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Practical Dynamic Entropy-Compressed Bitvectors with Applications

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Experimental Algorithms (SEA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9685))

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Abstract

Compressed data structures provide the same functionality as their classical counterparts while using entropy-bounded space. While they have succeeded in a wide range of static structures, which do not undergo updates, they are less mature in the dynamic case, where the theory-versus-practice gap is wider. We implement compressed dynamic bitvectors B using \(|B|H_0(B)+o(|B|)\) or \(|B|H_0(B)(1+o(1))\) bits of space, where \(H_0\) is the zero-order empirical entropy, and supporting queries and updates in \(\mathcal {O}(w)\) time on a w-bit word machine. This is the first implementation that provably achieves compressed space and is also practical, operating within microseconds. Bitvectors are the basis of most compressed data structures; we explore applications to sequences and graphs.

Funded by Basal Funds FB0001 and with Fondecyt Grant 1-140796, Conicyt, Chile.

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Notes

  1. 1.

    Measured with https://github.com/mpetri/mem_monitor.

  2. 2.

    A precise comparison is not possible since their results are not available. We use their plots as a reference.

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Authors and Affiliations

  1. Department of Computer Science, CeBiB — Center of Biotechnology and Bioengineering, University of Chile, Santiago, Chile

    Joshimar Cordova & Gonzalo Navarro

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  1. Joshimar Cordova
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  2. Gonzalo Navarro
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Correspondence to Joshimar Cordova .

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Editors and Affiliations

  1. Amazon.com, Inc., Palo Alto, California, USA

    Andrew V. Goldberg

  2. Russian Academy of Sciences, St. Petersburg, Russia

    Alexander S. Kulikov

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Cordova, J., Navarro, G. (2016). Practical Dynamic Entropy-Compressed Bitvectors with Applications. In: Goldberg, A., Kulikov, A. (eds) Experimental Algorithms. SEA 2016. Lecture Notes in Computer Science(), vol 9685. Springer, Cham. https://doi.org/10.1007/978-3-319-38851-9_8

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  • DOI: https://doi.org/10.1007/978-3-319-38851-9_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38850-2

  • Online ISBN: 978-3-319-38851-9

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