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Development of optimal time-space algorithms on pattern matching problems

Research Project

Project/Area Number 19K20208
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 60010:Theory of informatics-related
Research InstitutionTohoku University

Principal Investigator

HENDRIAN DIPTARAMA  東北大学, 情報科学研究科, 助教 (70823136)

Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2020: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2019: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsパターン照合アルゴリズム / 索引構造 / パラメタ化パターン照合 / 順序保存パターン照合 / 劣線形領域アルゴリズム / アルゴリズム理論 / カバー配列 / 有向無閉路文字列グラフ / 順列パターン照合 / アルゴリズム / 文字列処理 / リアルタイムアルゴリズム
Outline of Research at the Start

パターン照合問題はデータ解析において重要な基本問題である.近似的なパターン照合問題やデータの特徴に合わせたパターン照合問題を含めた,異なる応用に合わせて様々な拡張がなされている.データ解析を効率的に行うために高速なアルゴリズムだけではなく,小型ロボットや宇宙探査機といった容量が非常に限られたシステムにおいて,省メモリなアルゴリズムも非常に重要である.そこで本研究は,様々なパターン照合問題に対して最適な時間・領域のアルゴリズムを開発する.本研究で開発したアルゴリズムはDNAのような膨大なデータの解析や小型計算機が搭載されたロボットや探索機によるデータ解析,幅広い分野で応用できると期待している.

Outline of Final Research Achievements

The pattern matching problem is a task to find occurrences of pattern strings in text strings. Pattern matching algorithms are fundamental in computer science since pattern matching algorithms have broad applications such as data searching and data mining. In this study, we consider the exact pattern matching problem and its extension, such as parameterized pattern matching and order-preserving pattern matching problems. We proposed various linear time pattern matching algorithms and indexing structures for the exact pattern matching problem and its extension. Moreover, we designed a sub-linear extra-space algorithm for the parameterized pattern matching problem. Our algorithm is based on the Galil&Sefeiras sub-linear extra-space algorithm for exact pattern matching.

Academic Significance and Societal Importance of the Research Achievements

本研究はパラメタ化パターン照合問題に対して,初めて劣線形領域アルゴリズムを提案した.劣線形領域アルゴリズムは情報科学理論において学術的に非常に重要である.また,パターン照合アルゴリズムは文字列検索を使ったアプリケーションに応用されるとともに,バイオインフォマティクスや人工知能等,様々な分野の研究に用いられ,非常に重要な技術である.そのため,本研究の成果は社会のおける情報科学技術の発展およびこれからの研究の発展に貢献できたと考えられる,

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (16 results)

All 2023 2022 2020 2019

All Journal Article (15 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 15 results,  Open Access: 8 results) Presentation (1 results) (of which Int'l Joint Research: 1 results)

  • [Journal Article] Inferring Strings from Position Heaps in Linear Time2023

    • Author(s)
      Koshiro Kumagai, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the 17th International Conference and Workshops on Algorithms and Computation

      Volume: 13973 Pages: 115-126

    • DOI

      10.1007/978-3-031-27051-2_11

    • ISBN
      9783031270505, 9783031270512
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Parameterized DAWGs: Efficient constructions and bidirectional pattern searches2022

    • Author(s)
      Katsuhito Nakashima, Noriki Fujisato, Diptarama Hendrian, Yuto Nakashima, Ryo Yoshinaka, Shunsuke Inenaga, Hideo Bannai, Ayumi Shinohara, Masayuki Takeda
    • Journal Title

      Theoretical Computer Science

      Volume: 933 Pages: 21-42

    • DOI

      10.1016/j.tcs.2022.09.008

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computing the Parameterized Burrows-Wheeler Transform Online2022

    • Author(s)
      Daiki Hashimoto and Diptarama Hendrian and Dominik Koeppl and Ryo Yoshinaka and Ayumi Shinohara
    • Journal Title

      Proceedings of SPIRE

      Volume: 13617 Pages: 70-85

    • DOI

      10.1007/978-3-031-20643-6_6

    • ISBN
      9783031206429, 9783031206436
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Parallel Algorithm for Pattern Matching Problems Under Substring Consistent Equivalence Relations2022

    • Author(s)
      Davaajav Jargalsaikhan, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the 33rd Annual Symposium on Combinatorial Pattern Matching

