Rolf Fagerberg

Bio: Rolf Fagerberg is an academic researcher from University of Southern Denmark. The author has contributed to research in topics: Cache-oblivious algorithm & Vertex (geometry). The author has an hindex of 25, co-authored 97 publications receiving 1906 citations. Previous affiliations of Rolf Fagerberg include Aarhus University & Odense University.

Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

Abstract: We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds. In practical applications the space is likely to be a bottleneck and therefore this is of crucial importance.

On the Adaptiveness of Quicksort.

Abstract: Quicksort was first introduced in 1961 by Hoare. Many variants have been developed, the best of which are among the fastest generic-sorting algorithms available, as testified by the choice of Quicksort as the default sorting algorithm in most programming libraries. Some sorting algorithms are adaptive, i.e., they have a complexity analysis that is better for inputs, which are nearly sorted, according to some specified measure of presortedness. Quicksort is not among these, as it uses Ω(n log n) comparisons even for sorted inputs. However, in this paper, we demonstrate empirically that the actual running time of Quicksort is adaptive with respect to the presortedness measure Inv. Differences close to a factor of two are observed between instances with low and high Inv value. We then show that for the randomized version of Quicksort, the number of element swaps performed is provably adaptive with respect to the measure Inv. More precisely, we prove that randomized Quicksort performs expected O(n(1 + log(1 + Inv/n))) element swaps, where Inv denotes the number of inversions in the input sequence. This result provides a theoretical explanation for the observed behavior and gives new insights on the behavior of Quicksort. We also give some empirical results on the adaptive behavior of Heapsort and Mergesort.

Competitive Routing on a Bounded-Degree Plane Spanner

Abstract: We show that it is possible to route locally and competitively on two bounded-degree plane 6-spanners, one with maximum degree 12 and the other with maximum degree 9. Both spanners are subgraphs of the empty equilateral triangle Delaunay triangulation. First, in a weak routing model where the only information stored at each vertex is its neighbourhood, we show how to nd a path between any two vertices of a 6-spanner of maximum degree 12, such that the path has length at most 95= p 3 times the straight-line distance between the vertices. In a slightly stronger model, where in addition to the neighbourhood of each vertex, we store O(1) additional information, we show how to nd a path that has length at most 15= p 3 times the Euclidean distance both in a 6-spanner of maximum degree 12 and a 6-spanner of maximum degree 9.

Competitive Local Routing with Constraints

Abstract: Let $P$ be a set of $n$ vertices in the plane and $S$ a set of non-crossing line segments between vertices in $P$, called constraints. Two vertices are visible if the straight line segment connecting them does not properly intersect any constraints. The constrained $\Theta_m$-graph is constructed by partitioning the plane around each vertex into $m$ disjoint cones, each with aperture $\theta = 2 \pi/m$, and adding an edge to the `closest' visible vertex in each cone. We consider how to route on the constrained $\Theta_6$-graph. We first show that no deterministic 1-local routing algorithm is $o(\sqrt{n})$-competitive on all pairs of vertices of the constrained $\Theta_6$-graph. After that, we show how to route between any two visible vertices of the constrained $\Theta_6$-graph using only 1-local information. Our routing algorithm guarantees that the returned path is 2-competitive. Additionally, we provide a 1-local 18-competitive routing algorithm for visible vertices in the constrained half-$\Theta_6$-graph, a subgraph of the constrained $\Theta_6$-graph that is equivalent to the Delaunay graph where the empty region is an equilateral triangle. To the best of our knowledge, these are the first local routing algorithms in the constrained setting with guarantees on the length of the returned path.

Binary Search Trees: How Low Can You Go?

Abstract: We prove that no algorithm for balanced binary search trees performing insertions and deletions in amortized time O(f(n)) can guarantee a height smaller than [log(n + 1) + 1/f(n)] for all n. We improve the existing upper bound to [log(n + 1) + log2 (f(n))/f(n)], thus almost matching our lower bound. We also improve the existing upper bound for worst case algorithms, and give a lower bound for the semi-dynamic case.

Application of Phylogenetic Networks in Evolutionary Studies

Abstract: The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes–Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.