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Documents authored by Kociumaka, Tomasz

Document
DOI: 10.4230/LIPIcs.ISAAC.2023.10
Small-Space Algorithms for the Online Language Distance Problem for Palindromes and Squares

Authors: Gabriel Bathie, Tomasz Kociumaka, and Tatiana Starikovskaya

Published in: LIPIcs, Volume 283, 34th International Symposium on Algorithms and Computation (ISAAC 2023)

Abstract
We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit (Levenshtein) distance. In this problem, defined for a fixed formal language L, we are given a string T of length n, and the task is to compute the minimal distance to L from every prefix of T. We focus on the low-distance regime, where one must compute only the distances smaller than a given threshold k. In this work, our contribution is twofold: 1) First, we show streaming algorithms, which access the input string T only through a single left-to-right scan. Both for palindromes and squares, our algorithms use O(k polylog n) space and time per character in the Hamming-distance case and O(k² polylog n) space and time per character in the edit-distance case. These algorithms are randomised by necessity, and they err with probability inverse-polynomial in n. 2) Second, we show deterministic read-only online algorithms, which are also provided with read-only random access to the already processed characters of T. Both for palindromes and squares, our algorithms use O(k polylog n) space and time per character in the Hamming-distance case and O(k⁴ polylog n) space and amortised time per character in the edit-distance case.
Cite as

Gabriel Bathie, Tomasz Kociumaka, and Tatiana Starikovskaya. Small-Space Algorithms for the Online Language Distance Problem for Palindromes and Squares. In 34th International Symposium on Algorithms and Computation (ISAAC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 283, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bathie_et_al:LIPIcs.ISAAC.2023.10,
  author =	{Bathie, Gabriel and Kociumaka, Tomasz and Starikovskaya, Tatiana},
  title =	{{Small-Space Algorithms for the Online Language Distance Problem for Palindromes and Squares}},
  booktitle =	{34th International Symposium on Algorithms and Computation (ISAAC 2023)},
  pages =	{10:1--10:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-289-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{283},
  editor =	{Iwata, Satoru and Kakimura, Naonori},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2023.10},
  URN =		{urn:nbn:de:0030-drops-193124},
  doi =		{10.4230/LIPIcs.ISAAC.2023.10},
  annote =	{Keywords: Approximate pattern matching, streaming algorithms, palindromes, squares}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.72
Bellman-Ford Is Optimal for Shortest Hop-Bounded Paths

Authors: Tomasz Kociumaka and Adam Polak

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

Abstract
This paper is about the problem of finding a shortest s-t path using at most h edges in edge-weighted graphs. The Bellman-Ford algorithm solves this problem in O(hm) time, where m is the number of edges. We show that this running time is optimal, up to subpolynomial factors, under popular fine-grained complexity assumptions. More specifically, we show that under the APSP Hypothesis the problem cannot be solved faster already in undirected graphs with nonnegative edge weights. This lower bound holds even restricted to graphs of arbitrary density and for arbitrary h ∈ O(√m). Moreover, under a stronger assumption, namely the Min-Plus Convolution Hypothesis, we can eliminate the restriction h ∈ O(√m). In other words, the O(hm) bound is tight for the entire space of parameters h, m, and n, where n is the number of nodes. Our lower bounds can be contrasted with the recent near-linear time algorithm for the negative-weight Single-Source Shortest Paths problem, which is the textbook application of the Bellman-Ford algorithm.
Cite as

Tomasz Kociumaka and Adam Polak. Bellman-Ford Is Optimal for Shortest Hop-Bounded Paths. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 72:1-72:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{kociumaka_et_al:LIPIcs.ESA.2023.72,
  author =	{Kociumaka, Tomasz and Polak, Adam},
  title =	{{Bellman-Ford Is Optimal for Shortest Hop-Bounded Paths}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{72:1--72:10},
  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.2023.72},
  URN =		{urn:nbn:de:0030-drops-187257},
  doi =		{10.4230/LIPIcs.ESA.2023.72},
  annote =	{Keywords: Fine-grained complexity, graph algorithms, lower bounds, shortest paths}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.15
Linear-Time Computation of Cyclic Roots and Cyclic Covers of a String

Authors: Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba

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

Abstract
Cyclic versions of covers and roots of a string are considered in this paper. A prefix V of a string S is a cyclic root of S if S is a concatenation of cyclic rotations of V. A prefix V of S is a cyclic cover of S if the occurrences of the cyclic rotations of V cover all positions of S. We present 𝒪(n)-time algorithms computing all cyclic roots (using number-theoretic tools) and all cyclic covers (using tools related to seeds) of a length-n string over an integer alphabet. Our results improve upon 𝒪(n log log n) and 𝒪(n log n) time complexities of recent algorithms of Grossi et al. (WALCOM 2023) for the respective problems and provide novel approaches to the problems. As a by-product, we obtain an optimal data structure for Internal Circular Pattern Matching queries that generalize Internal Pattern Matching and Cyclic Equivalence queries of Kociumaka et al. (SODA 2015).
Cite as

Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba. Linear-Time Computation of Cyclic Roots and Cyclic Covers of a String. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{iliopoulos_et_al:LIPIcs.CPM.2023.15,
  author =	{Iliopoulos, Costas S. and Kociumaka, Tomasz and Radoszewski, Jakub and Rytter, Wojciech and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Linear-Time Computation of Cyclic Roots and Cyclic Covers of a String}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{15:1--15:15},
  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.2023.15},
  URN =		{urn:nbn:de:0030-drops-179697},
  doi =		{10.4230/LIPIcs.CPM.2023.15},
  annote =	{Keywords: cyclic cover, cyclic root, circular pattern matching, internal pattern matching}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2023.58
An Algorithmic Bridge Between Hamming and Levenshtein Distances

Authors: Elazar Goldenberg, Tomasz Kociumaka, Robert Krauthgamer, and Barna Saha

Published in: LIPIcs, Volume 251, 14th Innovations in Theoretical Computer Science Conference (ITCS 2023)

