67 Search Results for "Bannai, Hideo"

Volume

LIPIcs, Volume 223

33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

CPM 2022, June 27-29, 2022, Prague, Czech Republic

Editors: Hideo Bannai and Jan Holub

Document
DOI: 10.4230/LIPIcs.ESA.2024.18
Height-Bounded Lempel-Ziv Encodings

Authors: Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, and Simon J. Puglisi

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
We introduce height-bounded LZ encodings (LZHB), a new family of compressed representations that are variants of Lempel-Ziv parsings with a focus on bounding the worst-case access time to arbitrary positions in the text directly via the compressed representation. An LZ-like encoding is a partitioning of the string into phrases of length 1 which can be encoded literally, or phrases of length at least 2 which have a previous occurrence in the string and can be encoded by its position and length. An LZ-like encoding induces an implicit referencing forest on the set of positions of the string. An LZHB encoding is an LZ-like encoding where the height of the implicit referencing forest is bounded. An LZHB encoding with height constraint h allows access to an arbitrary position of the underlying text using O(h) predecessor queries. While computing the optimal (i.e., smallest) LZHB encoding efficiently seems to be difficult [Cicalese & Ugazio 2024, arXiv, to appear at DLT 2024], we give the first linear time algorithm for strings over a constant size alphabet that computes the greedy LZHB encoding, i.e., the string is processed from beginning to end, and the longest prefix of the remaining string that can satisfy the height constraint is taken as the next phrase. Our algorithms significantly improve both theoretically and practically, the very recently and independently proposed algorithms by Lipták et al. (CPM 2024). We also analyze the size of height bounded LZ encodings in the context of repetitiveness measures, and show that there exists a constant c such that the size ẑ_{HB(clog n)} of the optimal LZHB encoding whose height is bounded by clog n for any string of length n is O(ĝ_{rl}), where ĝ_{rl} is the size of the smallest run-length grammar. Furthermore, we show that there exists a family of strings such that ẑ_{HB(clog n)} = o(ĝ_{rl}), thus making ẑ_{HB(clog n)} one of the smallest known repetitiveness measures for which O(polylog n) time access is possible using linear (O(ẑ_{HB(clog n)})) space.
Cite as

Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, and Simon J. Puglisi. Height-Bounded Lempel-Ziv Encodings. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 18:1-18:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bannai_et_al:LIPIcs.ESA.2024.18,
  author =	{Bannai, Hideo and Funakoshi, Mitsuru and Hendrian, Diptarama and Matsuda, Myuji and Puglisi, Simon J.},
  title =	{{Height-Bounded Lempel-Ziv Encodings}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{18:1--18:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.18},
  URN =		{urn:nbn:de:0030-drops-210899},
  doi =		{10.4230/LIPIcs.ESA.2024.18},
  annote =	{Keywords: Lempel-Ziv parsing, data compression}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.75
Edit and Alphabet-Ordering Sensitivity of Lex-Parse

Authors: Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
We investigate the compression sensitivity [Akagi et al., 2023] of lex-parse [Navarro et al., 2021] for two operations: (1) single character edit and (2) modification of the alphabet ordering, and give tight upper and lower bounds for both operations (i.e., we show Θ(log n) bounds for strings of length n). For both lower bounds, we use the family of Fibonacci words. For the bounds on edit operations, our analysis makes heavy use of properties of the Lyndon factorization of Fibonacci words to characterize the structure of lex-parse.
Cite as

Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai. Edit and Alphabet-Ordering Sensitivity of Lex-Parse. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 75:1-75:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{nakashima_et_al:LIPIcs.MFCS.2024.75,
  author =	{Nakashima, Yuto and K\"{o}ppl, Dominik and Funakoshi, Mitsuru and Inenaga, Shunsuke and Bannai, Hideo},
  title =	{{Edit and Alphabet-Ordering Sensitivity of Lex-Parse}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{75:1--75:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.75},
  URN =		{urn:nbn:de:0030-drops-206314},
  doi =		{10.4230/LIPIcs.MFCS.2024.75},
  annote =	{Keywords: Compression sensitivity, Lex-parse, Fibonacci words}
}
Document
DOI: 10.4230/LIPIcs.CPM.2024.3
Maintaining the Size of LZ77 on Semi-Dynamic Strings

