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The SBC-tree: an index for run-length compressed sequences

Authors:

Mohamed Y. Eltabakh,

Jeffrey S. VitterAuthors Info & Claims

EDBT '08: Proceedings of the 11th international conference on Extending database technology: Advances in database technology

Pages 523 - 534

https://doi.org/10.1145/1353343.1353407

Published: 25 March 2008 Publication History

Abstract

Run-Length-Encoding (RLE) is a data compression technique that is used in various applications, e.g., time series, biological sequences, and multimedia databases. One of the main challenges is how to operate on (e.g., index, search, and retrieve) compressed data without decompressing it. In this paper, we introduce the <u>S</u>tring <u>B</u>-tree for <u>C</u>ompressed sequences, termed the SBC-tree, for indexing and searching RLE-compressed sequences of arbitrary length. The SBC-tree is a two-level index structure based on the well-known String B-tree and a 3-sided range query structure [7]. The SBC-tree supports pattern matching queries such as substring matching, prefix matching, and range search operations over RLE-compressed sequences. The SBC-tree has an optimal external-memory space complexity of O(N/B) pages, where N is the total length of the compressed sequences, and B is the disk page size. Substring matching, prefix matching, and range search execute in an optimal O(log_B N + |p|+T/B) I/O operations, where |p| is the length of the compressed query pattern and T is the query output size. The SBC-tree is also dynamic and supports insert and delete operations efficiently. The insertion and deletion of all suffixes of a compressed sequence of length m take O(m log_B(N + m)) amortized I/O operations. The SBC-tree index is realized inside PostgreSQL. Performance results illustrate that using the SBC-tree to index RLE-compressed sequences achieves up to an order of magnitude reduction in storage, while retains the optimal search performance achieved by the String B-tree over the uncompressed sequences.

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Cited By

Tamakoshi YGoto KInenaga SBannai HTakeda M(2015)An Opportunistic Text Indexing Structure Based on Run Length EncodingProceedings of the 9th International Conference on Algorithms and Complexity - Volume 907910.1007/978-3-319-18173-8_29(390-402)Online publication date: 20-May-2015
https://dl.acm.org/doi/10.1007/978-3-319-18173-8_29
Ann HYang CTseng CHor C(2012)Fast algorithms for computing the constrained LCS of run-length encoded stringsTheoretical Computer Science10.1016/j.tcs.2012.01.038432(1-9)Online publication date: 1-May-2012
https://dl.acm.org/doi/10.1016/j.tcs.2012.01.038
Thankachan S(2011)Compressed indexes for aligned pattern matchingProceedings of the 18th international conference on String processing and information retrieval10.5555/2051073.2051113(410-419)Online publication date: 17-Oct-2011
https://dl.acm.org/doi/10.5555/2051073.2051113
Show More Cited By

Index Terms

The SBC-tree: an index for run-length compressed sequences
1. Information systems
2. Mathematics of computing
  1. Discrete mathematics
    1. Graph theory
      1. Trees

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cover image ACM Other conferences

EDBT '08: Proceedings of the 11th international conference on Extending database technology: Advances in database technology

March 2008

762 pages

ISBN:9781595939265

DOI:10.1145/1353343

Conference Chair:
Noureddine Mouaddib,
General Chair:
Patrick Valduriez,
Program Chairs:
Alfons Kemper
Technische Universität München, Germany
,
Mokrane Bouzeghoub,
Volker Markl,
Laurent Amsaleg,
Ioana Manolescu,
Publications Chair:
Jens Teubner

Copyright © 2008 ACM.

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Publication History

Published: 25 March 2008

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EDBT '08

EDBT '08: 11th International Conference on Extending Database Technology

March 25 - 29, 2008

Nantes, France

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Cited By

Tamakoshi YGoto KInenaga SBannai HTakeda M(2015)An Opportunistic Text Indexing Structure Based on Run Length EncodingProceedings of the 9th International Conference on Algorithms and Complexity - Volume 907910.1007/978-3-319-18173-8_29(390-402)Online publication date: 20-May-2015
https://dl.acm.org/doi/10.1007/978-3-319-18173-8_29
Ann HYang CTseng CHor C(2012)Fast algorithms for computing the constrained LCS of run-length encoded stringsTheoretical Computer Science10.1016/j.tcs.2012.01.038432(1-9)Online publication date: 1-May-2012
https://dl.acm.org/doi/10.1016/j.tcs.2012.01.038
Thankachan S(2011)Compressed indexes for aligned pattern matchingProceedings of the 18th international conference on String processing and information retrieval10.5555/2051073.2051113(410-419)Online publication date: 17-Oct-2011
https://dl.acm.org/doi/10.5555/2051073.2051113
Lemire DKaser O(2011)Reordering columns for smaller indexesInformation Sciences: an International Journal10.1016/j.ins.2011.02.002181:12(2550-2570)Online publication date: 1-Jun-2011
https://dl.acm.org/doi/10.1016/j.ins.2011.02.002
Thankachan S(2011)Compressed Indexes for Aligned Pattern MatchingString Processing and Information Retrieval10.1007/978-3-642-24583-1_40(410-419)Online publication date: 2011
https://doi.org/10.1007/978-3-642-24583-1_40
Eltabakh MAref WElmagarmid A(2010)A database server for next-generation scientific data management2010 IEEE 26th International Conference on Data Engineering Workshops (ICDEW 2010)10.1109/ICDEW.2010.5452723(313-316)Online publication date: Mar-2010
https://doi.org/10.1109/ICDEW.2010.5452723
Peng YYang CHuang KAnn H(2010)Efficient indexing algorithms for one-dimensional discretely-scaled stringsInformation Processing Letters10.1016/j.ipl.2010.05.012110:16(730-734)Online publication date: 1-Jul-2010
https://dl.acm.org/doi/10.1016/j.ipl.2010.05.012
Vitter J(2008)Algorithms and data structures for external memoryFoundations and Trends® in Theoretical Computer Science10.1561/04000000142:4(305-474)Online publication date: 1-Jan-2008
https://dl.acm.org/doi/10.1561/0400000014

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