Abstract
The edit distance between strings classically assigns unit cost to every character insertion, deletion, and substitution, whereas the Hamming distance only allows substitutions. In many real-life scenarios, insertions and deletions (abbreviated indels) appear frequently but significantly less so than substitutions. To model this, we consider substitutions being cheaper than indels, with cost 1/a for a parameter a ≥ 1. This basic variant, denoted ED_a, bridges classical edit distance (a = 1) with Hamming distance (a → ∞), leading to interesting algorithmic challenges: Does the time complexity of computing ED_a interpolate between that of Hamming distance (linear time) and edit distance (quadratic time)? What about approximating ED_a? We first present a simple deterministic exact algorithm for ED_a and further prove that it is near-optimal assuming the Orthogonal Vectors Conjecture. Our main result is a randomized algorithm computing a (1+ε)-approximation of ED_a(X,Y), given strings X,Y of total length n and a bound k ≥ ED_a(X,Y). For simplicity, let us focus on k ≥ 1 and a constant ε > 0; then, our algorithm takes Õ(n/a + ak³) time. Unless a = Õ(1), in which case ED_a resembles the standard edit distance, and for the most interesting regime of small enough k, this running time is sublinear in n. We also consider a very natural version that asks to find a (k_I, k_S)-alignment, i.e., an alignment with at most k_I indels and k_S substitutions. In this setting, we give an exact algorithm and, more importantly, an Õ((nk_I)/k_S + k_S k_I³)-time (1,1+ε)-bicriteria approximation algorithm. The latter solution is based on the techniques we develop for ED_a for a = Θ(k_S/k_I), and its running time is again sublinear in n whenever k_I ≪ k_S and the overall distance is small enough. These bounds are in stark contrast to unit-cost edit distance, where state-of-the-art algorithms are far from achieving (1+ε)-approximation in sublinear time, even for a favorable choice of k.
Cite as

Elazar Goldenberg, Tomasz Kociumaka, Robert Krauthgamer, and Barna Saha. An Algorithmic Bridge Between Hamming and Levenshtein Distances. In 14th Innovations in Theoretical Computer Science Conference (ITCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 251, pp. 58:1-58:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{goldenberg_et_al:LIPIcs.ITCS.2023.58,
  author =	{Goldenberg, Elazar and Kociumaka, Tomasz and Krauthgamer, Robert and Saha, Barna},
  title =	{{An Algorithmic Bridge Between Hamming and Levenshtein Distances}},
  booktitle =	{14th Innovations in Theoretical Computer Science Conference (ITCS 2023)},
  pages =	{58:1--58:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-263-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{251},
  editor =	{Tauman Kalai, Yael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2023.58},
  URN =		{urn:nbn:de:0030-drops-175615},
  doi =		{10.4230/LIPIcs.ITCS.2023.58},
  annote =	{Keywords: edit distance, Hamming distance, Longest Common Extension queries}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.35
Approximate Circular Pattern Matching

Authors: Panagiotis Charalampopoulos, Tomasz Kociumaka, Jakub Radoszewski, Solon P. Pissis, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba

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

Abstract
We investigate the complexity of approximate circular pattern matching (CPM, in short) under the Hamming and edit distance. Under each of these two basic metrics, we are given a length-n text T, a length-m pattern P, and a positive integer threshold k, and we are to report all starting positions (called occurrences) of fragments of T that are at distance at most k from some cyclic rotation of P. In the decision version of the problem, we are to check if there is any such occurrence. All previous results for approximate CPM were either average-case upper bounds or heuristics, with the exception of the work of Charalampopoulos et al. [CKP^+, JCSS'21], who considered only the Hamming distance. For the reporting version of the approximate CPM problem, under the Hamming distance we improve upon the main algorithm of [CKP^+, JCSS'21] from 𝒪(n+(n/m) ⋅ k⁴) to 𝒪(n+(n/m) ⋅ k³ log log k) time; for the edit distance, we give an 𝒪(nk²)-time algorithm. Notably, for the decision versions and wide parameter-ranges, we give algorithms whose complexities are almost identical to the state-of-the-art for standard (i.e., non-circular) approximate pattern matching: - For the decision version of the approximate CPM problem under the Hamming distance, we obtain an 𝒪(n+(n/m) ⋅ k² log k / log log k)-time algorithm, which works in 𝒪(n) time whenever k = 𝒪(√{m log log m / log m}). In comparison, the fastest algorithm for the standard counterpart of the problem, by Chan et al. [CGKKP, STOC’20], runs in 𝒪(n) time only for k = 𝒪(√m). We achieve this result via a reduction to a geometric problem by building on ideas from [CKP^+, JCSS'21] and Charalampopoulos et al. [CKW, FOCS'20]. - For the decision version of the approximate CPM problem under the edit distance, the 𝒪(nklog³ k) runtime of our algorithm near matches the 𝒪(nk) runtime of the Landau-Vishkin algorithm [LV, J. Algorithms'89] for approximate pattern matching under edit distance; the latter algorithm remains the fastest known for k = Ω(m^{2/5}). As a stepping stone, we propose an 𝒪(nklog³ k)-time algorithm for solving the Longest Prefix k'-Approximate Match problem, proposed by Landau et al. [LMS, SICOMP'98], for all k' ∈ {1,…,k}. Our algorithm is based on Tiskin’s theory of seaweeds [Tiskin, Math. Comput. Sci.'08], with recent advancements (see Charalampopoulos et al. [CKW, FOCS'22]), and on exploiting the seaweeds' relation to Monge matrices. In contrast, we obtain a conditional lower bound that suggests a polynomial separation between approximate CPM under the Hamming distance over the binary alphabet and its non-circular counterpart. We also show that a strongly subquadratic-time algorithm for the decision version of approximate CPM under edit distance would refute the Strong Exponential Time Hypothesis.
Cite as

Panagiotis Charalampopoulos, Tomasz Kociumaka, Jakub Radoszewski, Solon P. Pissis, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba. Approximate Circular Pattern Matching. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 35:1-35:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{charalampopoulos_et_al:LIPIcs.ESA.2022.35,
  author =	{Charalampopoulos, Panagiotis and Kociumaka, Tomasz and Radoszewski, Jakub and Pissis, Solon P. and Rytter, Wojciech and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Approximate Circular Pattern Matching}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{35:1--35:19},
  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.2022.35},
  URN =		{urn:nbn:de:0030-drops-169738},
  doi =		{10.4230/LIPIcs.ESA.2022.35},
  annote =	{Keywords: approximate circular pattern matching, Hamming distance, edit distance}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2022.49
Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding

Authors: Debarati Das, Tomasz Kociumaka, and Barna Saha

Published in: LIPIcs, Volume 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)

Abstract
The Dyck language, which consists of well-balanced sequences of parentheses, is one of the most fundamental context-free languages. The Dyck edit distance quantifies the number of edits (character insertions, deletions, and substitutions) required to make a given length-n parenthesis sequence well-balanced. RNA Folding involves a similar problem, where a closing parenthesis can match an opening parenthesis of the same type irrespective of their ordering. For example, in RNA Folding, both () and )( are valid matches, whereas the Dyck language only allows () as a match. Both of these problems have been studied extensively in the literature. Using fast matrix multiplication, it is possible to compute their exact solutions in time O(n^2.687) (Chi, Duan, Xie, Zhang, STOC'22), and a (1+ε)-multiplicative approximation is known with a running time of Ω(n^2.372). The impracticality of fast matrix multiplication often makes combinatorial algorithms much more desirable. Unfortunately, it is known that the problems of (exactly) computing the Dyck edit distance and the folding distance are at least as hard as Boolean matrix multiplication. Thereby, they are unlikely to admit truly subcubic-time combinatorial algorithms. In terms of fast approximation algorithms that are combinatorial in nature, the state of the art for Dyck edit distance is an O(log n)-factor approximation algorithm that runs in near-linear time (Saha, FOCS'14), whereas for RNA Folding only an ε n-additive approximation in Õ(n²/ε) time (Saha, FOCS'17) is known. In this paper, we make substantial improvements to the state of the art for Dyck edit distance (with any number of parenthesis types). We design a constant-factor approximation algorithm that runs in Õ(n^1.971) time (the first constant-factor approximation in subquadratic time). Moreover, we develop a (1+ε)-factor approximation algorithm running in Õ(n²/ε) time, which improves upon the earlier additive approximation. Finally, we design a (3+ε)-approximation that takes Õ(nd/ε) time, where d ≥ 1 is an upper bound on the sought distance. As for RNA folding, for any s ≥ 1, we design a factor-s approximation algorithm that runs in O(n+(n/s)³) time. To the best of our knowledge, this is the first nontrivial approximation algorithm for RNA Folding that can go below the n² barrier. All our algorithms are combinatorial in nature.
Cite as

