Showing papers by "Gerth Stølting Brodal published in 2003"
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12 Jan 2003TL;DR: For both lower bound trade offs between the I/O complexity of member queries and insertions, data structures are described which give matching upper bounds for a wide range of parameters, thereby showing the lower bounds to be tight within these ranges.
Abstract: We study trade-offs between the update time and the query time for comparison based external memory dictionaries. The main contributions of this paper are two lower bound trade offs between the I/O complexity of member queries and insertions: If N
113 citations
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09 Jun 2003TL;DR: The results for sorting show the existence of an inherent trade-off in the cache-oblivious model between the strength of the tall cache assumption and the overhead for the case M » B, and show that Funnelsort and recursive binary mergesort are optimal algorithms in the sense that they attain this trade-offs.
Abstract: In this paper, we present lower bounds for permuting and sorting in the cache-oblivious model. We prove that (1) I/O optimal cache-oblivious comparison based sorting is not possible without a tall cache assumption, and (2) there does not exist an I/O optimal cache-oblivious algorithm for permuting, not even in the presence of a tall cache assumption.Our results for sorting show the existence of an inherent trade-off in the cache-oblivious model between the strength of the tall cache assumption and the overhead for the case M » B, and show that Funnelsort and recursive binary mergesort are optimal algorithms in the sense that they attain this trade-off.
73 citations
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11 Oct 2003TL;DR: It is shown that for a multilevel memory hierarchy, a simple cache-oblivious structure almost replicates the performance of an optimal parameterized k-level DAM structure, and it is demonstrated that as k grows, the search costs of the optimal k- level DAM search structure and the optimal cache-OBlivious search structure rapidly converge.
Abstract: Tight bounds on the cost of cache-oblivious searching are proved. It is shown that no cache-oblivious search structure can guarantee that a search performs fewer than lg e log/sub B/N block transfers between any two levels of the memory hierarchy. This lower bound holds even if all of the block sizes are limited to be powers of 2. A modified version of the van Emde Boas layout is proposed, whose expected block transfers between any two levels of the memory hierarchy arbitrarily close to [lg e + O(lg lg B/ lgB)] logB N + O(1). This factor approaches lg e /spl ap/ 1.443 as B increases. The expectation is taken over the random placement of the first element of the structure in memory. As searching in the disk access model (DAM) can be performed in log/sub B/N + 1 block transfers, this result shows a separation between the 2-level DAM and cache-oblivious memory-hierarchy models. By extending the DAM model to k levels, multilevel memory hierarchies can be modeled. It is shown that as k grows, the search costs of the optimal k-level DAM search structure and of the optimal cache-oblivious search structure rapidly converge. This demonstrates that for a multilevel memory hierarchy, a simple cache-oblivious structure almost replicates the performance of an optimal parameterized k-level DAM structure.
34 citations
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15 Sep 2003TL;DR: The improved complexity of the algorithm is presented, which makes the method of refined Buneman trees computational competitive to methods based on neighbor joining.
Abstract: Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor 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). The improved complexity of our algorithm makes the method of refined Buneman trees computational competitive to methods based on neighbor joining.
13 citations