of certain pairs of nodes despite the failure of a few edges or nodes. A celebrated result by Jain [Combinatorica'01] provides a…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
The Mutliagent Path Finding (MAPF) problem consists of identifying the trajectories that a set of agents should follow inside a given network in order to reach their desired destinations as soon as possible, but without colliding with each…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
Throughout the last decade, we have seen much progress towards characterising and computing the minimum hybridisation number for a set P of rooted phylogenetic trees. Roughly speaking, this minimum quantifies the number of hybridisation…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
In this work, we present an $\Omega\left(\min\{\log \Delta, \sqrt{\log n}\}\right)$ lower bound for Maximal Matching (MM) in $\Delta$-ary trees against randomized algorithms. By a folklore reduction, the same lower bound applies to Maximal…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we obtain two combinatorial results on the number…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Let $\mathcal{F}$ be a family of $r$-graphs. The Tur\'an number $ex_r(n;\mathcal{F})$ is defined to be the maximum number of edges in an $r$-graph of order $n$ that is $\mathcal{F}$-free. The famous Erd\H{o}s Matching Conjecture shows that…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
A widely studied problem in communication networks is that of finding the maximum number of communication requests that can be scheduled concurrently, subject to node and/or link capacity constraints. In this paper, we consider the problem…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…