research-article

The wavelet trie: maintaining an indexed sequence of strings in compressed space

Authors:

Roberto Grossi,

Giuseppe OttavianoAuthors Info & Claims

PODS '12: Proceedings of the 31st ACM SIGMOD-SIGACT-SIGAI symposium on Principles of Database Systems

Pages 203 - 214

https://doi.org/10.1145/2213556.2213586

Published: 21 May 2012 Publication History

Abstract

An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of column-oriented databases, log processing, and other storage and query tasks. In these applications each string can appear several times and the order of the strings in the sequence is relevant. The prefix structure of the strings is relevant as well: common prefixes are sought in strings to extract interesting features from the sequence. Moreover, space-efficiency is highly desirable as it translates directly into higher performance, since more data can fit in fast memory.

We introduce and study the problem of compressed indexed sequence of strings, representing indexed sequences of strings in nearly-optimal compressed space, both in the static and dynamic settings, while preserving provably good performance for the supported operations.

We present a new data structure for this problem, the Wavelet Trie, which combines the classical Patricia Trie with the Wavelet Tree, a succinct data structure for storing a compressed sequence. The resulting Wavelet Trie smoothly adapts to a sequence of strings that changes over time. It improves on the state-of-the-art compressed data structures by supporting a dynamic alphabet (i.e. the set of distinct strings) and prefix queries, both crucial requirements in the aforementioned applications, and on traditional indexes by reducing space occupancy to close to the entropy of the sequence.

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Michail TAlepis E(2023)Design of Real-Time Multiplayer Word Game for the Android Platform Using Firebase and Fuzzy Logic2023 14th International Conference on Information, Intelligence, Systems & Applications (IISA)10.1109/IISA59645.2023.10345901(1-8)Online publication date: 10-Jul-2023
https://doi.org/10.1109/IISA59645.2023.10345901
Marchet CBoucher CPuglisi SMedvedev PSalson MChikhi R(2020) Data structures based on k -mers for querying large collections of sequencing data sets Genome Research10.1101/gr.260604.11931:1(1-12)Online publication date: 16-Dec-2020
https://doi.org/10.1101/gr.260604.119
Gonzalez NArroyuelo D(2019)A Compact Rank/Select Data Structure for the Streaming Model2019 38th International Conference of the Chilean Computer Science Society (SCCC)10.1109/SCCC49216.2019.8966418(1-7)Online publication date: Nov-2019
https://doi.org/10.1109/SCCC49216.2019.8966418
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Index Terms

The wavelet trie: maintaining an indexed sequence of strings in compressed space
1. Information systems
  1. Data management systems
    1. Data structures
      1. Data layout
        Data compression
  2. Information storage systems
    1. Record storage systems
      1. Directory structures
        B-trees
2. Mathematics of computing
  1. Discrete mathematics
    1. Graph theory
      1. Trees

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cover image ACM Conferences

PODS '12: Proceedings of the 31st ACM SIGMOD-SIGACT-SIGAI symposium on Principles of Database Systems

May 2012

332 pages

ISBN:9781450312486

DOI:10.1145/2213556

Editor:
Markus Krötzsch
University of Oxford, UK
,
General Chair:
Maurizio Lenzerini
University of Rome La Sapienza, Italy
,
Program Chair:
Michael Benedikt
University of Oxford, UK

Copyright © 2012 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGMOD: ACM Special Interest Group on Management of Data

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 21 May 2012

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SIGMOD/PODS '12

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SIGMOD

SIGMOD/PODS '12: International Conference on Management of Data

May 21 - 23, 2012

Arizona, Scottsdale, USA

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PODS '12 Paper Acceptance Rate 26 of 101 submissions, 26%;

Overall Acceptance Rate 642 of 2,707 submissions, 24%

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Cited By

Michail TAlepis E(2023)Design of Real-Time Multiplayer Word Game for the Android Platform Using Firebase and Fuzzy Logic2023 14th International Conference on Information, Intelligence, Systems & Applications (IISA)10.1109/IISA59645.2023.10345901(1-8)Online publication date: 10-Jul-2023
https://doi.org/10.1109/IISA59645.2023.10345901
Marchet CBoucher CPuglisi SMedvedev PSalson MChikhi R(2020) Data structures based on k -mers for querying large collections of sequencing data sets Genome Research10.1101/gr.260604.11931:1(1-12)Online publication date: 16-Dec-2020
https://doi.org/10.1101/gr.260604.119
Gonzalez NArroyuelo D(2019)A Compact Rank/Select Data Structure for the Streaming Model2019 38th International Conference of the Chilean Computer Science Society (SCCC)10.1109/SCCC49216.2019.8966418(1-7)Online publication date: Nov-2019
https://doi.org/10.1109/SCCC49216.2019.8966418
Peng XWang QSun XGong CWang Y(2019)Succinct Representations in Collaborative Filtering: A Case Study using Wavelet Tree on 1,000 Cores2019 20th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)10.1109/PDCAT46702.2019.00083(427-432)Online publication date: Dec-2019
https://doi.org/10.1109/PDCAT46702.2019.00083
Kraska TBeutel AChi EDean JPolyzotis NDas GJermaine CBernstein P(2018)The Case for Learned Index StructuresProceedings of the 2018 International Conference on Management of Data10.1145/3183713.3196909(489-504)Online publication date: 27-May-2018
https://dl.acm.org/doi/10.1145/3183713.3196909
Mustafa HSchilken IKarasikov MEickhoff CRätsch GKahles A(2018)Dynamic compression schemes for graph coloringBioinformatics10.1093/bioinformatics/bty63235:3(407-414)Online publication date: 18-Jul-2018
https://doi.org/10.1093/bioinformatics/bty632
Navarro G(2016)SequencesCompact Data Structures10.1017/CBO9781316588284.007(120-166)Online publication date: 5-Sep-2016
https://doi.org/10.1017/CBO9781316588284.007
Klein SShapira D(2016)Random access to Fibonacci encoded filesDiscrete Applied Mathematics10.1016/j.dam.2015.11.003212:C(115-128)Online publication date: 30-Oct-2016
https://dl.acm.org/doi/10.1016/j.dam.2015.11.003
Babenko MGawrychowski PKociumaka TStarikovskaya TIndyk P(2015)Wavelet trees meet suffix treesProceedings of the twenty-sixth annual ACM-SIAM symposium on Discrete algorithms10.5555/2722129.2722168(572-591)Online publication date: 4-Jan-2015
https://dl.acm.org/doi/10.5555/2722129.2722168
Crochemore MGrossi RKärkkäinen JLandau G(2015)Computing the Burrows-Wheeler transform in place and in small spaceJournal of Discrete Algorithms10.1016/j.jda.2015.01.00432:C(44-52)Online publication date: 1-May-2015
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