Debarati Das, Tomasz Kociumaka, and Barna Saha. Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding. In 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 229, pp. 49:1-49:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{das_et_al:LIPIcs.ICALP.2022.49,
  author =	{Das, Debarati and Kociumaka, Tomasz and Saha, Barna},
  title =	{{Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding}},
  booktitle =	{49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)},
  pages =	{49:1--49:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-235-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{229},
  editor =	{Boja\'{n}czyk, Miko{\l}aj and Merelli, Emanuela and Woodruff, David P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2022.49},
  URN =		{urn:nbn:de:0030-drops-163902},
  doi =		{10.4230/LIPIcs.ICALP.2022.49},
  annote =	{Keywords: Dyck Edit Distance, RNA Folding, String Algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.18
The Dynamic k-Mismatch Problem

Authors: Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański

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

Abstract
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length m and all length-m substrings of a given text of length n ≥ m. We focus on the well-studied k-mismatch version of the problem, where a distance needs to be returned only if it does not exceed a threshold k. Moreover, we assume n ≤ 2m (in general, one can partition the text into overlapping blocks). In this work, we develop data structures for the dynamic version of the k-mismatch problem supporting two operations: An update performs a single-letter substitution in the pattern or the text, whereas a query, given an index i, returns the Hamming distance between the pattern and the text substring starting at position i, or reports that the distance exceeds k. First, we describe a simple data structure with 𝒪̃(1) update time and 𝒪̃(k) query time. Through considerably more sophisticated techniques, we show that 𝒪̃(k) update time and 𝒪̃(1) query time is also achievable. These two solutions likely provide an essentially optimal trade-off for the dynamic k-mismatch problem with m^{Ω(1)} ≤ k ≤ √m: we prove that, in that case, conditioned on the 3SUM conjecture, one cannot simultaneously achieve k^{1-Ω(1)} time for all operations (updates and queries) after n^{𝒪(1)}-time initialization. For k ≥ √m, the same lower bound excludes achieving m^{1/2-Ω(1)} time per operation. This is known to be essentially tight for constant-sized alphabets: already Clifford et al. (STACS 2018) achieved 𝒪̃(√m) time per operation in that case, but their solution for large alphabets costs 𝒪̃(m^{3/4}) time per operation. We improve and extend the latter result by developing a trade-off algorithm that, given a parameter 1 ≤ x ≤ k, achieves update time 𝒪̃(m/k +√{mk/x}) and query time 𝒪̃(x). In particular, for k ≥ √m, an appropriate choice of x yields 𝒪̃(∛{mk}) time per operation, which is 𝒪̃(m^{2/3}) when only the trivial threshold k = m is provided.
Cite as

Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański. The Dynamic k-Mismatch Problem. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 18:1-18:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{clifford_et_al:LIPIcs.CPM.2022.18,
  author =	{Clifford, Rapha\"{e}l and Gawrychowski, Pawe{\l} and Kociumaka, Tomasz and Martin, Daniel P. and Uzna\'{n}ski, Przemys{\l}aw},
  title =	{{The Dynamic k-Mismatch Problem}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{18:1--18:15},
  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.2022.18},
  URN =		{urn:nbn:de:0030-drops-161454},
  doi =		{10.4230/LIPIcs.CPM.2022.18},
  annote =	{Keywords: Pattern matching, Hamming distance, dynamic algorithms}
}
Document
DOI: 10.4230/LIPIcs.ESA.2021.30
Faster Algorithms for Longest Common Substring

Authors: Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)

Abstract
In the classic longest common substring (LCS) problem, we are given two strings S and T, each of length at most n, over an alphabet of size σ, and we are asked to find a longest string occurring as a fragment of both S and T. Weiner, in his seminal paper that introduced the suffix tree, presented an 𝒪(n log σ)-time algorithm for this problem [SWAT 1973]. For polynomially-bounded integer alphabets, the linear-time construction of suffix trees by Farach yielded an 𝒪(n)-time algorithm for the LCS problem [FOCS 1997]. However, for small alphabets, this is not necessarily optimal for the LCS problem in the word RAM model of computation, in which the strings can be stored in 𝒪(n log σ/log n) space and read in 𝒪(n log σ/log n) time. We show that, in this model, we can compute an LCS in time 𝒪(n log σ / √{log n}), which is sublinear in n if σ = 2^{o(√{log n})} (in particular, if σ = 𝒪(1)), using optimal space 𝒪(n log σ/log n). We then lift our ideas to the problem of computing a k-mismatch LCS, which has received considerable attention in recent years. In this problem, the aim is to compute a longest substring of S that occurs in T with at most k mismatches. Flouri et al. showed how to compute a 1-mismatch LCS in 𝒪(n log n) time [IPL 2015]. Thankachan et al. extended this result to computing a k-mismatch LCS in 𝒪(n log^k n) time for k = 𝒪(1) [J. Comput. Biol. 2016]. We show an 𝒪(n log^{k-1/2} n)-time algorithm, for any constant integer k > 0 and irrespective of the alphabet size, using 𝒪(n) space as the previous approaches. We thus notably break through the well-known n log^k n barrier, which stems from a recursive heavy-path decomposition technique that was first introduced in the seminal paper of Cole et al. [STOC 2004] for string indexing with k errors.
Cite as

Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski. Faster Algorithms for Longest Common Substring. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 30:1-30:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{charalampopoulos_et_al:LIPIcs.ESA.2021.30,
  author =	{Charalampopoulos, Panagiotis and Kociumaka, Tomasz and Pissis, Solon P. and Radoszewski, Jakub},
  title =	{{Faster Algorithms for Longest Common Substring}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{30:1--30:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus 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.2021.30},
  URN =		{urn:nbn:de:0030-drops-146114},
  doi =		{10.4230/LIPIcs.ESA.2021.30},
  annote =	{Keywords: longest common substring, k mismatches, wavelet tree}
}
Document
DOI: 10.4230/LIPIcs.ESA.2020.39
Practical Performance of Space Efficient Data Structures for Longest Common Extensions

