圧縮文字列上の高速パターン列挙に関する基盤技術開発

• Project/Area Number: 12J06417
• Research Category: Grant-in-Aid for JSPS Fellows
• Allocation Type: Single-year Grants
• Section: 国内
• Research Field: Fundamental theory of informatics
• Research Institution: Kyushu University
• Principal Investigator: 井 智弘 九州大学, 大学院・システム情報科学研究院, 特別研究員(PD)
• Project Period (FY): 2012 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥2,000,000 (Direct Cost: ¥2,000,000); Fiscal Year 2013: ¥1,000,000 (Direct Cost: ¥1,000,000); Fiscal Year 2012: ¥1,000,000 (Direct Cost: ¥1,000,000)
• Keywords: 圧縮文字列処理 / 文字列中の規則性発見 / 文字列パターン列挙

Research Abstract

本年度は, 本研究テーマの一つの集大成として, 圧縮された文字列データから規則性をもった部分文字列を高速に計算・列挙する手法を開発した. 繰り返し構造や回文構造といった文字列の規則性の発見は文字列処理の基礎であり, また, ゲノムデータの解析などに応用出来る. 圧縮文字列処理では展開文字列長に比例する計算資源を用いないことを目標としており, そのため圧縮文字列を全て展開せずに処理しなければいけないという難しさがあるが, 解の列挙においてはさらに出力の仕方も問題になる. 単純に出力すると出力サイズに比例する時間を避ける事ができず, 今回の出力である繰り返し構造や回文構造の数は展開文字列長に比例するためである. 本手法では, 圧縮された文字列を展開する事無く処理を行い, かつ, 出力の圧縮表現を計算することでこの問題を回避した. これにより, ゲノムデータなどの大規模文字列データも, それが良く圧縮されているならば省領域かつ高速に規則性を発見することが出来る. この結果は38th International Symposium on Mathematical Foundations of Computer Science (MFCS2013)に採択され発表を行った.
また, 圧縮された文字列上の組み合わせ的性質を探る研究として圧縮文字列とLyndon文字列との関連性を探った. Lyndon文字列およびそれを基にしたLyndon分解は代数学と深く関連しており古くから知られているが, 近年はアルゴリズムへの応用も注目されている. 申請者らは24th Annual Symposium on Combinatorial Pattern Matching (CPM2013)と20th Symposium on String Processing and Information Retrieval (SPIRE 2013)において圧縮文字列からLyndon分解を効率的に求めるアルゴリズムを開発した. その過程において, Lyndon分解の項数が文法圧縮サイズの下界になっているという興味深い知見を得ている.

Strategy for Future Research Activity

(抄録なし)

