40 Search Results for "I, Tomohiro"

Document
DOI: 10.4230/LIPIcs.IPEC.2025.16
Designing Compact ILPs via Fast Witness Verification

Authors: Michał Włodarczyk

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
The standard formalization of preprocessing in parameterized complexity is given by kernelization. In this work, we depart from this paradigm and study a different type of preprocessing for problems without polynomial kernels, still aiming at producing instances that are easily solvable in practice. Specifically, we ask for which parameterized problems an instance (I,k) can be reduced in polynomial time to an integer linear program (ILP) with poly(k) constraints. We show that this property coincides with the parameterized complexity class WK[1], previously studied in the context of Turing kernelization lower bounds. In turn, the class WK[1] enjoys an elegant characterization in terms of witness verification protocols: a yes-instance should admit a witness of size poly(k) that can be verified in time poly(k). By combining known data structures with new ideas, we design such protocols for several problems, such as r-Way Cut, Vertex Multiway Cut, Steiner Tree, and Minimum Common String Partition, thus showing that they can be modeled by compact ILPs. We also present explicit ILP and MILP formulations for Weighted Vertex Cover on graphs with small (unweighted) vertex cover number. We believe that these results will provide a background for a systematic study of ILP-oriented preprocessing procedures for parameterized problems.
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Michał Włodarczyk. Designing Compact ILPs via Fast Witness Verification. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wlodarczyk:LIPIcs.IPEC.2025.16,
  author =	{W{\l}odarczyk, Micha{\l}},
  title =	{{Designing Compact ILPs via Fast Witness Verification}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{16:1--16:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.16},
  URN =		{urn:nbn:de:0030-drops-251481},
  doi =		{10.4230/LIPIcs.IPEC.2025.16},
  annote =	{Keywords: integer programming, kernelization, nondeterminism, multiway cut}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2025.32
The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set

Authors: Mario Grobler and Sebastian Siebertz

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
The 10th iteration of the of the Parameterized Algorithms and Computational Experiments challenge (PACE) 2025 was devoted to engineer algorithms solving the Dominating Set problem as well as the Hitting Set problem. In contrast to the last iterations, these problems are (under standard assumptions) not fixed-parameter tractable (fpt) in general. However, restricting the structure of the input (e.g. to planar graphs or degenerate graphs for Dominating Set, or to set systems with sets of bounded size for Hitting Set) renders these problems fpt. Following the spirit of the last iterations of the PACE challenge, there is an exact track and a heuristic track for each problem; each track coming with a benchmark set of 100 public instances and 100 private instances. Overall, the PACE 2025 had 71 participants from 25 teams, 13 countries, and 3 continents. In this report, we briefly describe the setup of the challenge, the selection of benchmark instances, as well as the ranking of the participating teams. We also briefly outline the approaches used in the submitted solvers.
Cite as

Mario Grobler and Sebastian Siebertz. The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 32:1-32:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grobler_et_al:LIPIcs.IPEC.2025.32,
  author =	{Grobler, Mario and Siebertz, Sebastian},
  title =	{{The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{32:1--32:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.32},
  URN =		{urn:nbn:de:0030-drops-251644},
  doi =		{10.4230/LIPIcs.IPEC.2025.32},
  annote =	{Keywords: PACE 2025 Report, Dominating Set, Hitting Set, Algorithm Engineering, FPT, Heuristics}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.36
Streaming Periodicity with Mismatches, Wildcards, and Edits

Authors: Taha El Ghazi and Tatiana Starikovskaya

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
In this work, we study the problem of detecting periodic trends in strings. While detecting exact periodicity has been studied extensively, real-world data is often noisy, where small deviations or mismatches occur between repetitions. This work focuses on a generalized approach to period detection that efficiently handles noise. Given a string S of length n, the task is to identify integers p such that the prefix and the suffix of S, each of length n-p+1, are similar under a given distance measure. Ergün et al. [APPROX-RANDOM 2017] were the first to study this problem in the streaming model under the Hamming distance. In this work, we combine, in a non-trivial way, the Hamming distance sketch of Clifford et al. [SODA 2019] and the structural description of the k-mismatch occurrences of a pattern in a text by Charalampopoulos et al. [FOCS 2020] to present a more efficient streaming algorithm for period detection under the Hamming distance. As a corollary, we derive a streaming algorithm for detecting periods of strings which may contain wildcards, a special symbol that match any character of the alphabet. Our algorithm is not only more efficient than that of Ergün et al. [TCS 2020], but it also operates without their assumption that the string must be free of wildcards in its final characters. Additionally, we introduce the first two-pass streaming algorithm for computing periods under the edit distance by leveraging and extending the Bhattacharya-Koucký’s grammar decomposition technique [STOC 2023].
Cite as