Authors: Patrick Dinklage, Johannes Fischer, Alexander Herlez, Tomasz Kociumaka, and Florian Kurpicz

Published in: LIPIcs, Volume 173, 28th Annual European Symposium on Algorithms (ESA 2020)

Abstract
For a text T[1,n], a Longest Common Extension (LCE) query lce_T(i,j) asks for the length of the longest common prefix of the suffixes T[i,n] and T[j,n] identified by their starting positions 1 ≤ i,j ≤ n. A classic problem in stringology asks to preprocess a static text T[1,n] over an alphabet of size σ so that LCE queries can be efficiently answered on-line. Since its introduction in the 1980’s, this problem has found numerous applications: in suffix sorting, edit distance computation, approximate pattern matching, regularities finding, string mining, and many more. Text-book solutions offer O(n) preprocessing time and O(1) query time, but they employ memory-heavy data structures, such as suffix arrays, in practice several times bigger than the text itself. Very recently, more space efficient solutions using O(nlogσ) bits of total space or even only O(log n) bits of extra space have been proposed: string synchronizing sets [Kempa and Kociumaka, STOC'19, and Birenzwige et al., SODA'20] and in-place fingerprinting [Prezza, SODA'18]. The goal of this article is to present well-engineered implementations of these new solutions and study their practicality on a commonly agreed text corpus. We show that both perform extremely well in practice, with space consumption of only around 10% of the input size for string synchronizing sets (around 20% for highly repetitive texts), and essentially no extra space for fingerprinting. Interestingly, our experiments also show that both solutions become much faster than naive scanning even for finding common prefixes of moderate length, contradicting a common belief that sophisticated data structures for LCE queries are not competitive with naive approaches [Ilie and Tinta, SPIRE'09].
Cite as

Patrick Dinklage, Johannes Fischer, Alexander Herlez, Tomasz Kociumaka, and Florian Kurpicz. Practical Performance of Space Efficient Data Structures for Longest Common Extensions. In 28th Annual European Symposium on Algorithms (ESA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 173, pp. 39:1-39:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{dinklage_et_al:LIPIcs.ESA.2020.39,
  author =	{Dinklage, Patrick and Fischer, Johannes and Herlez, Alexander and Kociumaka, Tomasz and Kurpicz, Florian},
  title =	{{Practical Performance of Space Efficient Data Structures for Longest Common Extensions}},
  booktitle =	{28th Annual European Symposium on Algorithms (ESA 2020)},
  pages =	{39:1--39:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-162-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{173},
  editor =	{Grandoni, Fabrizio and Herman, Grzegorz and Sanders, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2020.39},
  URN =		{urn:nbn:de:0030-drops-129050},
  doi =		{10.4230/LIPIcs.ESA.2020.39},
  annote =	{Keywords: text indexing, longest common prefix, space efficient data structures}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2020.46
Improved Circular k-Mismatch Sketches

Authors: Shay Golan, Tomasz Kociumaka, Tsvi Kopelowitz, Ely Porat, and Przemysław Uznański

Published in: LIPIcs, Volume 176, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2020)

Abstract
The shift distance sh(S₁,S₂) between two strings S₁ and S₂ of the same length is defined as the minimum Hamming distance between S₁ and any rotation (cyclic shift) of S₂. We study the problem of sketching the shift distance, which is the following communication complexity problem: Strings S₁ and S₂ of length n are given to two identical players (encoders), who independently compute sketches (summaries) sk(S₁) and sk(S₂), respectively, so that upon receiving the two sketches, a third player (decoder) is able to compute (or approximate) sh(S₁,S₂) with high probability. This paper primarily focuses on the more general k-mismatch version of the problem, where the decoder is allowed to declare a failure if sh(S₁,S₂) > k, where k is a parameter known to all parties. Andoni et al. (STOC'13) introduced exact circular k-mismatch sketches of size Õ(k+D(n)), where D(n) is the number of divisors of n. Andoni et al. also showed that their sketch size is optimal in the class of linear homomorphic sketches. We circumvent this lower bound by designing a (non-linear) exact circular k-mismatch sketch of size Õ(k); this size matches communication-complexity lower bounds. We also design (1± ε)-approximate circular k-mismatch sketch of size Õ(min(ε^{-2}√k, ε^{-1.5}√n)), which improves upon an Õ(ε^{-2}√n)-size sketch of Crouch and McGregor (APPROX'11).
Cite as

Shay Golan, Tomasz Kociumaka, Tsvi Kopelowitz, Ely Porat, and Przemysław Uznański. Improved Circular k-Mismatch Sketches. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 176, pp. 46:1-46:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{golan_et_al:LIPIcs.APPROX/RANDOM.2020.46,
  author =	{Golan, Shay and Kociumaka, Tomasz and Kopelowitz, Tsvi and Porat, Ely and Uzna\'{n}ski, Przemys{\l}aw},
  title =	{{Improved Circular k-Mismatch Sketches}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2020)},
  pages =	{46:1--46:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-164-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{176},
  editor =	{Byrka, Jaros{\l}aw and Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2020.46},
  URN =		{urn:nbn:de:0030-drops-126492},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2020.46},
  annote =	{Keywords: Hamming distance, k-mismatch, sketches, rotation, cyclic shift, communication complexity}
}
Document
DOI: 10.4230/LIPIcs.CPM.2020.5
Time-Space Tradeoffs for Finding a Long Common Substring

Authors: Stav Ben-Nun, Shay Golan, Tomasz Kociumaka, and Matan Kraus

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract
We consider the problem of finding, given two documents of total length n, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic 𝒪(n)-time solution dating back to the discovery of suffix trees (Weiner, 1973) and their efficient construction for integer alphabets (Farach-Colton, 1997). However, these solutions require Θ(n) space, which is prohibitive in many applications. To address this issue, Starikovskaya and Vildhøj (CPM 2013) showed that for n^{2/3} ≤ s ≤ n, the LCS problem can be solved in 𝒪(s) space and 𝒪̃(n²/s) time. Kociumaka et al. (ESA 2014) generalized this tradeoff to 1 ≤ s ≤ n, thus providing a smooth time-space tradeoff from constant to linear space. In this paper, we obtain a significant speed-up for instances where the length L of the sought LCS is large. For 1 ≤ s ≤ n, we show that the LCS problem can be solved in 𝒪(s) space and 𝒪̃(n²/(L⋅s) +n) time. The result is based on techniques originating from the LCS with Mismatches problem (Flouri et al., 2015; Charalampopoulos et al., CPM 2018), on space-efficient locally consistent parsing (Birenzwige et al., SODA 2020), and on the structure of maximal repetitions (runs) in the input documents.
Cite as

