268,203 research outputs found

    Online Data Structures in External Memory

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    The original publication is available at www.springerlink.comThe data sets for many of today's computer applications are too large to t within the computer's internal memory and must instead be stored on external storage devices such as disks. A major performance bottleneck can be the input/output communication (or I/O) between the external and internal memories. In this paper we discuss a variety of online data structures for external memory, some very old and some very new, such as hashing (for dictionaries), B-trees (for dictionaries and 1-D range search), bu er trees (for batched dynamic problems), interval trees with weight-balanced B-trees (for stabbing queries), priority search trees (for 3-sided 2-D range search), and R-trees and other spatial structures. We also discuss several open problems along the way

    Online Sorting via Searching and Selection

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    In this paper, we present a framework based on a simple data structure and parameterized algorithms for the problems of finding items in an unsorted list of linearly ordered items based on their rank (selection) or value (search). As a side-effect of answering these online selection and search queries, we progressively sort the list. Our algorithms are based on Hoare's Quickselect, and are parameterized based on the pivot selection method. For example, if we choose the pivot as the last item in a subinterval, our framework yields algorithms that will answer q<=n unique selection and/or search queries in a total of O(n log q) average time. After q=\Omega(n) queries the list is sorted. Each repeated selection query takes constant time, and each repeated search query takes O(log n) time. The two query types can be interleaved freely. By plugging different pivot selection methods into our framework, these results can, for example, become randomized expected time or deterministic worst-case time. Our methods are easy to implement, and we show they perform well in practice

    Prospects and limitations of full-text index structures in genome analysis

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    The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

    I/O-Efficient Dynamic Planar Range Skyline Queries

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    We present the first fully dynamic worst case I/O-efficient data structures that support planar orthogonal \textit{3-sided range skyline reporting queries} in \bigO (\log_{2B^\epsilon} n + \frac{t}{B^{1-\epsilon}}) I/Os and updates in \bigO (\log_{2B^\epsilon} n) I/Os, using \bigO (\frac{n}{B^{1-\epsilon}}) blocks of space, for nn input planar points, tt reported points, and parameter 0ϵ10 \leq \epsilon \leq 1. We obtain the result by extending Sundar's priority queues with attrition to support the operations \textsc{DeleteMin} and \textsc{CatenateAndAttrite} in \bigO (1) worst case I/Os, and in \bigO(1/B) amortized I/Os given that a constant number of blocks is already loaded in main memory. Finally, we show that any pointer-based static data structure that supports \textit{dominated maxima reporting queries}, namely the difficult special case of 4-sided skyline queries, in \bigO(\log^{\bigO(1)}n +t) worst case time must occupy Ω(nlognloglogn)\Omega(n \frac{\log n}{\log \log n}) space, by adapting a similar lower bounding argument for planar 4-sided range reporting queries.Comment: Submitted to SODA 201

    Belga B-trees

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    We revisit self-adjusting external memory tree data structures, which combine the optimal (and practical) worst-case I/O performances of B-trees, while adapting to the online distribution of queries. Our approach is analogous to undergoing efforts in the BST model, where Tango Trees (Demaine et al. 2007) were shown to be O(loglogN)O(\log\log N)-competitive with the runtime of the best offline binary search tree on every sequence of searches. Here we formalize the B-Tree model as a natural generalization of the BST model. We prove lower bounds for the B-Tree model, and introduce a B-Tree model data structure, the Belga B-tree, that executes any sequence of searches within a O(loglogN)O(\log \log N) factor of the best offline B-tree model algorithm, provided B=logO(1)NB=\log^{O(1)}N. We also show how to transform any static BST into a static B-tree which is faster by a Θ(logB)\Theta(\log B) factor; the transformation is randomized and we show that randomization is necessary to obtain any significant speedup
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