Fast parameterized pattern matching algorithms based on data compression

2013 Fiscal Year Final Research Report

• Project/Area Number: 23700022
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Fundamental theory of informatics
• Research Institution: Kyushu University
• Principal Investigator: INENAGA Shunsuke 九州大学, システム情報科学研究科(研究院, 准教授 (60448404)
• Project Period (FY): 2011 – 2013
• Keywords: アルゴリズム / 文字列処理 / データ圧縮

Research Abstract

A sequence of characters or symbols is called a string. Many digital data can be regarded as a string. In order to process and utilize large-scale data, we proposed efficient string processing algorithms that are both fast and memory efficient. In particular, we developed efficient algorithms that work on strings given as straight-line programs (SLPs). We achieved fast and memory efficient solutions by an approach called compressed string processing, where given compressed data is not explicitly decompressed. The results of our work have been published in internal journals/proceedings, and presented in international/domestic conferences.

Research Products

• [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: Proc. the 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014) Pages: 675-686
  • DOI: 10.4230/LIPIcs.STACS.2014.675
  • Peer Reviewed
• [Journal Article] Shortest Unique Substrings Queries in Optimal Time (2014)
  • Author(s): Kazuya Tsuruta, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: Proc. the 40th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2014), Lecture Notes in Computer Science Volume: 8327 Pages: 503-513
  • DOI: 10.1007/978-3-319-04298-5_44
  • Peer Reviewed
• [Journal Article] Inferring Strings from Suffix Trees and Links on a Binary Alphabet (2014)
  • Author(s): Tomohiro I, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: Discrete Applied Mathematics Volume: 163(3) Pages: 316-325
  • DOI: 10.1016/j.dam.2013.02.033
  • Peer Reviewed
• [Journal Article] Faster Lyndon Factorization Algorithms for SLP and LZ78 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), Lecture Notes in Computer Science Volume: 8214 Pages: 174-185
  • DOI: 10.1007/978-3-319-02432-5_21
  • 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 2013 (PSC 2013) Pages: 107-118
  • URL: http://www.stringology.org/event/2013/p10.html
  • 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, Ayumi Shinohara
  • Journal Title: In Proc. the 38th International Symposium on Mathematical Foundations of Computer Science (MFCS 2013), Lecture Notes in Computer Science Volume: 8087 Pages: 571-582
  • DOI: 10.1007/978-3-642-40313-2_51
  • 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), Lecture Notes in Computer Science Volume: 7982 Pages: 319-330
  • DOI: 10.1007/978-3-642-39274-0_28
  • Peer Reviewed
• [Journal Article] Converting SLP to LZ78 in almost linear time (2013)
  • Author(s): Hideo Bannai, Pawel Gawrychowski, Shunsuke Inenaga, and Masayuki Takeda
  • Journal Title: In Proc. 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013), Lecture Notes in Computer Science Volume: 7922 Pages: 38-49
  • DOI: 10.1007/978-3-642-38905-4_6
  • 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. 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013), Lecture Notes in Computer Science Volume: 7922 Pages: 153-164
  • DOI: 10.1007/978-3-642-38905-4_16
  • 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
  • DOI: 10.1016/j.tcs.2012.01.047
  • Peer Reviewed
• [Journal Article] Computing convolution on grammar-compressed text (2013)
  • Author(s): Toshiya Tanaka, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: In Proc. Data Compression Conference 2013 (DCC 2013), (IEEE Computer Society Press) Pages: 451-460
  • DOI: 10.1109/DCC.2013.53
  • Peer Reviewed
• [Journal Article] From Run Length Encoding to LZ78 and Back Again (2013)
  • Author(s): Yuya Tamakoshi, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: In Proc. Data Compression Conference 2013 (DCC 2013), (IEEE Computer Society Press) Pages: 143-152
  • DOI: 10.1109/DCC.2013.22
  • Peer Reviewed
• [Journal Article] Permuted Pattern Matching on Multi-Track Strings (2013)
  • Author(s): Takashi Katsura, Kazuyuki Narisawa, Ayumi Shinohara, Hideo Bannai, and Shunsuke Inenaga
  • Journal Title: In Proc. The 39th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2013), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7741 Pages: 280-291
  • DOI: 10.1007/978-3-642-35843-2_25
  • Peer Reviewed
• [Journal Article] Fast q-gram mining on SLP compressed strings (2013)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: Journal of Discrete Algorithms Volume: 18 Pages: 89-99
  • DOI: 10.1016/j.jda.2012.07.006
  • 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, and Moshe Lewenstein
  • Journal Title: Information Processing Letters Volume: 122(9) 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, and Masayuki Takeda
