A Static Optimality Transformation with Applications to Planar Point Location

Over the last decade, there have been several data structures that, given a planar subdivision and a probability distribution over the plane, provide a way for answering point location queries that is fine-tuned for the distribution. All these methods suffer from the requirement that the query distribution must be known in advance. We present a new data structure for point location queries in planar triangulations. Our structure is asymptotically as fast as the optimal structures, but it requires no prior information about the queries. This is a 2D analogue of the jump from Knuth's optimum binary search trees (discovered in 1971) to the splay trees of Sleator and Tarjan in 1985. While the former need to know the query distribution, the latter are statically optimal. This means that we can adapt to the query sequence and achieve the same asymptotic performance as an optimum static structure, without needing any additional information.Comment: 13 pages, 1 figure, a preliminary version appeared at SoCG 201

Burning a Graph is Hard

Graph burning is a model for the spread of social contagion. The burning number is a graph parameter associated with graph burning that measures the speed of the spread of contagion in a graph; the lower the burning number, the faster the contagion spreads. We prove that the corresponding graph decision problem is \textbf{NP}-complete when restricted to acyclic graphs with maximum degree three, spider graphs and path-forests. We provide polynomial time algorithms for finding the burning number of spider graphs and path-forests if the number of arms and components, respectively, are fixed.Comment: 20 Pages, 4 figures, presented at GRASTA-MAC 2015 (October 19-23rd, 2015, Montr\'eal, Canada

A Fast Quartet Tree Heuristic for Hierarchical Clustering

The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the $3{n \choose 4}$ weighted quartet topologies on $n$ objects, where optimality means that the summed weight of the embedded quartet topologies is optimal (so it can be the case that the optimal tree embeds all quartets as nonoptimal topologies). We present a Monte Carlo heuristic, based on randomized hill climbing, for approximating the optimal weight tree, given the quartet topology weights. The method repeatedly transforms a dendrogram, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. The problem and the solution heuristic has been extensively used for general hierarchical clustering of nontree-like (non-phylogeny) data in various domains and across domains with heterogeneous data. We also present a greatly improved heuristic, reducing the running time by a factor of order a thousand to ten thousand. All this is implemented and available, as part of the CompLearn package. We compare performance and running time of the original and improved versions with those of UPGMA, BioNJ, and NJ, as implemented in the SplitsTree package on genomic data for which the latter are optimized. Keywords: Data and knowledge visualization, Pattern matching--Clustering--Algorithms/Similarity measures, Hierarchical clustering, Global optimization, Quartet tree, Randomized hill-climbing,Comment: LaTeX, 40 pages, 11 figures; this paper has substantial overlap with arXiv:cs/0606048 in cs.D

A New Quartet Tree Heuristic for Hierarchical Clustering

We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the case that the optimal tree embeds all quartets as non-optimal topologies). We present a heuristic for reconstructing the optimal-weight tree, and a canonical manner to derive the quartet-topology weights from a given distance matrix. The method repeatedly transforms a bifurcating tree, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. This contrasts to other heuristic search methods from biological phylogeny, like DNAML or quartet puzzling, which, repeatedly, incrementally construct a solution from a random order of objects, and subsequently add agreement values.Comment: 22 pages, 14 figure

Communication tree problems

In this paper, we consider random communication requirements and several cost measures for a particular model of tree routing on a complete network. First we show that a random tree does not give any approximation. Then give approximation algorithms for the case for two random models of requirements.Postprint (published version