Stav Ben-Nun, Shay Golan, Tomasz Kociumaka, and Matan Kraus. Time-Space Tradeoffs for Finding a Long Common Substring. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{bennun_et_al:LIPIcs.CPM.2020.5,
  author =	{Ben-Nun, Stav and Golan, Shay and Kociumaka, Tomasz and Kraus, Matan},
  title =	{{Time-Space Tradeoffs for Finding a Long Common Substring}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{5:1--5:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.5},
  URN =		{urn:nbn:de:0030-drops-121302},
  doi =		{10.4230/LIPIcs.CPM.2020.5},
  annote =	{Keywords: longest common substring, time-space tradeoff, local consistency, periodicity}
}
Document
DOI: 10.4230/LIPIcs.CPM.2020.8
Counting Distinct Patterns in Internal Dictionary Matching

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

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract
We consider the problem of preprocessing a text T of length n and a dictionary 𝒟 in order to be able to efficiently answer queries CountDistinct(i,j), that is, given i and j return the number of patterns from 𝒟 that occur in the fragment T[i..j]. The dictionary is internal in the sense that each pattern in 𝒟 is given as a fragment of T. This way, the dictionary takes space proportional to the number of patterns d=|𝒟| rather than their total length, which could be Θ(n⋅ d). An 𝒪̃(n+d)-size data structure that answers CountDistinct(i,j) queries 𝒪(log n)-approximately in 𝒪̃(1) time was recently proposed in a work that introduced internal dictionary matching [ISAAC 2019]. Here we present an 𝒪̃(n+d)-size data structure that answers CountDistinct(i,j) queries 2-approximately in 𝒪̃(1) time. Using range queries, for any m, we give an 𝒪̃(min(nd/m,n²/m²)+d)-size data structure that answers CountDistinct(i,j) queries exactly in 𝒪̃(m) time. We also consider the special case when the dictionary consists of all square factors of the string. We design an 𝒪(n log² n)-size data structure that allows us to count distinct squares in a text fragment T[i..j] in 𝒪(log n) time.
Cite as

Panagiotis Charalampopoulos, Tomasz Kociumaka, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, and Wiktor Zuba. Counting Distinct Patterns in Internal Dictionary Matching. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 8:1-8:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{charalampopoulos_et_al:LIPIcs.CPM.2020.8,
  author =	{Charalampopoulos, Panagiotis and Kociumaka, Tomasz and Mohamed, Manal and Radoszewski, Jakub and Rytter, Wojciech and Straszy\'{n}ski, Juliusz and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Counting Distinct Patterns in Internal Dictionary Matching}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{8:1--8:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.8},
  URN =		{urn:nbn:de:0030-drops-121336},
  doi =		{10.4230/LIPIcs.CPM.2020.8},
  annote =	{Keywords: dictionary matching, internal pattern matching, squares}
}
Document
DOI: 10.4230/LIPIcs.CPM.2020.9
Dynamic String Alignment

Authors: Panagiotis Charalampopoulos, Tomasz Kociumaka, and Shay Mozes

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract
We consider the problem of dynamically maintaining an optimal alignment of two strings, each of length at most n, as they undergo insertions, deletions, and substitutions of letters. The string alignment problem generalizes the longest common subsequence (LCS) problem and the edit distance problem (also with non-unit costs, as long as insertions and deletions cost the same). The conditional lower bound of Backurs and Indyk [J. Comput. 2018] for computing the LCS in the static case implies that strongly sublinear update time for the dynamic string alignment problem would refute the Strong Exponential Time Hypothesis. We essentially match this lower bound when the alignment weights are constants, by showing how to process each update in 𝒪̃(n) time. When the weights are integers bounded in absolute value by some w=n^{𝒪(1)}, we can maintain the alignment in 𝒪̃(n ⋅ min {√ n,w}) time per update. For the 𝒪̃(nw)-time algorithm, we heavily rely on Tiskin’s work on semi-local LCS, and in particular, in an implicit way, on his algorithm for computing the (min,+)-product of two simple unit-Monge matrices [Algorithmica 2015]. As for the 𝒪̃(n√n)-time algorithm, we employ efficient data structures for computing distances in planar graphs.
Cite as

Panagiotis Charalampopoulos, Tomasz Kociumaka, and Shay Mozes. Dynamic String Alignment. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 9:1-9:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{charalampopoulos_et_al:LIPIcs.CPM.2020.9,
  author =	{Charalampopoulos, Panagiotis and Kociumaka, Tomasz and Mozes, Shay},
  title =	{{Dynamic String Alignment}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{9:1--9:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.9},
  URN =		{urn:nbn:de:0030-drops-121344},
  doi =		{10.4230/LIPIcs.CPM.2020.9},
  annote =	{Keywords: string alignment, edit distance, longest common subsequence, (unit-)Monge matrices, (min,+)-product}
}
Document
DOI: 10.4230/LIPIcs.CPM.2020.15
The Streaming k-Mismatch Problem: Tradeoffs Between Space and Total Time

Authors: Shay Golan, Tomasz Kociumaka, Tsvi Kopelowitz, and Ely Porat

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract
We revisit the k-mismatch problem in the streaming model on a pattern of length m and a streaming text of length n, both over a size-σ alphabet. The current state-of-the-art algorithm for the streaming k-mismatch problem, by Clifford et al. [SODA 2019], uses Õ(k) space and Õ(√k) worst-case time per character. The space complexity is known to be (unconditionally) optimal, and the worst-case time per character matches a conditional lower bound. However, there is a gap between the total time cost of the algorithm, which is Õ(n√k), and the fastest known offline algorithm, which costs Õ(n + min(nk/√m, σn)) time. Moreover, it is not known whether improvements over the Õ(n√k) total time are possible when using more than O(k) space. We address these gaps by designing a randomized streaming algorithm for the k-mismatch problem that, given an integer parameter k≤s≤m, uses Õ(s) space and costs Õ(n+min(nk²/m, nk/√s, σnm/s)) total time. For s=m, the total runtime becomes Õ(n + min(nk/√m, σn)), which matches the time cost of the fastest offline algorithm. Moreover, the worst-case time cost per character is still Õ(√k).
Cite as

Shay Golan, Tomasz Kociumaka, Tsvi Kopelowitz, and Ely Porat. The Streaming k-Mismatch Problem: Tradeoffs Between Space and Total Time. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{golan_et_al:LIPIcs.CPM.2020.15,
  author =	{Golan, Shay and Kociumaka, Tomasz and Kopelowitz, Tsvi and Porat, Ely},
  title =	{{The Streaming k-Mismatch Problem: Tradeoffs Between Space and Total Time}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{15:1--15:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.15},
  URN =		{urn:nbn:de:0030-drops-121406},
  doi =		{10.4230/LIPIcs.CPM.2020.15},
  annote =	{Keywords: Streaming pattern matching, Hamming distance, k-mismatch}
}
Document
DOI: 10.4230/LIPIcs.CPM.2020.16
Approximating Longest Common Substring with k mismatches: Theory and Practice

Authors: Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski, and Tatiana Starikovskaya