  • Journal Title: In Proc. the 19th Symposium on String Processing and Information Retrieval (SPIRE 2012), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7608 Pages: 360-371
  • DOI: 10.1007/978-3-642-34109-0_38
  • Peer Reviewed
• [Journal Article] Efficient LZ78 Factorization of Grammar Compressed Text (2012)
  • Author(s): Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Journal Title: In Proc. the 19th Symposium on String Processing and Information Retrieval (SPIRE 2012), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7608 Pages: 86-98
  • DOI: 10.1007/978-3-642-34109-0_10
  • Peer Reviewed
• [Journal Article] Speeding-up q-gram mining on grammar-based compressed texts (2012)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Journal Title: In Proc. the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7354 Pages: 220-231
  • DOI: 10.1007/978-3-642-31265-6_18
  • Peer Reviewed
• [Journal Article] Finding Characteristic Substrings from Compressed Texts (2012)
  • Author(s): Shunsuke Inenaga and Hideo Bannai
  • Journal Title: International Journal of Foundations of Computer Science Volume: 23(2) Pages: 261-280
  • DOI: 10.1142/S0129054112400126
  • Peer Reviewed
• [Journal Article] Computing q-gram Non-overlapping Frequencies on SLP Compressed Texts (2012)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Journal Title: In Proc. the 38th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2012), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7147 Pages: 301-312
  • DOI: 10.1007/978-3-642-27660-6_25
  • Peer Reviewed
• [Journal Article] Verifying and Enumerating Parameterized Border Arrays (2011)
  • Author(s): Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: Theoretical Computer Science Volume: 412(50) Pages: 6959-6981
  • DOI: 10.1016/j.tcs.2011.09.008
  • Peer Reviewed
• [Journal Article] Fast q-gram Mining on SLP Compressed Strings (2011)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Journal Title: In Proc. the 18th Symposium on String Processing and Information Retrieval (SPIRE 2011), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 7024 Pages: 278-289
  • DOI: 10.1007/978-3-642-24583-1_27
  • Peer Reviewed
• [Journal Article] Computing Longest Common Substring/Subsequence of Non-linear Texts (2011)
  • Author(s): Kouji Shimohira, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: In Proc. The Prague Stringology Conference 2011 (PSC 2011), (Czech Technical University) Pages: 197-208
  • URL: http://www.stringology.org/event/2011/p17.html
  • Peer Reviewed
• [Journal Article] Inferring Strings from Suffix Trees and Links on a Binary Alphabet (2011)
  • Author(s): Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Journal Title: In Proc. The Prague Stringology Conference 2011 (PSC 2011), (Czech Technical University) Pages: 121-131
  • URL: http://www.stringology.org/event/2011/p11.html
  • Peer Reviewed
• [Journal Article] Faster Subsequence and Don't-Care Pattern Matching on Compressed Texts (2011)
  • Author(s): Takanori Yamamoto, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: In Proc. the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 6661 Pages: 309-322
  • DOI: 10.1007/978-3-642-21458-5_27
  • Peer Reviewed
• [Journal Article] Palindrome Pattern Matching (2011)
  • Author(s): Tomohiro I, Shunsuke Inenaga and Masayuki Takeda
  • Journal Title: In Proc. the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), Lecture Notes in Computer Science, (Springer-Verlag) Volume: 6661 Pages: 232-245
  • DOI: 10.1007/978-3-642-21458-5_21
  • Peer Reviewed
• [Journal Article] Finding Missing Patterns (2011)
  • Author(s): Stanislav Angelov, Shunsuke Inenaga, Teemu Kivioja, and Veli Makinen
  • Journal Title: Journal of Discrete Algorithms Volume: 9(2) Pages: 153-165
  • DOI: 10.1016/j.jda.2010.08.005
  • Peer Reviewed
• [Presentation] Faster Compact On-Line Lempel-Ziv Factorization (2014)
  • Author(s): Jun'ichi Yamamoto, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 31st Symposium on Theoretical Aspects of Computer Science (STACS 2014)
  • Place of Presentation: Lyon, France
  • Year and Date: 20140305-08
• [Presentation] Shortest Unique Substrings Queries in Optimal Time (2014)
  • Author(s): Kazuya Tsuruta, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: 40th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2014)
  • Place of Presentation: High Tatras, Slovakia
  • Year and Date: 20140125-30
• [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: 20th Symposium on String Processing and Information Retrieval (SPIRE 2013)
  • Place of Presentation: Jerusalem, Israel
  • Year and Date: 20131007-09
• [Presentation] Computing Reversed Lempel-Ziv Factorization Online (2013)
  • Author(s): Shiho Sugimoto, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: Prague Stringology Conference 2013 (PSC 2013)
