4 Search Results for "Shibuya, Tetsuo"

Document
Invited Talk
DOI: 10.4230/LIPIcs.CPM.2022.3
Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk)

Authors: Sharma V. Thankachan

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
In the past two decades, we have witnessed the design of various compact data structures for pattern matching over an indexed text [Navarro, 2016]. Popular indexes like the FM-index [Paolo Ferragina and Giovanni Manzini, 2005], compressed suffix arrays/trees [Roberto Grossi and Jeffrey Scott Vitter, 2005; Kunihiko Sadakane, 2007], the recent r-index [Travis Gagie et al., 2020; Takaaki Nishimoto and Yasuo Tabei, 2021], etc., capture the key functionalities of classic suffix arrays/trees [Udi Manber and Eugene W. Myers, 1993; Peter Weiner, 1973] in compact space. Mostly, they rely on the Burrows-Wheeler Transform (BWT) and its associated operations [Burrows and Wheeler, 1994]. However, compactly encoding some advanced suffix tree (ST) variants, like parameterized ST [Brenda S. Baker, 1993; S. Rao Kosaraju, 1995; Juan Mendivelso et al., 2020], order-isomorphic/preserving ST [Maxime Crochemore et al., 2016], two-dimensional ST [Raffaele Giancarlo, 1995; Dong Kyue Kim et al., 1998], etc. [Sung Gwan Park et al., 2019; Tetsuo Shibuya, 2000]- collectively known as suffix trees with missing suffix links [Richard Cole and Ramesh Hariharan, 2003], has been challenging. The previous techniques are not easily extendable because these variants do not hold some structural properties of the standard ST that enable compression. However, some limited progress has been made in these directions recently [Arnab Ganguly et al., 2017; Travis Gagie et al., 2017; Gianni Decaroli et al., 2017; Dhrumil Patel and Rahul Shah, 2021; Arnab Ganguly et al., 2021; Sung{-}Hwan Kim and Hwan{-}Gue Cho, 2021; Sung{-}Hwan Kim and Hwan{-}Gue Cho, 2021; Arnab Ganguly et al., 2017; Arnab Ganguly et al., 2022; Arnab Ganguly et al., 2021]. This talk will briefly survey them and highlight some interesting open problems.
Cite as

Sharma V. Thankachan. Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk). In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 3:1-3:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{thankachan:LIPIcs.CPM.2022.3,
  author =	{Thankachan, Sharma V.},
  title =	{{Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc.}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{3:1--3:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.3},
  URN =		{urn:nbn:de:0030-drops-161300},
  doi =		{10.4230/LIPIcs.CPM.2022.3},
  annote =	{Keywords: Text Indexing, Suffix Trees, String Matching}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.12
Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition

Authors: Kazushi Kitaya and Tetsuo Shibuya

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
A set of k-mers is used in many bioinformatics tasks, and much work has been done on methods to efficiently represent or compress a single set of k-mers. However, methods for compressing multiple k-mer sets have been less studied in spite of their obvious benefits for researchers and genome-related database maintainers. This paper proposes an algorithm to compress multiple k-mer sets, which works by iteratively splitting SPSS (spectrum-preserving string sets). In experiments with 3292 k-mer sets constructed from E. coli whole-genome sequencing data and 2555 k-mer sets constructed from human RNA-Seq data, the proposed algorithm could reduce the compressed file sizes by 34.7% and 13.2% respectively compared to one of the state-of-the-art colored de Bruijn graph representations. Also, our method used less memory than the colored de Bruijn graph method. This paper also introduces various methods to make the compression algorithm efficient in terms of time and memory, one of which is a parallelizable small-weight SPSS construction algorithm.
Cite as

Kazushi Kitaya and Tetsuo Shibuya. Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 12:1-12:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{kitaya_et_al:LIPIcs.WABI.2021.12,
  author =	{Kitaya, Kazushi and Shibuya, Tetsuo},
  title =	{{Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{12:1--12:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.12},
  URN =		{urn:nbn:de:0030-drops-143659},
  doi =		{10.4230/LIPIcs.WABI.2021.12},
  annote =	{Keywords: sequencing data, k-mer, de Bruijn graph, compression, colored de Bruijn graph}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2020.65
Wear Leveling Revisited