Authors: Hideo Bannai, Panagiotis Charalampopoulos, and Jakub Radoszewski

Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)

Abstract
We consider the problem of maintaining the size of the LZ77 factorization of a string S of length at most n under the following operations: (a) appending a given letter to S and (b) deleting the first letter of S. Our main result is an algorithm for this problem with amortized update time Õ(√n). As a corollary, we obtain an Õ(n√n)-time algorithm for computing the most LZ77-compressible rotation of a length-n string - a naive approach for this problem would compute the LZ77 factorization of each possible rotation and would thus take quadratic time in the worst case. We also show an Ω(√n) lower bound for the additive sensitivity of LZ77 with respect to the rotation operation. Our algorithm employs dynamic trees to maintain the longest-previous-factor array information and depends on periodicity-based arguments that bound the number of the required updates and enable their efficient computation.
Cite as

Hideo Bannai, Panagiotis Charalampopoulos, and Jakub Radoszewski. Maintaining the Size of LZ77 on Semi-Dynamic Strings. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 3:1-3:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bannai_et_al:LIPIcs.CPM.2024.3,
  author =	{Bannai, Hideo and Charalampopoulos, Panagiotis and Radoszewski, Jakub},
  title =	{{Maintaining the Size of LZ77 on Semi-Dynamic Strings}},
  booktitle =	{35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)},
  pages =	{3:1--3:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-326-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{296},
  editor =	{Inenaga, Shunsuke and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.3},
  URN =		{urn:nbn:de:0030-drops-201134},
  doi =		{10.4230/LIPIcs.CPM.2024.3},
  annote =	{Keywords: Lempel-Ziv, compression, LZ77, semi-dynamic algorithm, cyclic rotation}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.14
Lyndon Arrays in Sublinear Time

Authors: Hideo Bannai and Jonas Ellert

Published in: LIPIcs, Volume 274, 31st Annual European Symposium on Algorithms (ESA 2023)

Abstract
A Lyndon word is a string that is lexicographically smaller than all of its non-trivial suffixes. For example, airbus is a Lyndon word, but amtrak is not a Lyndon word due to its suffix ak. The Lyndon array stores the length of the longest Lyndon prefix of each suffix of a string. For a length-n string over a general ordered alphabet, the array can be computed in O(n) time (Bille et al., ICALP 2020). However, on a word-RAM of word-width w ≥ log₂ n, linear time is not optimal if the string is over integer alphabet {0, … , σ} with σ ≪ n. In this case, the string can be stored in O(n log σ) bits (or O(n / log_σ n) words) of memory, and reading it takes only O(n / log_σ n) time. We show that O(n / log_σ n) time and words of space suffice to compute the succinct 2n-bit version of the Lyndon array. The time is optimal for w = O(log n). The algorithm uses precomputed lookup tables to perform significant parts of the computation in constant time. This is possible due to properties of periodic substrings, which we carefully analyze to achieve the desired result. We envision that the algorithm has applications in the computation of runs (maximal periodic substrings), where the Lyndon array plays a central role in both theoretically and practically fast algorithms.
Cite as

Hideo Bannai and Jonas Ellert. Lyndon Arrays in Sublinear Time. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 14:1-14:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bannai_et_al:LIPIcs.ESA.2023.14,
  author =	{Bannai, Hideo and Ellert, Jonas},
  title =	{{Lyndon Arrays in Sublinear Time}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{14:1--14:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2023.14},
  URN =		{urn:nbn:de:0030-drops-186670},
  doi =		{10.4230/LIPIcs.ESA.2023.14},
  annote =	{Keywords: Lyndon forest, Lyndon table, Lyndon array, sublinear time algorithms, word RAM algorithms, word packing, tabulation, lookup tables, periodicity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.13
Acceleration of FM-Index Queries Through Prefix-Free Parsing