  • Place of Presentation: Prague, Czech Republic
  • Year and Date: 20130902-03
• [Presentation] Detecting Regularities on Grammar-compressed Strings (2013)
  • Author(s): Tomohiro I, Wataru Matsubara, Kouji Shimohira, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda, Kazuyuki Narisawa, Ayumi Shinohara
  • Organizer: 38th International Symposium on Mathematical Foundations of Computer Science (MFCS 2013)
  • Place of Presentation: Klosterneuburg, Austria
  • Year and Date: 20130826-30
• [Presentation] Compressed Automata for Dictionary Matching (2013)
  • Author(s): Tomohiro I, Takaaki Nishimoto, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: 18th International Conference on Implementation and Application of Automata (CIAA 2013)
  • Place of Presentation: Halifax, Canada
  • Year and Date: 20130716-19
• [Presentation] Converting SLP to LZ78 in almost linear time (2013)
  • Author(s): Hideo Bannai, Pawel Gawrychowski, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013)
  • Place of Presentation: Bad Herrenalb, Germany
  • Year and Date: 20130617-19
• [Presentation] Efficient Lyndon factorization of grammar compressed text (2013)
  • Author(s): Tomohiro I, Yuto Nakashima, Shunsuke Inenaga, Hideo Bannai and Masayuki Takeda
  • Organizer: 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013)
  • Place of Presentation: Bad Herrenalb, Germany
  • Year and Date: 20130617-19
• [Presentation] Computing convolution on grammar-compressed text (2013)
  • Author(s): Toshiya Tanaka, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: Data Compression Conference 2013 (DCC 2013)
  • Place of Presentation: Snowbird, USA
  • Year and Date: 20130320-22
• [Presentation] From Run Length Encoding to LZ78 and Back Again (2013)
  • Author(s): Yuya Tamakoshi, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: Data Compression Conference 2013 (DCC 2013)
  • Place of Presentation: Snowbird, USA
  • Year and Date: 20130320-22
• [Presentation] Permuted Pattern Matching on Multi-Track Strings (2013)
  • Author(s): Takashi Katsura, Kazuyuki Narisawa, Ayumi Shinohara, Hideo Bannai, and Shunsuke Inenaga
  • Organizer: 39th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2013)
  • Place of Presentation: Spindleruv Mlyn, Czech Republic
  • Year and Date: 20130126-31
• [Presentation] The Position Heap of a Trie (2012)
  • Author(s): Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: 19th Symposium on String Processing and Information Retrieval (SPIRE 2012)
  • Place of Presentation: Cartagena, Colombia
  • Year and Date: 20121021-25
• [Presentation] Efficient LZ78 Factorization of Grammar Compressed Text (2012)
  • Author(s): Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 19th Symposium on String Processing and Information Retrieval (SPIRE 2012)
  • Place of Presentation: Cartagena, Colombia
  • Year and Date: 20121021-25
• [Presentation] Speeding-up q-gram mining on grammar-based compressed texts (2012)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012)
  • Place of Presentation: Helsinki, Finland
  • Year and Date: 20120703-05
• [Presentation] Computing q-gram Non-overlapping Frequencies on SLP Compressed Texts (2012)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 38th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2012)
  • Place of Presentation: Spindleruv Mlyn, Czech Republic
  • Year and Date: 20120121-27
• [Presentation] Fast q-gram Mining on SLP Compressed Strings (2011)
  • Author(s): Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, and Masayuki Takeda
  • Organizer: 18th Symposium on String Processing and Information Retrieval (SPIRE 2011)
  • Place of Presentation: Pisa, Italy
  • Year and Date: 20111017-21
• [Presentation] Computing Longest Common Substring/Subsequence of Non-linear Texts (2011)
  • Author(s): Kouji Shimohira, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: Prague Stringology Conference 2011 (PSC 2011)
  • Place of Presentation: Prague, Czech Republic
  • Year and Date: 20110829-31
• [Presentation] Inferring Strings from Suffix Trees and Links on a Binary Alphabet (2011)
  • Author(s): Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda
  • Organizer: Prague Stringology Conference 2011 (PSC 2011)
  • Place of Presentation: Czech Republic
  • Year and Date: 20110829-31
• [Presentation] Faster Subsequence and Don't-Care Pattern Matching on Compressed Texts (2011)
  • Author(s): Takanori Yamamoto, Hideo Bannai, Shunsuke Inenaga and Masayuki Takeda
  • Organizer: 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011)
  • Place of Presentation: Palermo, Italy
  • Year and Date: 20110627-29
• [Presentation] Palindrome Pattern Matching (2011)
  • Author(s): Tomohiro I, Shunsuke Inenaga and Masayuki Takeda
  • Organizer: 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011)
  • Place of Presentation: Palermo, Italy
  • Year and Date: 20110627-19