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.

Optimal Resilient Dynamic Dictionaries

Abstract: . In the resilient memory model any memory cell can get cor- rupted at any time, and corrupted cells cannot be distinguished from uncorrupted cells. An upper bound, , on the number of corruptions and O(1) reliable memory cells are provided. In this model, a data structure is denoted resilient if it gives the correct output on the set of uncor- rupted elements. We propose two optimal resilient static dictionaries, a randomized one and a deterministic one. The randomized dictionary supports searches in O(log n + ) expected time using O(log ) random bits in the worst case, under the assumption that corruptions are not performed by an adaptive adversary. The deterministic static dictionary supports searches in O(log n + ) time in the worst case. We also in- troduce a deterministic dynamic resilient dictionary supporting searches in O(log n + ) time in the worst case, which is optimal, and updates in O(log n + ) amortized time. Our dynamic dictionary supports range queries in O(log n + + k) worst case time, where k is the size of the output.

De-amortizing binary search trees

Abstract: We present a general method for de-amortizing essentially any Binary Search Tree (BST) algorithm. In particular, by transforming Splay Trees, our method produces a BST that has the same asymptotic cost as Splay Trees on any access sequence while performing each search in O(logn) worst case time. By transforming Multi-Splay Trees, we obtain a BST that is O(loglogn) competitive, satisfies the scanning theorem, the static optimality theorem, the static finger theorem, the working set theorem, and performs each search in O(logn) worst case time. Transforming OPT proves the existence of an O(1)-competitive offline BST algorithm which performs at most O(log n) BST operations between each access to the keys in the input sequence. Finally, we obtain that if there is an O(1)-competitive online BST algorithm, then there is also one that performs every search in O(logn) operations worst case.

De-amortizing Binary Search Trees

Abstract: We present a general method for de-amortizing essentially any Binary Search Tree (BST) algorithm. In particular, by transforming Splay Trees, our method produces a BST that has the same asymptotic cost as Splay Trees on any access sequence while performing each search in O(log n) worst case time. By transforming Multi-Splay Trees, we obtain a BST that is O(log log n) competitive, satisfies the scanning theorem, the static optimality theorem, the static finger theorem, the working set theorem, and performs each search in O(log n) worst case time. Moreover, we prove that if there is a dynamically optimal BST algorithm, then there is a dynamically optimal BST algorithm that answers every search in O(log n) worst case time.

Fragile Complexity of Comparison-Based Algorithms

Abstract: We initiate a study of algorithms with a focus on the computational complexity of individual elements, and introduce the fragile complexity of comparison-based algorithms as the maximal number of comparisons any individual element takes part in. We give a number of upper and lower bounds on the fragile complexity for fundamental problems, including Minimum, Selection, Sorting and Heap Construction. The results include both deterministic and randomized upper and lower bounds, and demonstrate a separation between the two settings for a number of problems. The depth of a comparator network is a straight-forward upper bound on the worst case fragile complexity of the corresponding fragile algorithm. We prove that fragile complexity is a different and strictly easier property than the depth of comparator networks, in the sense that for some problems a fragile complexity equal to the best network depth can be achieved with less total work and that with randomization, even a lower fragile complexity is possible.

Computing Refined Buneman Trees in Cubic Time

Abstract: Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbour joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n^5) and a space consumption of O(n^4). In this paper, we present an algorithm with running time O(n^3) and space consumption O(n^2).

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.