Authors: Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [Ferragina and Fischer, 2007] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. Last year, Deng et al. [Deng et al., 2022] proposed parsing genomic data by induced suffix sorting, and showed the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing - which takes parameters that let us tune the average length of the phrases - instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38. And was consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it is very clear that our method accelerates the performance of count over all state-of-the-art methods with a minor increase in the memory.
Cite as

Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie. Acceleration of FM-Index Queries Through Prefix-Free Parsing. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{hong_et_al:LIPIcs.WABI.2023.13,
  author =	{Hong, Aaron and Oliva, Marco and K\"{o}ppl, Dominik and Bannai, Hideo and Boucher, Christina and Gagie, Travis},
  title =	{{Acceleration of FM-Index Queries Through Prefix-Free Parsing}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.13},
  URN =		{urn:nbn:de:0030-drops-186390},
  doi =		{10.4230/LIPIcs.WABI.2023.13},
  annote =	{Keywords: FM-index, pangenomics, scalability, word-based indexing, random access}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.3
Optimal LZ-End Parsing Is Hard

Authors: Hideo Bannai, Mitsuru Funakoshi, Kazuhiro Kurita, Yuto Nakashima, Kazuhisa Seto, and Takeaki Uno

Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

Abstract
LZ-End is a variant of the well-known Lempel-Ziv parsing family such that each phrase of the parsing has a previous occurrence, with the additional constraint that the previous occurrence must end at the end of a previous phrase. LZ-End was initially proposed as a greedy parsing, where each phrase is determined greedily from left to right, as the longest factor that satisfies the above constraint [Kreft & Navarro, 2010]. In this work, we consider an optimal LZ-End parsing that has the minimum number of phrases in such parsings. We show that a decision version of computing the optimal LZ-End parsing is NP-complete by showing a reduction from the vertex cover problem. Moreover, we give a MAX-SAT formulation for the optimal LZ-End parsing adapting an approach for computing various NP-hard repetitiveness measures recently presented by [Bannai et al., 2022]. We also consider the approximation ratio of the size of greedy LZ-End parsing to the size of the optimal LZ-End parsing, and give a lower bound of the ratio which asymptotically approaches 2.
Cite as

Hideo Bannai, Mitsuru Funakoshi, Kazuhiro Kurita, Yuto Nakashima, Kazuhisa Seto, and Takeaki Uno. Optimal LZ-End Parsing Is Hard. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 3:1-3:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bannai_et_al:LIPIcs.CPM.2023.3,
  author =	{Bannai, Hideo and Funakoshi, Mitsuru and Kurita, Kazuhiro and Nakashima, Yuto and Seto, Kazuhisa and Uno, Takeaki},
  title =	{{Optimal LZ-End Parsing Is Hard}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{3:1--3:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.3},
  URN =		{urn:nbn:de:0030-drops-179571},
  doi =		{10.4230/LIPIcs.CPM.2023.3},
  annote =	{Keywords: Data Compression, LZ-End, Repetitiveness measures}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.12
Computing NP-Hard Repetitiveness Measures via MAX-SAT

Authors: Hideo Bannai, Keisuke Goto, Masakazu Ishihata, Shunsuke Kanda, Dominik Köppl, and Takaaki Nishimoto

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract
Repetitiveness measures reveal profound characteristics of datasets, and give rise to compressed data structures and algorithms working in compressed space. Alas, the computation of some of these measures is NP-hard, and straight-forward computation is infeasible for datasets of even small sizes. Three such measures are the smallest size of a string attractor, the smallest size of a bidirectional macro scheme, and the smallest size of a straight-line program. While a vast variety of implementations for heuristically computing approximations exist, exact computation of these measures has received little to no attention. In this paper, we present MAX-SAT formulations that provide the first non-trivial implementations for exact computation of smallest string attractors, smallest bidirectional macro schemes, and smallest straight-line programs. Computational experiments show that our implementations work for texts of length up to a few hundred for straight-line programs and bidirectional macro schemes, and texts even over a million for string attractors.
Cite as