Taha El Ghazi and Tatiana Starikovskaya. Streaming Periodicity with Mismatches, Wildcards, and Edits. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 36:1-36:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{elghazi_et_al:LIPIcs.ISAAC.2025.36,
  author =	{El Ghazi, Taha and Starikovskaya, Tatiana},
  title =	{{Streaming Periodicity with Mismatches, Wildcards, and Edits}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{36:1--36:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.36},
  URN =		{urn:nbn:de:0030-drops-249446},
  doi =		{10.4230/LIPIcs.ISAAC.2025.36},
  annote =	{Keywords: approximate periods, pattern matching, streaming algorithms}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.5
Graph Coloring Below Guarantees via Co-Triangle Packing

Authors: Shyan Akmal and Tomohiro Koana

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
In the 𝓁-Coloring problem, we are given a graph on n nodes, and tasked with determining if its vertices can be properly colored using 𝓁 colors. In this paper we study below-guarantee graph coloring, which tests whether an n-vertex graph can be properly colored using g-k colors, where g is a trivial upper bound such as n. We introduce an algorithmic framework that builds on a packing of co-triangles K₃ (independent sets of three vertices): the algorithm greedily finds co-triangles and employs a win-win analysis. If many are found, we immediately return yes; otherwise these co-triangles form a small co-triangle modulator, whose deletion makes the graph co-triangle-free. Extending the work of [Gutin et al., SIDMA 2021], who solved 𝓁-Coloring (for any 𝓁) in randomized O^∗(2^k) time when given a K₂-free modulator of size k, we show that this problem can likewise be solved in randomized O^*(2^{k}) time when given a K₃-free modulator of size k. This result in turn yields a randomized O^*(2^{3k/2}) algorithm for (n-k)-Coloring (also known as Dual Coloring), improving the previous O^*(4^k) bound. We then introduce a smaller parameterization, (ω+μ-k)-Coloring, where ω is the clique number and μ is the size of a maximum matching in the complement graph; since ω+μ ≤ n for any graph, this problem is strictly harder. Using the same co-triangle-packing argument, we obtain a randomized O^*(2^{6k}) algorithm, establishing its fixed-parameter tractability for a smaller parameter. Complementing this finding, we show that no fixed-parameter tractable algorithm exists for (ω-k)-Coloring or (μ-k)-Coloring under standard complexity assumptions.
Cite as

Shyan Akmal and Tomohiro Koana. Graph Coloring Below Guarantees via Co-Triangle Packing. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{akmal_et_al:LIPIcs.ISAAC.2025.5,
  author =	{Akmal, Shyan and Koana, Tomohiro},
  title =	{{Graph Coloring Below Guarantees via Co-Triangle Packing}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.5},
  URN =		{urn:nbn:de:0030-drops-249130},
  doi =		{10.4230/LIPIcs.ISAAC.2025.5},
  annote =	{Keywords: coloring, parameterized algorithms, algebraic algorithms, above-guarantee, below-guarantee, subset convolution, determinants}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.9
Small Space Encoding and Recognition of k-Palindromic Prefixes

Authors: Gabriel Bathie, Jonas Ellert, and Tatiana Starikovskaya

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
Palindromes are non-empty strings that read the same forward and backward. We study the problem of recognizing so-called k-palindromic strings, which can be represented as the concatenation of exactly k palindromes. [Rubinchik and Shur, MFCS 2020] showed that the problem is solvable in linear space and time. We present a read-only algorithm that recognizes all k-palindromic prefixes of a string T of length n in O(n ⋅ 6^{k²} ⋅ log^k n) time and O(6^{k²} ⋅ log^k n) space. As a corollary, we also obtain a read-only algorithm for computing the palindromic length of T, i.e., the smallest k such that T is k-palindromic, in O(n ⋅ 6^{k²} ⋅ log^⌈k/2⌉ n) time and O(6^{k²} ⋅ log^⌈k/2⌉ n) space.
Cite as