Research Products

• [Journal Article] Faster Sparse Suffix Sorting (2014)
  • Author(s): Tomohiro I, Juha Kärkainen and Dominik Kempa
  • Journal Title: In Proc. the 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014) Pages: 386-396
  • Peer Reviewed
• [Journal Article] Faster Compact On-Line Lempel-Ziv Factorization (2014)
  • Author(s): Jun-ichi Yamamoto, Tomohiro I, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: In Proc. the 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014) Pages: 675-686
  • Peer Reviewed
• [Journal Article] Computing palindromic factorizations and palindromic covers on-line (2014)
  • Author(s): Tomohiro I, Shiho Sugimoto, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: In proc. the 25th Annual Symposium on Combinatorial Pattern Matching (CPM 2014) Volume: (To appear)
  • Peer Reviewed
• [Journal Article] Palindrome pattern matching (2013)
  • Author(s): Tomohiro I, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: Theoretical Computer Science Volume: 483 Pages: 162-170
  • Peer Reviewed
• [Journal Article] Inferring Strings from Suffix Trees and Links on a Binary Alphabet (2013)
  • Author(s): Tomohiro I, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: Discrete Applied Mathematics Volume: 163(3) Pages: 316-325
  • Peer Reviewed
• [Journal Article] Efficient Lyndon factorization of grammar compressed text (2013)
  • Author(s): Tomohiro I, Yuto Nakashima, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: In Proc. the 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013) Volume: LNCS 7922 Pages: 153-164
  • Peer Reviewed
• [Journal Article] Compressed Automata for Dictionary Matching (2013)
  • Author(s): Tomohiro I, Takaaki Nishimoto, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: In Proc. the 18th International Conference on Implementation and Application of Automata (CIAA 2013) Volume: LNCS 7982 Pages: 319-330
  • Peer Reviewed
• [Journal Article] Detecting regularities on grammar-compressed strings (2013)
  • Author(s): Tomohiro I, Wataru Matsubara, Kouji Shimohira, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda, Kazuyuki Narisawa and Ayumi Shinohara
  • Journal Title: In Proc. the 38th International Symposium on Mathematical Foundations of Computer Science (MFCS 2013) Volume: LNCS 8087 Pages: 571-582
  • Peer Reviewed
• [Journal Article] Computing Reversed Lempel-Ziv Factorization Online (2013)
  • Author(s): Shiho Sugimoto, Tomohiro I, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: In Proc. The Prague Stringology Conference (PSC 2013) Pages: 107-118
  • Peer Reviewed
• [Journal Article] Faster Lyndon factorization algorithms for SLP and 1278 compressed text (2013)
  • Author(s): Tomohiro I, Yuto Nakashima, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Journal Title: In Proc. the 20th Symposium on String Processing and Information Retrieval (SPIRE 2013) Volume: LNCS 8214 Pages: 174-185
  • Peer Reviewed
• [Journal Article] From Run Length Encoding to LZ78 and Back Again (2013)
  • Author(s): Yuya Tamakoshi, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Journal Title: Proceedings of the Data Compression Conference 20 Pages: 143-152
  • Peer Reviewed
• [Journal Article] Computing convolution on grammar-compressed text (2013)
  • Author(s): Toshiya Tanaka, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Journal Title: Proceedings of the Data Compression Conference 20 Pages: 451-460
  • Peer Reviewed
• [Journal Article] Inferring Strings from Suffix Trees and Links on a Binary Alphabet (2013)
  • Author(s): Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Journal Title: Journal of Discrete Applied Mathematics Volume: (in press) Pages: 316-325
  • DOI: 10.1016/j.dam.2013.02.033
  • Peer Reviewed
• [Journal Article] General Algorithms for Mining Closed Flexible Patterns under Various Equivalence Relations (2012)
  • Author(s): Tomohiro I, Yuki Enokuna, Hideo Bannai, Masayuki Takeda
  • Journal Title: In Proceedings of the European Conference on Machine Learning and Principles and Practice of knowledge Discovery in Databases Volume: LNCS 7524 Pages: 435-450
  • DOI: 10.1007/978-3-642-33486-3_28
  • ISBN: 9783642334856, 9783642334863
  • Peer Reviewed
• [Journal Article] An efficient algorithm to test square-freeness of strings compressed by straight-line programs (2012)
  • Author(s): Hideo Bannai, Travis Gagie, Tomohiro I, Shunsuke Inenaga, Gad M. Landau, Moshe Lewenstein
  • Journal Title: Journal of Information Processing Letters Volume: 112(19) Issue: 19 Pages: 711-714
  • DOI: 10.1016/j.ipl.2012.06.017
  • Peer Reviewed
• [Journal Article] The position heap of a trie (2012)
  • Author(s): Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Journal Title: In Proceedings of the 19th Symposium on String Processing and Information Retrieval Volume: LNCS 7608 Pages: 360-371
  • DOI: 10.1007/978-3-642-34109-0_38
  • ISBN: 9783642341083, 9783642341090
  • Peer Reviewed
• [Presentation] Faster Compact On-Line Lempel-Ziv Factorization (2014)