Hideo Bannai, Keisuke Goto, Masakazu Ishihata, Shunsuke Kanda, Dominik Köppl, and Takaaki Nishimoto. Computing NP-Hard Repetitiveness Measures via MAX-SAT. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bannai_et_al:LIPIcs.ESA.2022.12,
  author =	{Bannai, Hideo and Goto, Keisuke and Ishihata, Masakazu and Kanda, Shunsuke and K\"{o}ppl, Dominik and Nishimoto, Takaaki},
  title =	{{Computing NP-Hard Repetitiveness Measures via MAX-SAT}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.12},
  URN =		{urn:nbn:de:0030-drops-169505},
  doi =		{10.4230/LIPIcs.ESA.2022.12},
  annote =	{Keywords: repetitiveness measures, string attractor, bidirectional macro scheme}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.CPM.2022
LIPIcs, Volume 223, CPM 2022, Complete Volume

Authors: Hideo Bannai and Jan Holub

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

Abstract
LIPIcs, Volume 223, CPM 2022, Complete Volume
Cite as

33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 1-470, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Proceedings{bannai_et_al:LIPIcs.CPM.2022,
  title =	{{LIPIcs, Volume 223, CPM 2022, Complete Volume}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{1--470},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022},
  URN =		{urn:nbn:de:0030-drops-161265},
  doi =		{10.4230/LIPIcs.CPM.2022},
  annote =	{Keywords: LIPIcs, Volume 223, CPM 2022, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.CPM.2022.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Hideo Bannai and Jan Holub

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

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 0:i-0:xviii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bannai_et_al:LIPIcs.CPM.2022.0,
  author =	{Bannai, Hideo and Holub, Jan},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{0:i--0:xviii},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.0},
  URN =		{urn:nbn:de:0030-drops-161271},
  doi =		{10.4230/LIPIcs.CPM.2022.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.CPM.2022.1
Invitation to Combinatorial Reconfiguration (Invited Talk)

Authors: Takehiro Ito

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

Abstract
Combinatorial reconfiguration studies reachability and related questions over the solution space formed by feasible solutions of an instance of a combinatorial search problem. For example, as the solution space for the satisfiability problem, we may consider the subgraph of the hypercube induced by the satisfying truth assignments of a given CNF formula. Then, the reachability problem for satisfiability is the problem of asking whether two given satisfying truth assignments are contained in the same connected component of the solution space. The study of reconfiguration problems has motivation from a variety of fields such as puzzles, statistical physics, and industry. In this decade, reconfiguration problems have been studied intensively for many central combinatorial search problems, such as satisfiability, independent set and coloring, from the algorithmic viewpoints. Many reconfiguration problems are PSPACE-complete in general, although several efficiently solvable cases have been obtained. In this talk, I will give a broad introduction of combinatorial reconfiguration.
Cite as

Takehiro Ito. Invitation to Combinatorial Reconfiguration (Invited Talk). In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, p. 1:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{ito:LIPIcs.CPM.2022.1,
  author =	{Ito, Takehiro},
  title =	{{Invitation to Combinatorial Reconfiguration}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{1:1--1:1},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.1},
  URN =		{urn:nbn:de:0030-drops-161281},
  doi =		{10.4230/LIPIcs.CPM.2022.1},
  annote =	{Keywords: Combinatorial reconfiguration, graph algorithm}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.CPM.2022.2
Using Automata and a Decision Procedure to Prove Results in Pattern Matching (Invited Talk)

