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Documents authored by Shibuya, Tetsuo

Document
DOI: 10.4230/LIPIcs.SWAT.2024.5
Recognition and Proper Coloring of Unit Segment Intersection Graphs

Authors: Robert D. Barish and Tetsuo Shibuya

Published in: LIPIcs, Volume 294, 19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024)

Abstract
In this work, we concern ourselves with the fine-grained complexity of recognition and proper coloring problems on highly restricted classes of geometric intersection graphs of "thin" objects (i.e., objects with unbounded aspect ratios). As a point of motivation, we remark that there has been significant interest in finding algorithmic lower bounds for classic decision and optimization problems on these types of graphs, as they appear to escape the net of known planar or geometric separator theorems for "fat" objects (i.e., objects with bounded aspect ratios). In particular, letting n be the order of a geometric intersection graph, and assuming a geometric ply bound, per what is known as the "square root phenomenon", these separator theorems often imply the existence of 𝒪(2^√n) algorithms for problems ranging from finding proper colorings to finding Hamiltonian cycles. However, in contrast, it is known for instance that no 2^o(n) time algorithm can exist under the Exponential Time Hypothesis (ETH) for proper 6-coloring intersection graphs of line segments embedded in the plane (Biró et. al.; J. Comput. Geom. 9(2); pp. 47-80; 2018). We begin by establishing algorithmic lower bounds for proper k-coloring and recognition problems of intersection graphs of line segments embedded in the plane under the most stringent constraints possible that allow either problem to be non-trivial. In particular, we consider the class UNIT-PURE-k-DIR of unit segment geometric intersection graphs, in which segments are constrained to lie in at most k directions in the plane, and no two parallel segments are permitted to intersect. Here, under the ETH, we show for every k ≥ 3 that no 2^o(√{n/k}) time algorithm can exist for either recognizing or proper k-coloring UNIT-PURE-k-DIR graphs of order n. In addition, for every k ≥ 4, we establish the same algorithmic lower bound under the ETH for the problem of proper (k-1)-coloring UNIT-PURE-k-DIR graphs when provided a list of segment coordinates specified using 𝒪(n ⋅ k) bits witnessing graph class membership. As a consequence of our approach, we are also able to show that the problem of properly 3-coloring an arbitrary graph on m edges can be reduced in 𝒪(m²) time to the problem of properly (k-1)-coloring a UNIT-PURE-k-DIR graph. Finally, we consider a slightly less constrained class of geometric intersection graphs of lines (of unbounded length) in which line-line intersections must occur on any one of (r = 3) parallel planes in ℝ³. In this context, for every k ≥ 3, we show that no 2^o(n/k) time algorithm can exist for proper k-coloring these graphs unless the ETH is false.
Cite as

Robert D. Barish and Tetsuo Shibuya. Recognition and Proper Coloring of Unit Segment Intersection Graphs. In 19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 294, pp. 5:1-5:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{barish_et_al:LIPIcs.SWAT.2024.5,
  author =	{Barish, Robert D. and Shibuya, Tetsuo},
  title =	{{Recognition and Proper Coloring of Unit Segment Intersection Graphs}},
  booktitle =	{19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024)},
  pages =	{5:1--5:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-318-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{294},
  editor =	{Bodlaender, Hans L.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2024.5},
  URN =		{urn:nbn:de:0030-drops-200452},
  doi =		{10.4230/LIPIcs.SWAT.2024.5},
  annote =	{Keywords: graph class recognition, proper coloring, geometric intersection graph, segment intersection graph, fine-grained complexity, Exponential Time Hypothesis}
}
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.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.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.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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