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract
In the problem of the longest common substring with k mismatches we are given two strings X, Y and must find the maximal length 𝓁 such that there is a length-𝓁 substring of X and a length-𝓁 substring of Y that differ in at most k positions. The length 𝓁 can be used as a robust measure of similarity between X, Y. In this work, we develop new approximation algorithms for computing 𝓁 that are significantly more efficient that previously known solutions from the theoretical point of view. Our approach is simple and practical, which we confirm via an experimental evaluation, and is probably close to optimal as we demonstrate via a conditional lower bound.
Cite as

Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski, and Tatiana Starikovskaya. Approximating Longest Common Substring with k mismatches: Theory and Practice. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 16:1-16:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{gourdel_et_al:LIPIcs.CPM.2020.16,
  author =	{Gourdel, Garance and Kociumaka, Tomasz and Radoszewski, Jakub and Starikovskaya, Tatiana},
  title =	{{Approximating Longest Common Substring with k mismatches: Theory and Practice}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{16:1--16:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.16},
  URN =		{urn:nbn:de:0030-drops-121410},
  doi =		{10.4230/LIPIcs.CPM.2020.16},
  annote =	{Keywords: approximation algorithms, string similarity, LSH, conditional lower bounds}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2019.22
Internal Dictionary Matching

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

Published in: LIPIcs, Volume 149, 30th International Symposium on Algorithms and Computation (ISAAC 2019)

Abstract
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary D in fragments of a given string T of length n. The dictionary is internal in the sense that each pattern in D is given as a fragment of T. This way, D takes space proportional to the number of patterns d=|D| rather than their total length, which could be Theta(n * d). In particular, we consider the following types of queries: reporting and counting all occurrences of patterns from D in a fragment T[i..j] (operations Report(i,j) and Count(i,j) below, as well as operation Exists(i,j) that returns true iff Count(i,j)>0) and reporting distinct patterns from D that occur in T[i..j] (operation ReportDistinct(i,j)). We show how to construct, in O((n+d) log^{O(1)} n) time, a data structure that answers each of these queries in time O(log^{O(1)} n+|output|) - see the table below for specific time and space complexities. Query | Preprocessing time | Space | Query time Exists(i,j) | O(n+d) | O(n) | O(1) Report(i,j) | O(n+d) | O(n+d) | O(1+|output|) ReportDistinct(i,j) | O(n log n+d) | O(n+d) | O(log n+|output|) Count(i,j) | O({n log n}/{log log n} + d log^{3/2} n) | O(n+d log n) | O({log^2n}/{log log n}) The case of counting patterns is much more involved and needs a combination of a locally consistent parsing with orthogonal range searching. Reporting distinct patterns, on the other hand, uses the structure of maximal repetitions in strings. Finally, we provide tight - up to subpolynomial factors - upper and lower bounds for the case of a dynamic dictionary.
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Panagiotis Charalampopoulos, Tomasz Kociumaka, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, and Tomasz Waleń. Internal Dictionary Matching. In 30th International Symposium on Algorithms and Computation (ISAAC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 149, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{charalampopoulos_et_al:LIPIcs.ISAAC.2019.22,
  author =	{Charalampopoulos, Panagiotis and Kociumaka, Tomasz and Mohamed, Manal and Radoszewski, Jakub and Rytter, Wojciech and Wale\'{n}, Tomasz},
  title =	{{Internal Dictionary Matching}},
  booktitle =	{30th International Symposium on Algorithms and Computation (ISAAC 2019)},
  pages =	{22:1--22:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-130-6},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{149},
  editor =	{Lu, Pinyan and Zhang, Guochuan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2019.22},
  URN =		{urn:nbn:de:0030-drops-115182},
  doi =		{10.4230/LIPIcs.ISAAC.2019.22},
  annote =	{Keywords: string algorithms, dictionary matching, internal pattern matching}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2019.66
RLE Edit Distance in Near Optimal Time

Authors: Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)

Abstract
We show that the edit distance between two run-length encoded strings of compressed lengths m and n respectively, can be computed in O(mn log(mn)) time. This improves the previous record by a factor of O(n/log(mn)). The running time of our algorithm is within subpolynomial factors of being optimal, subject to the standard SETH-hardness assumption. This effectively closes a line of algorithmic research first started in 1993.
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Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański. RLE Edit Distance in Near Optimal Time. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 66:1-66:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{clifford_et_al:LIPIcs.MFCS.2019.66,
  author =	{Clifford, Rapha\"{e}l and Gawrychowski, Pawe{\l} and Kociumaka, Tomasz and Martin, Daniel P. and Uzna\'{n}ski, Przemys{\l}aw},
  title =	{{RLE Edit Distance in Near Optimal Time}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{66:1--66:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.66},
  URN =		{urn:nbn:de:0030-drops-110109},
  doi =		{10.4230/LIPIcs.MFCS.2019.66},
  annote =	{Keywords: String algorithms, Compression, Pattern matching, Run-length encoding}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2019.109
Graph and String Parameters: Connections Between Pathwidth, Cutwidth and the Locality Number (Track B: Automata, Logic, Semantics, and Theory of Programming)

Authors: Katrin Casel, Joel D. Day, Pamela Fleischmann, Tomasz Kociumaka, Florin Manea, and Markus L. Schmid

Published in: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)

Abstract
We investigate the locality number, a recently introduced structural parameter for strings (with applications in pattern matching with variables), and its connection to two important graph-parameters, cutwidth and pathwidth. These connections allow us to show that computing the locality number is NP-hard but fixed-parameter tractable (when the locality number or the alphabet size is treated as a parameter), and can be approximated with ratio O(sqrt{log{opt}} log n). As a by-product, we also relate cutwidth via the locality number to pathwidth, which is of independent interest, since it improves the best currently known approximation algorithm for cutwidth. In addition to these main results, we also consider the possibility of greedy-based approximation algorithms for the locality number.
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Katrin Casel, Joel D. Day, Pamela Fleischmann, Tomasz Kociumaka, Florin Manea, and Markus L. Schmid. Graph and String Parameters: Connections Between Pathwidth, Cutwidth and the Locality Number (Track B: Automata, Logic, Semantics, and Theory of Programming). In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 109:1-109:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{casel_et_al:LIPIcs.ICALP.2019.109,
  author =	{Casel, Katrin and Day, Joel D. and Fleischmann, Pamela and Kociumaka, Tomasz and Manea, Florin and Schmid, Markus L.},
  title =	{{Graph and String Parameters: Connections Between Pathwidth, Cutwidth and the Locality Number}},
  booktitle =	{46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)},
  pages =	{109:1--109:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-109-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{132},
  editor =	{Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.109},
  URN =		{urn:nbn:de:0030-drops-106858},
  doi =		{10.4230/LIPIcs.ICALP.2019.109},
  annote =	{Keywords: Graph and String Parameters, NP-Completeness, Approximation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2019.25
Quasi-Linear-Time Algorithm for Longest Common Circular Factor