Gabriel Bathie, Jonas Ellert, and Tatiana Starikovskaya. Small Space Encoding and Recognition of k-Palindromic Prefixes. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bathie_et_al:LIPIcs.ISAAC.2025.9,
  author =	{Bathie, Gabriel and Ellert, Jonas and Starikovskaya, Tatiana},
  title =	{{Small Space Encoding and Recognition of k-Palindromic Prefixes}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{9:1--9:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.9},
  URN =		{urn:nbn:de:0030-drops-249178},
  doi =		{10.4230/LIPIcs.ISAAC.2025.9},
  annote =	{Keywords: palindromic length, read-only algorithms, palindromes}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.8
Fast Computation of k-Runs, Parameterized Squares, and Other Generalised Squares

Authors: Yuto Nakashima, Jakub Radoszewski, and Tomasz Waleń

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

Abstract
A k-mismatch square is a string of the form XY where X and Y are two equal-length strings that have at most k mismatches. Kolpakov and Kucherov [Theor. Comput. Sci., 2003] defined two notions of k-mismatch repeats, called k-repetitions and k-runs, each representing a sequence of consecutive k-mismatch squares of equal length. They proposed algorithms for computing k-repetitions and k-runs working in 𝒪(nklog k+output) time for a string of length n over an integer alphabet, where output is the number of the reported repeats. We show that output = 𝒪(nk log k), both in case of k-repetitions and k-runs, which implies that the complexity of their algorithms is actually 𝒪(nk log k). We apply this result to computing parameterized squares. A parameterized square is a string of the form XY such that X and Y parameterized-match, i.e., there exists a bijection f on the alphabet such that f(X) = Y. Two parameterized squares XY and X'Y' are equivalent if they parameterized match. Recently Hamai et al. [SPIRE 2024] showed that a string of length n over an alphabet of size σ contains less than nσ non-equivalent parameterized squares, improving an earlier bound by Kociumaka et al. [Theor. Comput. Sci., 2016]. We apply our bound for k-mismatch repeats to propose an algorithm that reports all non-equivalent parameterized squares in 𝒪(nσ log σ) time. We also show that the number of non-equivalent parameterized squares can be computed in 𝒪(n log n) time. This last algorithm applies to squares under any substring compatible equivalence relation and also to counting squares that are distinct as strings. In particular, this improves upon the 𝒪(nσ)-time algorithm of Gawrychowski et al. [CPM 2023] for counting order-preserving squares that are distinct as strings if σ = ω(log n).
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Yuto Nakashima, Jakub Radoszewski, and Tomasz Waleń. Fast Computation of k-Runs, Parameterized Squares, and Other Generalised Squares. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nakashima_et_al:LIPIcs.ESA.2025.8,
  author =	{Nakashima, Yuto and Radoszewski, Jakub and Wale\'{n}, Tomasz},
  title =	{{Fast Computation of k-Runs, Parameterized Squares, and Other Generalised Squares}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{8:1--8:18},
  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.2025.8},
  URN =		{urn:nbn:de:0030-drops-244768},
  doi =		{10.4230/LIPIcs.ESA.2025.8},
  annote =	{Keywords: string algorithm, k-mismatch square, parameterized square, order-preserving square, maximum gapped repeat}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.60
Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars

Authors: Jannik Olbrich

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

Abstract
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the entire dataset in main memory. Fortunately, such large datasets are often highly repetitive. It can thus be beneficial to compute the BWT from a compressed representation. We propose an algorithm for computing the BWT via the Lyndon straight-line program, a grammar based on the standard factorization of Lyndon words. Our algorithm can also be used to compute the extended BWT (eBWT) of a multiset of sequences. We empirically evaluate our implementation and find that we can compute the BWT and eBWT of very large datasets faster and/or with less memory than competing methods.
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Jannik Olbrich. Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 60:1-60:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{olbrich:LIPIcs.ESA.2025.60,
  author =	{Olbrich, Jannik},
  title =	{{Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{60:1--60:19},
  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.2025.60},
  URN =		{urn:nbn:de:0030-drops-245286},
  doi =		{10.4230/LIPIcs.ESA.2025.60},
  annote =	{Keywords: Burrows-Wheeler Transform, Grammar compression}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.13
Solving Partial Dominating Set and Related Problems Using Twin-Width

