3 Search Results for "Takasu, Atsuhiro"

Document
DOI: 10.4230/LIPIcs.CPM.2026.10
R-Enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies

Authors: Kotaro Kimura and Tomohiro I

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
A repeat is a substring that occurs at least twice in a string, and is called a maximal repeat if it cannot be extended outwards without reducing its frequency. Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string T of length n in O(r) words of compressed working space, where r ≤ n is the number of runs in the Burrows-Wheeler transform (BWT) of T. Given the run-length encoded BWT (RLBWT) of T, r-enum runs in O(n log log_w (n/r)) time in addition to the time linear to the number of output strings, where w = Θ(log n) is the word size. In this paper, we first improve the O(n log log_w (n/r)) term to O(n). We next extend r-enum to compute other context-sensitive repeats such as near-supermaximal repeats (NSMRs) and supermaximal repeats, as well as the context diversity for every maximal repeat in the same complexities. Furthermore, we study net occurrences: An occurrence of a repeat is called a net occurrence if it is not covered by another repeat, and the net frequency of a repeat is the number of its net occurrences. With this terminology, an NSMR is a repeat with a positive net frequency. Given the RLBWT of T, we show how to compute the set 𝒮^{nsmr} of all NSMRs in T together with their net frequency/occurrences in O(n) time and O(r) space. We also show that an O(r)-space data structure can be built from the RLBWT to compute the net frequency/occurrences of any pattern in optimal time. The data structure is built in O(r) space and in O(n) time with high probability or deterministic O(n + |𝒮^{nsmr}| log log min(σ, |𝒮^{nsmr}|)) time, where σ ≤ r is the alphabet size of T. To achieve this, we prove that the total number of net occurrences is less than 2r. With the duality between net occurrences and minimal unique substrings (MUSs), we get a new upper bound 2r of the number of MUSs in T, which may be of independent interest.
Cite as

Kotaro Kimura and Tomohiro I. R-Enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kimura_et_al:LIPIcs.CPM.2026.10,
  author =	{Kimura, Kotaro and I, Tomohiro},
  title =	{{R-Enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.10},
  URN =		{urn:nbn:de:0030-drops-259361},
  doi =		{10.4230/LIPIcs.CPM.2026.10},
  annote =	{Keywords: Supermaximal repeats, Largest maximal repeats, Net frequencies, Run-length Burrows-Wheeler transform, Compressed data mining}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.94
Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime

Authors: Tomasz Kociumaka and Ali Shahali

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet Σ. It is defined as the minimum number of node edits - insertions, deletions, and relabelings - required to transform one tree into the other. The weighted variant assigns costs ≥ 1 to edits (based on node labels), minimizing total cost rather than edit count. The unweighted tree edit distance between two trees of total size n can be computed in 𝒪(n^{2.6857}) time; in contrast, determining the weighted tree edit distance is fine-grained equivalent to the All-Pairs Shortest Paths (APSP) problem and requires n³/2^Ω(√{log n}) time [Nogler, Polak, Saha, Vassilevska Williams, Xu, Ye; STOC'25]. These impractical super-quadratic times for large, similar trees motivate the bounded version, parameterizing runtime by the distance k to enable faster algorithms for k ≪ n. Prior algorithms for bounded unweighted edit distance achieve 𝒪(nk²log n) [Akmal & Jin; ICALP’21] and 𝒪(n + k⁷log k) [Das, Gilbert, Hajiaghayi, Kociumaka, Saha; STOC'23]. For weighted, only 𝒪(n + k^{15}) is known [Das, Gilbert, Hajiaghayi, Kociumaka, Saha; STOC'23]. We present an 𝒪(n + k⁶ log k)-time algorithm for bounded tree edit distance in both weighted/unweighted settings. First, we devise a simpler weighted 𝒪(nk² log n)-time algorithm. Next, we exploit periodic structures in input trees via an optimized universal kernel: modifying prior 𝒪(n)-time 𝒪(k⁵)-size kernels to generate such structured instances, enabling efficient analysis.
Cite as

Tomasz Kociumaka and Ali Shahali. Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 94:1-94:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kociumaka_et_al:LIPIcs.ESA.2025.94,
  author =	{Kociumaka, Tomasz and Shahali, Ali},
  title =	{{Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{94:1--94:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.94},
  URN =		{urn:nbn:de:0030-drops-245634},
  doi =		{10.4230/LIPIcs.ESA.2025.94},
  annote =	{Keywords: tree edit distance, edit distance, kernelization, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2018.27
New and Improved Algorithms for Unordered Tree Inclusion

Authors: Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, and Takeyuki Tamura

Published in: LIPIcs, Volume 123, 29th International Symposium on Algorithms and Computation (ISAAC 2018)

Abstract
The tree inclusion problem is, given two node-labeled trees P and T (the "pattern tree" and the "text tree"), to locate every minimal subtree in T (if any) that can be obtained by applying a sequence of node insertion operations to P. Although the ordered tree inclusion problem is solvable in polynomial time, the unordered tree inclusion problem is NP-hard. The currently fastest algorithm for the latter is from 1995 and runs in O(poly(m,n) * 2^{2d}) = O^*(2^{2d}) time, where m and n are the sizes of the pattern and text trees, respectively, and d is the maximum outdegree of the pattern tree. Here, we develop a new algorithm that improves the exponent 2d to d by considering a particular type of ancestor-descendant relationships and applying dynamic programming, thus reducing the time complexity to O^*(2^d). We then study restricted variants of the unordered tree inclusion problem where the number of occurrences of different node labels and/or the input trees' heights are bounded. We show that although the problem remains NP-hard in many such cases, it can be solved in polynomial time for c = 2 and in O^*(1.8^d) time for c = 3 if the leaves of P are distinctly labeled and each label occurs at most c times in T. We also present a randomized O^*(1.883^d)-time algorithm for the case that the heights of P and T are one and two, respectively.
Cite as

Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, and Takeyuki Tamura. New and Improved Algorithms for Unordered Tree Inclusion. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 27:1-27:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{akutsu_et_al:LIPIcs.ISAAC.2018.27,
  author =	{Akutsu, Tatsuya and Jansson, Jesper and Li, Ruiming and Takasu, Atsuhiro and Tamura, Takeyuki},
  title =	{{New and Improved Algorithms for Unordered Tree Inclusion}},
  booktitle =	{29th International Symposium on Algorithms and Computation (ISAAC 2018)},
  pages =	{27:1--27:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-094-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{123},
  editor =	{Hsu, Wen-Lian and Lee, Der-Tsai and Liao, Chung-Shou},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2018.27},
  URN =		{urn:nbn:de:0030-drops-99752},
  doi =		{10.4230/LIPIcs.ISAAC.2018.27},
  annote =	{Keywords: parameterized algorithms, tree inclusion, unordered trees, dynamic programming}
}
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