Authors: Jeffrey Shallit

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

Abstract
The first-order theory of automatic sequences with addition is decidable, and this means that one can often prove combinatorial properties of these sequences "automatically", using the free software Walnut written by Hamoon Mousavi. In this talk I will explain how this is done, using as an example the measure of minimize size string attractor, introduced by Kempa and Prezza in 2018. Using the logic-based approach, we can also prove more general properties of string attractors for automatic sequences. This is joint work with Luke Schaeffer.
Cite as

Jeffrey Shallit. Using Automata and a Decision Procedure to Prove Results in Pattern Matching (Invited Talk). In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 2:1-2:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{shallit:LIPIcs.CPM.2022.2,
  author =	{Shallit, Jeffrey},
  title =	{{Using Automata and a Decision Procedure to Prove Results in Pattern Matching}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{2:1--2:3},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.2},
  URN =		{urn:nbn:de:0030-drops-161297},
  doi =		{10.4230/LIPIcs.CPM.2022.2},
  annote =	{Keywords: finite automata, decision procedure, automatic sequence, Thue-Morse sequence, Fibonacci word, string attractor}
}
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.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.CPM.2022.4
The Fine-Grained Complexity of Episode Matching

Authors: Philip Bille, Inge Li Gørtz, Shay Mozes, Teresa Anna Steiner, and Oren Weimann

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

Abstract
Given two strings S and P, the Episode Matching problem is to find the shortest substring of S that contains P as a subsequence. The best known upper bound for this problem is Õ(nm) by Das et al. (1997), where n,m are the lengths of S and P, respectively. Although the problem is well studied and has many applications in data mining, this bound has never been improved. In this paper we show why this is the case by proving that no O((nm)^{1-ε}) algorithm (even for binary strings) exists, unless the Strong Exponential Time Hypothesis (SETH) is false. We then consider the indexing version of the problem, where S is preprocessed into a data structure for answering episode matching queries P. We show that for any τ, there is a data structure using O(n+(n/(τ)) ^k) space that answers episode matching queries for any P of length k in O(k⋅ τ ⋅ log log n) time. We complement this upper bound with an almost matching lower bound, showing that any data structure that answers episode matching queries for patterns of length k in time O(n^δ), must use Ω(n^{k-kδ-o(1)}) space, unless the Strong k-Set Disjointness Conjecture is false. Finally, for the special case of k = 2, we present a faster construction of the data structure using fast min-plus multiplication of bounded integer matrices.
Cite as

Philip Bille, Inge Li Gørtz, Shay Mozes, Teresa Anna Steiner, and Oren Weimann. The Fine-Grained Complexity of Episode Matching. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bille_et_al:LIPIcs.CPM.2022.4,
  author =	{Bille, Philip and G{\o}rtz, Inge Li and Mozes, Shay and Steiner, Teresa Anna and Weimann, Oren},
  title =	{{The Fine-Grained Complexity of Episode Matching}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{4:1--4:12},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.4},
  URN =		{urn:nbn:de:0030-drops-161312},
  doi =		{10.4230/LIPIcs.CPM.2022.4},
  annote =	{Keywords: Pattern matching, fine-grained complexity, longest common subsequence}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.5
Mechanical Proving with Walnut for Squares and Cubes in Partial Words

Authors: John Machacek

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

Abstract
Walnut is a software that can prove theorems in combinatorics on words about automatic sequences. We are able to apply this software to both prove new results as well as reprove some old results on avoiding squares and cubes in partial words. We also define the notion of an antisquare in a partial word and begin the study of binary partial words which contain only a fixed number of distinct squares and antisquares.
Cite as

John Machacek. Mechanical Proving with Walnut for Squares and Cubes in Partial Words. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 5:1-5:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{machacek:LIPIcs.CPM.2022.5,
  author =	{Machacek, John},
  title =	{{Mechanical Proving with Walnut for Squares and Cubes in Partial Words}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{5:1--5:11},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.5},
  URN =		{urn:nbn:de:0030-drops-161320},
  doi =		{10.4230/LIPIcs.CPM.2022.5},
  annote =	{Keywords: Partial words, squares, antisquares, cubes, Walnut}
}
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