Authors: Jakub Balabán, Daniel Mock, and Peter Rossmanith

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
Partial vertex cover and partial dominating set are two well-investigated optimization problems. While they are W[1]-hard on general graphs, they have been shown to be fixed-parameter tractable on many sparse graph classes, including nowhere-dense classes. In this paper, we demonstrate that these problems are also fixed-parameter tractable with respect to the twin-width of a graph. Indeed, we establish a more general result: every graph property that can be expressed by a logical formula of the form ϕ≡∃ x₁⋯ ∃ x_k ∑_{α ∈ I} #y ψ_α(x₁,…,x_k,y) ≥ t, where ψ_α is a quantifier-free formula for each α ∈ I, t is an arbitrary number, and #y is a counting quantifier, can be evaluated in time f(d,k)n, where n is the number of vertices and d is the width of a contraction sequence that is part of the input. In addition to the aforementioned problems, this includes also connected partial dominating set and independent partial dominating set.
Cite as

Jakub Balabán, Daniel Mock, and Peter Rossmanith. Solving Partial Dominating Set and Related Problems Using Twin-Width. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 13:1-13:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{balaban_et_al:LIPIcs.MFCS.2025.13,
  author =	{Balab\'{a}n, Jakub and Mock, Daniel and Rossmanith, Peter},
  title =	{{Solving Partial Dominating Set and Related Problems Using Twin-Width}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{13:1--13:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.13},
  URN =		{urn:nbn:de:0030-drops-241203},
  doi =		{10.4230/LIPIcs.MFCS.2025.13},
  annote =	{Keywords: Partial Dominating Set, Partial Vertex Cover, meta-algorithm, counting logic, twin-width}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.36
Counting Distinct Square Substrings in Sublinear Time

Authors: Panagiotis Charalampopoulos, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
We show that the number of distinct squares in a packed string of length n over an alphabet of size σ can be computed in 𝒪(n/log_{σ}n) time in the word-RAM model of computation. This paper is the first to introduce a sublinear time algorithm for the packed version of squares counting. The packed representation of a string of length n over an alphabet of size σ is given as a sequence of 𝒪(n/ log_{σ} n) machine words in the word-RAM model (a machine word consists of ω ≥ log₂ n bits). Previously it was known how to count distinct squares in 𝒪(n) time [Gusfield and Stoye, JCSS 2004], even for a string over an integer alphabet, see [Crochemore et al., TCS 2014; Bannai et al., CPM 2017; Charalampopoulos et al., SPIRE 2020]. We use techniques of squares extraction from runs described by Crochemore et al. [TCS 2014]. However, the packed model requires novel approaches. In particular, we need an 𝒪(n/log_{σ}n) sized representation of all long-period runs (runs with periods that are Ω(log_{σ}n)) which guarantees sublinear time counting of potentially linearly-many implied squares. The long-period runs with a string period that is periodic itself (called layer runs) are an obstacle, since their number can be Ω(n). Fortunately, the number of all other long-period runs is 𝒪(n/log_{σ}n) and we can construct an implicit representation of all long-period runs in 𝒪(n/log_{σ}n) time by adopting the insights of Amir et al. [ESA 2019], combined with sublinear time tools provided by the PILLAR model of computations in case of packed strings. We count squares in layer runs in sublinear time by exploiting combinatorial properties of types of pyramidally-shaped groups of layer runs. As a by-product, we discover several new structural properties of runs. Another difficulty is to compute, in sublinear time, locations of Lyndon roots of runs in packed strings, which is needed for grouping of runs that can generate equal squares. To overcome this difficulty, we introduce sparse-Lyndon roots which are based on the notion of string synchronizers proposed by Kempa and Kociumaka [STOC 2019].
Cite as

Panagiotis Charalampopoulos, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba. Counting Distinct Square Substrings in Sublinear Time. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 36:1-36:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{charalampopoulos_et_al:LIPIcs.MFCS.2025.36,
  author =	{Charalampopoulos, Panagiotis and Mohamed, Manal and Radoszewski, Jakub and Rytter, Wojciech and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Counting Distinct Square Substrings in Sublinear Time}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{36:1--36:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.36},
  URN =		{urn:nbn:de:0030-drops-241439},
  doi =		{10.4230/LIPIcs.MFCS.2025.36},
  annote =	{Keywords: square in a string, packed model, run (maximal repetition), Lyndon word}
}
Document
DOI: 10.4230/OASIcs.Manzini.3
BWT for String Collections

