Label Placement in Road Maps

A road map can be interpreted as a graph embedded in the plane, in which each vertex corresponds to a road junction and each edge to a particular road section. We consider the cartographic problem to place non-overlapping road labels along the edges so that as many road sections as possible are identified by their name, i.e., covered by a label. We show that this is NP-hard in general, but the problem can be solved in polynomial time if the road map is an embedded tree.Comment: extended version of a CIAC 2015 pape

Fast and compact self-stabilizing verification, computation, and fault detection of an MST

This paper demonstrates the usefulness of distributed local verification of proofs, as a tool for the design of self-stabilizing algorithms.In particular, it introduces a somewhat generalized notion of distributed local proofs, and utilizes it for improving the time complexity significantly, while maintaining space optimality. As a result, we show that optimizing the memory size carries at most a small cost in terms of time, in the context of Minimum Spanning Tree (MST). That is, we present algorithms that are both time and space efficient for both constructing an MST and for verifying it.This involves several parts that may be considered contributions in themselves.First, we generalize the notion of local proofs, trading off the time complexity for memory efficiency. This adds a dimension to the study of distributed local proofs, which has been gaining attention recently. Specifically, we design a (self-stabilizing) proof labeling scheme which is memory optimal (i.e., $O(\log n)$ bits per node), and whose time complexity is $O(\log ^2 n)$ in synchronous networks, or $O(\Delta \log ^3 n)$ time in asynchronous ones, where $\Delta$ is the maximum degree of nodes. This answers an open problem posed by Awerbuch and Varghese (FOCS 1991). We also show that $\Omega(\log n)$ time is necessary, even in synchronous networks. Another property is that if $f$ faults occurred, then, within the requireddetection time above, they are detected by some node in the $O(f\log n)$ locality of each of the faults.Second, we show how to enhance a known transformer that makes input/output algorithms self-stabilizing. It now takes as input an efficient construction algorithm and an efficient self-stabilizing proof labeling scheme, and produces an efficient self-stabilizing algorithm. When used for MST, the transformer produces a memory optimal self-stabilizing algorithm, whose time complexity, namely, $O(n)$, is significantly better even than that of previous algorithms. (The time complexity of previous MST algorithms that used $\Omega(\log^2 n)$ memory bits per node was $O(n^2)$, and the time for optimal space algorithms was $O(n|E|)$.) Inherited from our proof labelling scheme, our self-stabilising MST construction algorithm also has the following two properties: (1) if faults occur after the construction ended, then they are detected by some nodes within $O(\log ^2 n)$ time in synchronous networks, or within $O(\Delta \log ^3 n)$ time in asynchronous ones, and (2) if $f$ faults occurred, then, within the required detection time above, they are detected within the $O(f\log n)$ locality of each of the faults. We also show how to improve the above two properties, at the expense of some increase in the memory

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work and are publicly available. We also apply our methods to real data

On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

Approximation Algorithms for Union and Intersection Covering Problems

In a classical covering problem, we are given a set of requests that we need to satisfy (fully or partially), by buying a subset of items at minimum cost. For example, in the k-MST problem we want to find the cheapest tree spanning at least k nodes of an edge-weighted graph. Here nodes and edges represent requests and items, respectively. In this paper, we initiate the study of a new family of multi-layer covering problems. Each such problem consists of a collection of h distinct instances of a standard covering problem (layers), with the constraint that all layers share the same set of requests. We identify two main subfamilies of these problems: - in a union multi-layer problem, a request is satisfied if it is satisfied in at least one layer; - in an intersection multi-layer problem, a request is satisfied if it is satisfied in all layers. To see some natural applications, consider both generalizations of k-MST. Union k-MST can model a problem where we are asked to connect a set of users to at least one of two communication networks, e.g., a wireless and a wired network. On the other hand, intersection k-MST can formalize the problem of connecting a subset of users to both electricity and water. We present a number of hardness and approximation results for union and intersection versions of several standard optimization problems: MST, Steiner tree, set cover, facility location, TSP, and their partial covering variants