      Volume: 223

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computing Covers Under Substring Consistent Equivalence Relations2020

    • Author(s)
      Natsumi Kikuchi, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the 27th International Symposium on String Processing and Information Retrieval, Lecture Notes in Computer Science

      Volume: 12303 Pages: 131-146

    • DOI

      10.1007/978-3-030-59212-7_10

    • ISBN
      9783030592110, 9783030592127
    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] In-Place Bijective Burrows-Wheeler Transforms2020

    • Author(s)
      Dominik Koppl, Daiki Hashimoto, Diptarama Hendrian, Ayumi Shinohara
    • Journal Title

      Proceedings of the 31st Annual Symposium on Combinatorial Pattern Matching, Leibniz International Proceedings in Informatics

      Volume: 161

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] DAWGs for parameterized matching: online construction and related indexing structures2020

    • Author(s)
      Katsuhito Nakashima, Noriki Fujisato, Diptarama Hendrian, Yuto Nakashima, Ryo Yoshinaka, Shunsuke Inenaga, Hideo Bannai, Ayumi Shinohara, Masayuki Takeda
    • Journal Title

      Proceedings of the 31st Annual Symposium on Combinatorial Pattern Matching, Leibniz International Proceedings in Informatics

      Volume: 161

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fast and linear-time string matching algorithms based on the distances of q-gram occurrences2020

    • Author(s)
      Satoshi Kobayashi, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of 18th Symposium on Experimental Algorithms, Leibniz International Proceedings in Informatics

      Volume: 160

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Generalized Dictionary Matching Under Substring Consistent Equivalence Relations2020

    • Author(s)
      Hendrian Diptarama
    • Journal Title

      Proceedings of the 14th International Conference and Workshop on Algorithms and Computation, Lecture Notes in Computer Science

      Volume: 12049 Pages: 120-132

    • DOI

      10.1007/978-3-030-39881-1_11

    • ISBN
      9783030398804, 9783030398811
    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Parallel Duel-and-Sweep Algorithm for the Order-Preserving Pattern Matching2020

    • Author(s)
      Davaajav Jargalsaikhan, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the 46th International Conference on Current Trends in Theory and Practice of Computer Science, Lecture Notes in Computer Science

      Volume: 12011 Pages: 211-222

    • DOI

      10.1007/978-3-030-38919-2_18

    • ISBN
      9783030389185, 9783030389192
    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] AOBA: An Online Benchmark tool for Algorithms in stringology2020

    • Author(s)
      Ryu Wakimoto, Satoshi Kobayashi, Yuki Igarashi, Davaajav Jargalsaikhan, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the SOFSEM 2020 Student Research Forum, CEUR Workshop Proceedings

      Volume: 2568 Pages: 1-12

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An Extension of Linear-size Suffix Tries for Parameterized Strings2020

    • Author(s)
      Katsuhito Nakashima, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the SOFSEM 2020 Student Research Forum, CEUR Workshop Proceedings

      Volume: 2568 Pages: 97-108

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An improvement of the Franek-Jennings-Smyth pattern matching algorithm2019

    • Author(s)
      Satoshi Kobayashi, Diptarama Hendrian, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Proceedings of the Prague Stringology Conference 2019

      Volume: - Pages: 56-68

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Online Algorithms for Constructing Linear-size Suffix Trie2019

    • Author(s)
      Diptarama Hendrian, Takuya Takagi, Shunsuke Inenaga
    • Journal Title

      Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, Leibniz International Proceedings in Informatics

      Volume: 128

    • DOI

      10.4230/LIPICS.CPM.2019.30

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Permuted Pattern Matching Algorithms on Multi-Track Strings2019

    • Author(s)
      Diptarama Hendrian, Yohei Ueki, Kazuyuki Narisawa, Ryo Yoshinaka, Ayumi Shinohara
    • Journal Title

      Algorithms

      Volume: 12 Issue: 4 Pages: 73-73

    • DOI

      10.3390/a12040073

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] In-Place Bijective Burrows Wheeler Transformations2020

    • Author(s)
      Dominik Koppl, Daiki Hashimoto, Diptarama Hendrian, Ayumi Shinohara
    • Organizer
      Workshop Data Structures in Bioinformatics
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research

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Published: 2019-04-18   Modified: 2024-01-30  

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