Authors: Taku Onodera and Tetsuo Shibuya

Published in: LIPIcs, Volume 181, 31st International Symposium on Algorithms and Computation (ISAAC 2020)

Abstract
Wear leveling - a technology designed to balance the write counts among memory cells regardless of the requested accesses - is vital in prolonging the lifetime of certain computer memory devices, especially the type of next-generation non-volatile memory, known as phase change memory (PCM). Although researchers have been working extensively on wear leveling, almost all existing studies mainly focus on the practical aspects and lack rigorous mathematical analyses. The lack of theory is particularly problematic for security-critical applications. We address this issue by revisiting wear leveling from a theoretical perspective. First, we completely determine the problem parameter regime for which Security Refresh - one of the most well-known existing wear leveling schemes for PCM - works effectively by providing a positive result and a matching negative result. In particular, Security Refresh is not competitive for the practically relevant regime of large-scale memory. Then, we propose a novel scheme that achieves better lifetime, time/space overhead, and wear-free space for the relevant regime not covered by Security Refresh. Unlike existing studies, we give rigorous theoretical lifetime analyses, which is necessary to assess and control the security risk.
Cite as

Taku Onodera and Tetsuo Shibuya. Wear Leveling Revisited. In 31st International Symposium on Algorithms and Computation (ISAAC 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 181, pp. 65:1-65:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{onodera_et_al:LIPIcs.ISAAC.2020.65,
  author =	{Onodera, Taku and Shibuya, Tetsuo},
  title =	{{Wear Leveling Revisited}},
  booktitle =	{31st International Symposium on Algorithms and Computation (ISAAC 2020)},
  pages =	{65:1--65:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-173-3},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{181},
  editor =	{Cao, Yixin and Cheng, Siu-Wing and Li, Minming},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2020.65},
  URN =		{urn:nbn:de:0030-drops-134092},
  doi =		{10.4230/LIPIcs.ISAAC.2020.65},
  annote =	{Keywords: Wear leveling, Randomized algorithm, Non-volatile memory}
}
Document
DOI: 10.4230/LIPIcs.STACS.2018.52
Succinct Oblivious RAM

Authors: Taku Onodera and Tetsuo Shibuya

Published in: LIPIcs, Volume 96, 35th Symposium on Theoretical Aspects of Computer Science (STACS 2018)

Abstract
As online storage services become increasingly common, it is important that users' private information is protected from database access pattern analyses. Oblivious RAM (ORAM) is a cryptographic primitive that enables users to perform arbitrary database accesses without revealing any information about the access pattern to the server. Previous ORAM studies focused mostly on reducing the access overhead. Consequently, the access overhead of the state-of-the-art ORAM constructions are almost at practical levels in certain application scenarios such as secure processors. However, we assume that the server space usage could become a new important issue in the coming big-data era. To enable large-scale computation in security-aware settings, it is necessary to rethink the ORAM server space cost using big-data standards. In this paper, we introduce "succinctness" as a theoretically tractable and practically relevant criterion of the ORAM server space efficiency in the big-data era. We, then, propose two succinct ORAM constructions that also exhibit state-of-the-art performance in terms of the bandwidth blowup and the user space. We also give non-asymptotic analyses and simulation results which indicate that the proposed ORAM constructions are practically effective.
Cite as

Taku Onodera and Tetsuo Shibuya. Succinct Oblivious RAM. In 35th Symposium on Theoretical Aspects of Computer Science (STACS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 96, pp. 52:1-52:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{onodera_et_al:LIPIcs.STACS.2018.52,
  author =	{Onodera, Taku and Shibuya, Tetsuo},
  title =	{{Succinct Oblivious RAM}},
  booktitle =	{35th Symposium on Theoretical Aspects of Computer Science (STACS 2018)},
  pages =	{52:1--52:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-062-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{96},
  editor =	{Niedermeier, Rolf and Vall\'{e}e, Brigitte},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2018.52},
  URN =		{urn:nbn:de:0030-drops-85014},
  doi =		{10.4230/LIPIcs.STACS.2018.52},
  annote =	{Keywords: Oblivious RAM, Succinct data structure, Balls-into-bins}
}
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