Related papers: Constructing minimal phylogenetic networks from so…

We resolve positively a long standing open question regarding the fixed-parameter tractability of the parameterized Directed Feedback Vertex Set problem. In particular, we propose an algorithm which solves this problem in…

In this paper we present decomposable priors, a family of priors over structure and parameters of tree belief nets for which Bayesian learning with complete observations is tractable, in the sense that the posterior is also decomposable and…

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…

Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…

Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…

Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…

There has lately been increased interest in describing complex systems not merely as single networks but rather as collections of networks that are coupled to one another. We introduce an analytically tractable model that enables one to…

We study an extensive class of movement minimization problems which arise from many practical scenarios but so far have little theoretical study. In general, these problems involve planning the coordinated motion of a collection of agents…

We report on parallel observations in two seemingly unrelated areas of dynamical network research. The one is the so-called small world phenomenon and/or the observation of scale freeness in certain types of large (empirical) networks and…

The solvable Farb growth of a group quantifies how well-approximated the group is by its finite solvable quotients. In this note we present a new characterization of polycyclic groups which are virtually nilpotent. That is, we show that a…

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…

We consider a the minimum k-way cut problem for unweighted graphs with a size bound s on the number of cut edges allowed. Thus we seek to remove as few edges as possible so as to split a graph into k components, or report that this requires…

We apply classical quartet techniques to the problem of phylogenetic decisiveness and find a value $k$ such that all collections of at least $k$ quartets are decisive. Moreover, we prove that this bound is optimal and give a lower-bound on…

Connected clustering denotes a family of constrained clustering problems in which we are given a distance metric and an undirected connectivity graph $G$ that can be completely unrelated to the metric. The aim is to partition the $n$…

In a recursive way and by including a parameter, we introduce a family of deterministic scale-free networks. The resulting networks exhibit small-world effects. We calculate the exact results for the degree exponent, the clustering…

We investigate the problem asking whether the intersection of a context-free language (CFL) and a Petri net language (PNL) is empty. Our contribution to solve this long-standing problem which relates, for instance, to the reachability…

Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…

A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…

We study the approximation of high-dimensional rank one tensors using point evaluations and consider deterministic as well as randomized algorithms. We prove that for certain parameters (smoothness and norm of the $r$th derivative) this…

The cyclability of a graph is the maximum integer $k$ for which every $k$ vertices lie on a cycle. The algorithmic version of the problem, given a graph $G$ and a non-negative integer $k,$ decide whether the cyclability of $G$ is at least…