Authors: Mai Alzamel, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, and Wiktor Zuba

Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)

Abstract
We introduce the Longest Common Circular Factor (LCCF) problem in which, given strings S and T of length at most n, we are to compute the longest factor of S whose cyclic shift occurs as a factor of T. It is a new similarity measure, an extension of the classic Longest Common Factor. We show how to solve the LCCF problem in O(n log^4 n) time using O(n log^2 n) space.
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Mai Alzamel, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, and Wiktor Zuba. Quasi-Linear-Time Algorithm for Longest Common Circular Factor. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 25:1-25:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{alzamel_et_al:LIPIcs.CPM.2019.25,
  author =	{Alzamel, Mai and Crochemore, Maxime and Iliopoulos, Costas S. and Kociumaka, Tomasz and Radoszewski, Jakub and Rytter, Wojciech and Straszy\'{n}ski, Juliusz and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Quasi-Linear-Time Algorithm for Longest Common Circular Factor}},
  booktitle =	{30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)},
  pages =	{25:1--25:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-103-0},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{128},
  editor =	{Pisanti, Nadia and P. Pissis, Solon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.25},
  URN =		{urn:nbn:de:0030-drops-104961},
  doi =		{10.4230/LIPIcs.CPM.2019.25},
  annote =	{Keywords: longest common factor, circular pattern matching, internal pattern matching, intersection of hyperrectangles}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2018.70
Longest Unbordered Factor in Quasilinear Time

Authors: Tomasz Kociumaka, Ritu Kundu, Manal Mohamed, and Solon P. Pissis

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

Abstract
A border u of a word w is a proper factor of w occurring both as a prefix and as a suffix. The maximal unbordered factor of w is the longest factor of w which does not have a border. Here an O(n log n)-time with high probability (or O(n log n log^2 log n)-time deterministic) algorithm to compute the Longest Unbordered Factor Array of w for general alphabets is presented, where n is the length of w. This array specifies the length of the maximal unbordered factor starting at each position of w. This is a major improvement on the running time of the currently best worst-case algorithm working in O(n^{1.5}) time for integer alphabets [Gawrychowski et al., 2015].
Cite as

Tomasz Kociumaka, Ritu Kundu, Manal Mohamed, and Solon P. Pissis. Longest Unbordered Factor in Quasilinear Time. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 70:1-70:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{kociumaka_et_al:LIPIcs.ISAAC.2018.70,
  author =	{Kociumaka, Tomasz and Kundu, Ritu and Mohamed, Manal and Pissis, Solon P.},
  title =	{{Longest Unbordered Factor in Quasilinear Time}},
  booktitle =	{29th International Symposium on Algorithms and Computation (ISAAC 2018)},
  pages =	{70:1--70:13},
  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.2018.70},
  URN =		{urn:nbn:de:0030-drops-100184},
  doi =		{10.4230/LIPIcs.ISAAC.2018.70},
  annote =	{Keywords: longest unbordered factor, factorisation, period, border, strings}
}
Document
DOI: 10.4230/LIPIcs.ESA.2018.33
Edit Distance with Block Operations

Authors: Michal Ganczorz, Pawel Gawrychowski, Artur Jez, and Tomasz Kociumaka

Published in: LIPIcs, Volume 112, 26th Annual European Symposium on Algorithms (ESA 2018)

Abstract
We consider the problem of edit distance in which block operations are allowed, i.e. we ask for the minimal number of (block) operations that are needed to transform a string s to t. We give O(log n) approximation algorithms, where n is the total length of the input strings, for the variants of the problem which allow the following sets of operations: block move; block move and block delete; block move and block copy; block move, block copy, and block uncopy. The results still hold if we additionally allow any of the following operations: character insert, character delete, block reversal, or block involution (involution is a generalisation of the reversal). Previously, algorithms only for the first and last variant were known, and they had approximation ratios O(log n log^*n) and O(log n (log^*n)^2), respectively. The edit distance with block moves is equivalent, up to a constant factor, to the common string partition problem, in which we are given two strings s, t and the goal is to partition s into minimal number of parts such that they can be permuted in order to obtain t. Thus we also obtain an O(log n) approximation for this problem (compared to the previous O(log n log^* n)). The results use a simplification of the previously used technique of locally consistent parsing, which groups short substrings of a string into phrases so that similar substrings are guaranteed to be grouped in a similar way. Instead of a sophisticated parsing technique relying on a deterministic coin tossing, we use a simple one based on a partition of the alphabet into two subalphabets. In particular, this lowers the running time from O(n log^* n) to O(n). The new algorithms (for block copy or block delete) use a similar algorithm, but the analysis is based on a specially tuned combinatorial function on sets of numbers.
Cite as

Michal Ganczorz, Pawel Gawrychowski, Artur Jez, and Tomasz Kociumaka. Edit Distance with Block Operations. In 26th Annual European Symposium on Algorithms (ESA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 112, pp. 33:1-33:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{ganczorz_et_al:LIPIcs.ESA.2018.33,
  author =	{Ganczorz, Michal and Gawrychowski, Pawel and Jez, Artur and Kociumaka, Tomasz},
  title =	{{Edit Distance with Block Operations}},
  booktitle =	{26th Annual European Symposium on Algorithms (ESA 2018)},
  pages =	{33:1--33:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-081-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{112},
  editor =	{Azar, Yossi and Bast, Hannah 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.2018.33},
  URN =		{urn:nbn:de:0030-drops-94963},
  doi =		{10.4230/LIPIcs.ESA.2018.33},
  annote =	{Keywords: Edit distance, Block operations, Common string partition}
}
Document
DOI: 10.4230/LIPIcs.CPM.2018.23
Linear-Time Algorithm for Long LCF with k Mismatches

Authors: Panagiotis Charalampopoulos, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Walen

Published in: LIPIcs, Volume 105, 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)

Abstract
In the Longest Common Factor with k Mismatches (LCF_k) problem, we are given two strings X and Y of total length n, and we are asked to find a pair of maximal-length factors, one of X and the other of Y, such that their Hamming distance is at most k. Thankachan et al. [Thankachan et al. 2016] show that this problem can be solved in O(n log^k n) time and O(n) space for constant k. We consider the LCF_k(l) problem in which we assume that the sought factors have length at least l. We use difference covers to reduce the LCF_k(l) problem with l=Omega(log^{2k+2}n) to a task involving m=O(n/log^{k+1}n) synchronized factors. The latter can be solved in O(m log^{k+1}m) time, which results in a linear-time algorithm for LCF_k(l) with l=Omega(log^{2k+2}n). In general, our solution to the LCF_k(l) problem for arbitrary l takes O(n + n log^{k+1} n/sqrt{l}) time.
Cite as