Authors: Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics.
Cite as

Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino. BWT for String Collections. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 3:1-3:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cenzato_et_al:OASIcs.Manzini.3,
  author =	{Cenzato, Davide and Lipt\'{a}k, Zsuzsanna and Pisanti, Nadia and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT for String Collections}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{3:1--3:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.3},
  URN =		{urn:nbn:de:0030-drops-239113},
  doi =		{10.4230/OASIcs.Manzini.3},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, compressed text indexes, text compression, string collections, bioinformatics}
}
Document
DOI: 10.4230/OASIcs.Manzini.1
BWT and Combinatorics on Words

Authors: Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Burrows-Wheeler Transform (BWT) is a reversible transformation on words (strings) introduced in 1994 in the context of data compression, which is a permutation of the characters in the word. Its clustering effect, i.e., the remarkable property of grouping identical characters (BWT runs) when they share common contexts, has made it a powerful tool for boosting compression performances and enabling efficient pattern searching in highly repetitive string collections. In this chapter, we analyze the Burrows-Wheeler transform under the combinatorial point of view, and we survey known properties and connections with different aspects of combinatorics on words. In particular, we focus on the properties of words in relation to the number of their BWT runs. The value r, which counts the number of BWT runs, impacts both compression performance and indexing efficiency, and is considered a measure to evaluate the above-mentioned clustering effect and, consequently, the repetitiveness of a word. We give an overview of the results relating r to other combinatorial repetitiveness measures related to the factor complexity. The chapter also explores extremal cases of the clustering effect. Finally, some results on the sensitivity of the measure r are considered, where the effects of combinatorial operations are studied, such as reversal, edits, and the application of morphisms.
Cite as

Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino. BWT and Combinatorics on Words. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fici_et_al:OASIcs.Manzini.1,
  author =	{Fici, Gabriele and Mantaci, Sabrina and Restivo, Antonio and Romana, Giuseppe and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT and Combinatorics on Words}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{1:1--1:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.1},
  URN =		{urn:nbn:de:0030-drops-239090},
  doi =		{10.4230/OASIcs.Manzini.1},
  annote =	{Keywords: Burrows-Wheeler Transform, Combinatorics on Words, Clustering Effect, BWT Runs}
}
Document
DOI: 10.4230/OASIcs.Manzini.2
A Survey of the Bijective Burrows-Wheeler Transform

Authors: Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Bijective BWT (BBWT), conceived by Scott in 2007, later summarized in a preprint by Gil and Scott in 2009 (arXiv 2012), is a variant of the Burrows-Wheeler Transform which is bijective: every string is the BBWT of some string. Indeed, the BBWT of a string is the extended BWT [Mantaci et al., 2007] of the factors of its Lyndon factorization. The BBWT has been receiving increasing interest in recent years. In this paper, we survey existing research on the BBWT, starting with its history and motivation. We then present algorithmic topics including construction algorithms with various complexities and an index on top of the BBWT for pattern matching. We subsequently address some properties of the BBWT as a compressor, discussing robustness to operations such as reversal, edits, rotation, as well as compression power. We close with listing other bijective variants of the BWT and open problems concerning the BBWT.
Cite as

Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták. A Survey of the Bijective Burrows-Wheeler Transform. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 2:1-2:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bannai_et_al:OASIcs.Manzini.2,
  author =	{Bannai, Hideo and K\"{o}ppl, Dominik and Lipt\'{a}k, Zsuzsanna},
  title =	{{A Survey of the Bijective Burrows-Wheeler Transform}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{2:1--2:26},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.2},
  URN =		{urn:nbn:de:0030-drops-239100},
  doi =		{10.4230/OASIcs.Manzini.2},
  annote =	{Keywords: Burrows-Wheeler Transform, compression, text indexing, repetitiveness measure, Lyndon words, index construction algorithms, bijective string transformation}
}
Document
DOI: 10.4230/OASIcs.Manzini.6
Optimizing the Performance of the FM-Index for Large-Scale Data

Authors: Eddie Ferro and Christina Boucher

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The FM-index is a fundamental data structure used in bioinformatics to efficiently search for strings and index genomes. However, the FM-index can pose computational challenges, particularly in the context of large-scale genomic datasets, due to the complexity of its underlying components and data encodings. In this paper, we present a comprehensive review of efficient variants of the FM-index and the encoding strategies used to improve performance. We examine hardware-accelerated techniques, such as memory-efficient data layouts and cache-aware structures, as well as software-level innovations, including algorithmic refinements and compact representations. The reviewed work demonstrates substantial gains in both speed and scalability, making methods that use the FM-index more practical for high-throughput genomic applications. By analyzing the trade-offs and design choices of these variants, we highlight how combining hardware-aware and software-centric strategies enables more efficient FM-index construction and usage across a range of bioinformatics tasks.
Cite as

