Related papers: Additive Approximation for Near-Perfect Phylogeny …
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
We consider the ``minimum degree spanning tree'' problem. As input, we receive an undirected, connected graph $G=(V, E)$ with $n$ nodes and $m$ edges, and our task is to find a spanning tree $T$ of $G$ that minimizes $\max_{u \in V}…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
We consider the problem of constructing a single spanning tree for the single-source buy-at-bulk network design problem for doubling-dimension graphs. We compute a spanning tree to route a set of demands (or data) along a graph to or from a…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
In the Priority Steiner Tree (PST) problem, we are given an undirected graph $G=(V,E)$ with a source $s \in V$ and terminals $T \subseteq V \setminus \{s\}$, where each terminal $v \in T$ requires a nonnegative priority $P(v)$. The goal is…
Min-Cut queries are fundamental: Preprocess an undirected edge-weighted graph, to quickly report a minimum-weight cut that separates a query pair of nodes $s,t$. The best data structure known for this problem simply builds a cut-equivalent…
We propose a data structure in $d$-dimensional hyperbolic space that can be considered a natural counterpart to quadtrees in Euclidean spaces. Based on this data structure we propose a so-called L-order for hyperbolic point sets, which is…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
We give a new general approach for designing exact exponential-time algorithms for subset problems. In a subset problem the input implicitly describes a family of sets over a universe of size n and the task is to determine whether the…
Given a set $P$ of terminals in the plane and a partition of $P$ into $k$ subsets $P_1, ..., P_k$, a two-level rectilinear Steiner tree consists of a rectilinear Steiner tree $T_i$ connecting the terminals in each set $P_i$ ($i=1,...,k$)…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We consider the $k$-prize-collecting Steiner tree problem. An instance is composed of an integer $k$ and a graph $G$ with costs on edges and penalties on vertices. The objective is to find a tree spanning at least $k$ vertices which…
An important goal in algorithm design is determining the best running time for solving a problem (approximately). For some problems, we know the optimal running time, assuming certain conditional lower bounds. In this work, we study the…
We study the multi-level Steiner tree problem: a generalization of the Steiner tree problem in graphs where terminals $T$ require varying priority, level, or quality of service. In this problem, we seek to find a minimum cost tree…
The \emph{Steiner tree} problem is one of the fundamental and classical problems in combinatorial optimization. In this paper, we study this problem in the $\mathcal{CONGESTED}$ $\mathcal{CLIQUE}$ model of distributed computing and present…
An algorithm is developed for finding a close to optimal junction tree of a given graph G. The algorithm has a worst case complexity O(c^k n^a) where a and c are constants, n is the number of vertices, and k is the size of the largest…
We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…
A spanning tree $T$ of graph $G$ is a $\rho$-approximate universal Steiner tree (UST) for root vertex $r$ if, for any subset of vertices $S$ containing $r$, the cost of the minimal subgraph of $T$ connecting $S$ is within a $\rho$ factor of…
Approximation algorithms for the prize-collecting Steiner forest problem (PCSF) have been a subject of research for over three decades, starting with the seminal works of Agrawal, Klein, and Ravi and Goemans and Williamson on Steiner forest…