  • Author(s): Jun-ichi Yamamoto, Tomiro I, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Organizer: the 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014)
  • Place of Presentation: Lyon, France
  • Year and Date: 2014-03-08
• [Presentation] Faster Sparse Suffix Sorting (2014)
  • Author(s): Tomohiro I, Juha Kärkkäinen and Dominik Kempa
  • Organizer: the 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014)
  • Place of Presentation: Lyon, France
  • Year and Date: 2014-03-06
• [Presentation] 回文による文字列の分解と被覆 (2014)
  • Author(s): 杉本志穂, 井智弘, 稲永俊介, 坂内英夫, 竹田正幸
  • Organizer: 冬のLAシンポジウム2013
  • Place of Presentation: 日本, 京都
  • Year and Date: 2014-01-30
• [Presentation] LZ78圧縮されたテキストに対するLyndon分解アルゴリズ (2014)
  • Author(s): 井智弘, 中島祐人, 稲永俊介, 坂内英夫, 竹田正幸
  • Organizer: 冬のLAシンポジウム2013
  • Place of Presentation: 日本, 京都
  • Year and Date: 2014-01-30
• [Presentation] 省スペースオンラインLZ分解 (2014)
  • Author(s): 山本淳一, 井智弘, 坂内英夫, 稲永俊介, 竹田正幸
  • Organizer: 冬のLAシンポジウム2013
  • Place of Presentation: 日本, 京都
  • Year and Date: 2014-01-29
• [Presentation] Faster Compact On-Line Lempel-Ziv Factorization (2013)
  • Author(s): Tomohiro I
  • Organizer: the 8th Workshop on Compression, Text, and Algorithms (WCTA 2013)
  • Place of Presentation: Jerusalem, Israel
  • Year and Date: 2013-10-10
• [Presentation] Faster Lyndon factorization algorithms for SLP and LZ78 compressed text (2013)
  • Author(s): Tomohiro I, Yuto Nakashima, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: the 20th Symposium on String Processing and Information Retrieval (SPIRE 2013)
  • Place of Presentation: Jerusalem, Israel
  • Year and Date: 2013-10-08
• [Presentation] Computing Reversed Lempel-Ziv Factorization Online (2013)
  • Author(s): Shiho Sugimoto, Tomohiro I, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: the Prague Stringology Conference (PSC 2013)
  • Place of Presentation: Prague, Czech
  • Year and Date: 2013-09-03
• [Presentation] Detecting regularities on grammar-compressed strings (2013)
  • Author(s): Tomohiro I, Wataru Matsubara, Kouji Shimohira, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda, Kazuyuki Narisawa and Ayumi Shinohara
  • Organizer: the 38th International Symposium on Mathematic al Foundations of Computer Science (MFCS 2013)
  • Place of Presentation: Klosterneuburg, Austria
  • Year and Date: 2013-08-27
• [Presentation] Lyndon分解の逆問題 (2013)
  • Author(s): 中島祐人, 岡部駿志, 井智弘, 稲永俊介, 坂内英夫, 竹田正幸
  • Organizer: 夏のLAシンポジウム2013
  • Place of Presentation: 日本, 福岡
  • Year and Date: 2013-07-17
• [Presentation] Compressed Automata for Dictionary Matching (2013)
  • Author(s): Tomohiro I, Takaaki Nishimoto, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: the 18th International Conference on Implementa tion and Application of Automata (CIAA 2013)
  • Place of Presentation: Halifax, Nova Scotia, Canada
  • Year and Date: 2013-07-16
• [Presentation] Efficient Lyndon factorization of grammar compressed text (2013)
  • Author(s): Tomohiro I, Yuto Nakashima, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: the 24th Annual Symposium on Combinatorial Pattern Matchine (CPM 2013)
  • Place of Presentation: Bad Herrenalb, Germany
  • Year and Date: 2013-06-19
• [Presentation] Computing convolution on grammar-compressed text (2013)
  • Author(s): Toshiya Tanaka, Tomohiro I. Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Organizer: Data Compression Conference 2013 (DCC 2013)
  • Place of Presentation: アメリカ・, スノーバード
  • Year and Date: 2013-03-22
• [Presentation] From Run Length Encoding to LZ78 and Back Again (2013)
  • Author(s): Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Organizer: Data Compression Conference 2013 (DCC 2013)
  • Place of Presentation: アメリカ・, スノーバード
  • Year and Date: 2013-03-20
• [Presentation] The position heap of a trie (2012)
  • Author(s): Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda
  • Organizer: Synposiun on String Processing and Information Retrieval (SPIRE 2012)
  • Place of Presentation: コロンビア, カルタヘナ
  • Year and Date: 2012-10-23
• [Presentation] General Algorithms for Mining Closed Flexible Patterns under Various Equivalence Relations (2012)
  • Author(s): Tomohiro I, Yuki Enokuma, Hideo Bannai, Masayuki Takeda
  • Organizer: the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD 2012)
  • Place of Presentation: イギリス, ブリストル
  • Year and Date: 2012-09-25
• [Presentation] 直線的プログラムで圧縮された文字列の非反復性検証アルゴリズム (2012)
  • Author(s): 井智弘, 坂内英夫, 稲永俊介
  • Organizer: 夏のLAシンポジウム2012
  • Place of Presentation: 京都, 天橋立
  • Year and Date: 2012-07-19
• [Presentation] 木構造で表現された複数文字列に対するポジションヒープ (2012)
  • Author(s): 中島祐人, 井智弘, 稲永俊介, 坂内英夫, 竹田正幸
  • Organizer: 夏のLAシンポジウム2012
  • Place of Presentation: 京都, 天橋立
  • Year and Date: 2012-07-17
• [Presentation] General Algorithms for Mining Closed Flexible Patterns under Various Equivalence Relations (2012)
  • Author(s): 井智弘, 荏隈勇樹, 坂内英夫, 竹田正幸
  • Organizer: ERATO湊離散構造処理系プロジェクト「2012年度 初夏のワークショップ」
  • Place of Presentation: 北海道, 札幌
  • Year and Date: 2012-06-23