Eddie Ferro and Christina Boucher. Optimizing the Performance of the FM-Index for Large-Scale Data. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ferro_et_al:OASIcs.Manzini.6,
  author =	{Ferro, Eddie and Boucher, Christina},
  title =	{{Optimizing the Performance of the FM-Index for Large-Scale Data}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{6:1--6:21},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.6},
  URN =		{urn:nbn:de:0030-drops-239140},
  doi =		{10.4230/OASIcs.Manzini.6},
  annote =	{Keywords: FM-Index Acceleration, Run-Length Encoding, Suffix Array Optimization, Burrows-Wheeler Transform, Efficient Backward Search}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.14
Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing

Authors: Diego Díaz-Domínguez

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
We present compression algorithms designed to process terabyte-sized datasets in parallel. Our approach builds on locally consistent grammars, a lightweight form of compression, combined with simple post-processing techniques to achieve further space reductions. Locally consistent grammar algorithms are suitable for scaling as they need minimal satellite information to compact the text, but they are not inherently parallel. To enable parallelisation, we introduce a novel concept that we call stable local consistency. A grammar algorithm ALG is stable if for any pattern P occurring in a collection 𝒯 = {T_1, T_2, …, T_k}, instances ALG(T_1), ALG(T_2), …, ALG(T_k) independently produce cores for P with the same topology. In a locally consistent grammar, the core of P is a subset of nodes and edges in the parse tree of 𝒯 that remains the same in all the occurrences of P. This feature enables compression, but it only holds if ALG defines a common set of nonterminal symbols for the strings. Stability removes this restriction, allowing us to run ALG(T_1), ALG(T_2), …, ALG(T_k) in parallel and subsequently merge their grammars into a single output equivalent to that of ALG(𝒯). We implemented our ideas and tested them on massive datasets. Our experiments showed that our method could process 7.9 TB of bacterial genomes in around nine hours, using 16 threads and 0.43 bits/symbol of working memory, achieving a compression ratio of 85x.
Cite as

Diego Díaz-Domínguez. Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 14:1-14:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{diazdominguez:LIPIcs.SEA.2025.14,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego},
  title =	{{Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{14:1--14:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra 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.SEA.2025.14},
  URN =		{urn:nbn:de:0030-drops-232525},
  doi =		{10.4230/LIPIcs.SEA.2025.14},
  annote =	{Keywords: Grammar compression, locally consistent parsing, hashing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.12
Bit Packed Encodings for Grammar-Compressed Strings Supporting Fast Random Access

Authors: Alan M. Cleary, Joseph Winjum, Jordan Dood, Hiroki Shibata, and Shunsuke Inenaga

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Grammar-based compression is a powerful compression technique that allows for computation over the compressed data. While there has been extensive theoretical work on grammar and encoding size, there has been little work on practical grammar encodings. In this work, we consider the canonical array-of-arrays grammar representation and present a general bit packing approach for reducing its space requirements in practice. We then present three bit packing strategies based on this approach - one online and two offline - with different space-time trade-offs. This technique can be used to encode any grammar-compressed string while preserving the virtues of the array-of-arrays representation. We show that our encodings are Nlog₂ N away from the information-theoretic bound, where N is the number of symbols in the grammar, and that they are much smaller than methods that meet the information-theoretic bound in practice. Moreover, our experiments show that by using bit packed encodings we can achieve state-of-the-art performance both in grammar encoding size and run-time performance of random-access queries.
Cite as

Alan M. Cleary, Joseph Winjum, Jordan Dood, Hiroki Shibata, and Shunsuke Inenaga. Bit Packed Encodings for Grammar-Compressed Strings Supporting Fast Random Access. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 12:1-12:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cleary_et_al:LIPIcs.SEA.2025.12,
  author =	{Cleary, Alan M. and Winjum, Joseph and Dood, Jordan and Shibata, Hiroki and Inenaga, Shunsuke},
  title =	{{Bit Packed Encodings for Grammar-Compressed Strings Supporting Fast Random Access}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{12:1--12:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra 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.SEA.2025.12},
  URN =		{urn:nbn:de:0030-drops-232506},
  doi =		{10.4230/LIPIcs.SEA.2025.12},
  annote =	{Keywords: String algorithms, data compression, random access, grammar-based compression}
}
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