Panagiotis Charalampopoulos, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Walen. Linear-Time Algorithm for Long LCF with k Mismatches. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{charalampopoulos_et_al:LIPIcs.CPM.2018.23,
  author =	{Charalampopoulos, Panagiotis and Crochemore, Maxime and Iliopoulos, Costas S. and Kociumaka, Tomasz and Pissis, Solon P. and Radoszewski, Jakub and Rytter, Wojciech and Walen, Tomasz},
  title =	{{Linear-Time Algorithm for Long LCF with k Mismatches}},
  booktitle =	{29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)},
  pages =	{23:1--23:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-074-3},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{105},
  editor =	{Navarro, Gonzalo and Sankoff, David and Zhu, Binhai},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2018.23},
  URN =		{urn:nbn:de:0030-drops-86869},
  doi =		{10.4230/LIPIcs.CPM.2018.23},
  annote =	{Keywords: longest common factor, longest common substring, Hamming distance, heavy-light decomposition, difference cover}
}
Document
DOI: 10.4230/LIPIcs.STACS.2018.38
String Periods in the Order-Preserving Model

Authors: Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Arseny Shur, and Tomasz Walen

Published in: LIPIcs, Volume 96, 35th Symposium on Theoretical Aspects of Computer Science (STACS 2018)

Abstract
The order-preserving model (op-model, in short) was introduced quite recently but has already attracted significant attention because of its applications in data analysis. We introduce several types of periods in this setting (op-periods). Then we give algorithms to compute these periods in time O(n), O(n log log n), O(n log^2 log n/log log log n), O(n log n) depending on the type of periodicity. In the most general variant the number of different periods can be as big as Omega(n^2), and a compact representation is needed. Our algorithms require novel combinatorial insight into the properties of such periods.
Cite as

Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Arseny Shur, and Tomasz Walen. String Periods in the Order-Preserving Model. In 35th Symposium on Theoretical Aspects of Computer Science (STACS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 96, pp. 38:1-38:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{gourdel_et_al:LIPIcs.STACS.2018.38,
  author =	{Gourdel, Garance and Kociumaka, Tomasz and Radoszewski, Jakub and Rytter, Wojciech and Shur, Arseny and Walen, Tomasz},
  title =	{{String Periods in the Order-Preserving Model}},
  booktitle =	{35th Symposium on Theoretical Aspects of Computer Science (STACS 2018)},
  pages =	{38:1--38:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-062-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{96},
  editor =	{Niedermeier, Rolf and Vall\'{e}e, Brigitte},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2018.38},
  URN =		{urn:nbn:de:0030-drops-85064},
  doi =		{10.4230/LIPIcs.STACS.2018.38},
  annote =	{Keywords: order-preserving pattern matching, period, efficient algorithm}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2016.46
Pattern Matching and Consensus Problems on Weighted Sequences and Profiles

Authors: Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski

Published in: LIPIcs, Volume 64, 27th International Symposium on Algorithms and Computation (ISAAC 2016)

Abstract
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version, in which only the pattern or only the text is uncertain, we obtain efficient algorithms with theoretically-provable running times using a variation of the lookahead scoring technique. We also consider a general variant of the pattern matching problems in which both the pattern and the text are uncertain. Central to our solution is a special case where the sequences have equal length, called the consensus problem. We propose algorithms for the consensus problem parameterized by the number of strings that match one of the sequences. As our basic approach, a careful adaptation of the classic meet-in-the-middle algorithm for the knapsack problem is used. On the lower bound side, we prove that our dependence on the parameter is optimal up to lower-order terms conditioned on the optimality of the original algorithm for the knapsack problem.
Cite as

Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski. Pattern Matching and Consensus Problems on Weighted Sequences and Profiles. In 27th International Symposium on Algorithms and Computation (ISAAC 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 64, pp. 46:1-46:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{kociumaka_et_al:LIPIcs.ISAAC.2016.46,
  author =	{Kociumaka, Tomasz and Pissis, Solon P. and Radoszewski, Jakub},
  title =	{{Pattern Matching and Consensus Problems on Weighted Sequences and Profiles}},
  booktitle =	{27th International Symposium on Algorithms and Computation (ISAAC 2016)},
  pages =	{46:1--46:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-026-2},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{64},
  editor =	{Hong, Seok-Hee},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2016.46},
  URN =		{urn:nbn:de:0030-drops-68166},
  doi =		{10.4230/LIPIcs.ISAAC.2016.46},
  annote =	{Keywords: weighted sequence, position weight matrix, profile matching}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.4
Efficient Index for Weighted Sequences

Authors: Carl Barton, Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to support efficient on-line pattern queries. We study this problem in the case where the text is weighted: for every position of the text and every letter of the alphabet a probability of occurrence of this letter at this position is given. Sequences of this type, also called position weight matrices, are commonly used to represent imprecise or uncertain data. A weighted sequence may represent many different strings, each with probability of occurrence equal to the product of probabilities of its letters at subsequent positions. Given a probability threshold 1/z, we say that a pattern string P matches a weighted text at position i if the product of probabilities of the letters of P at positions i,...,i+|P|-1 in the text is at least 1/z. In this article, we present an O(nz)-time construction of an O(nz)-sized index that can answer pattern matching queries in a weighted text in optimal time improving upon the state of the art by a factor of z log z. Other applications of this data structure include an O(nz)-time construction of the weighted prefix table and an O(nz)-time computation of all covers of a weighted sequence, which improve upon the state of the art by the same factor.
Cite as

Carl Barton, Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski. Efficient Index for Weighted Sequences. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{barton_et_al:LIPIcs.CPM.2016.4,
  author =	{Barton, Carl and Kociumaka, Tomasz and Pissis, Solon P. and Radoszewski, Jakub},
  title =	{{Efficient Index for Weighted Sequences}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{4:1--4:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.4},
  URN =		{urn:nbn:de:0030-drops-60807},
  doi =		{10.4230/LIPIcs.CPM.2016.4},
  annote =	{Keywords: weighted sequence, position weight matrix, indexing, weighted suffix tree}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.5
Faster Longest Common Extension Queries in Strings over General Alphabets

Authors: Pawel Gawrychowski, Tomasz Kociumaka, Wojciech Rytter, and Tomasz Walen

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of q LCE queries for a string of size n over a general ordered alphabet can be realized in O(q log log n + n log* n) time making only O(q + n) symbol comparisons. Consequently, all runs in a string over a general ordered alphabets can be computed in O(n log log n) time making O(n) symbol comparisons. Our results improve upon a solution by Kosolobov (Information Processing Letters, 2016), who designed an algorithm with O(n log^⅔ n) running time and conjectured that O(n) time is possible. Our paper makes a significant progress towards resolving this conjecture. Our techniques extend to the case of general unordered alphabets, when the time increases to O(q log n + n log* n). The main tools are difference covers and a variant of the disjoint-sets data structure by La Poutré (SODA 1990).
Cite as

Pawel Gawrychowski, Tomasz Kociumaka, Wojciech Rytter, and Tomasz Walen. Faster Longest Common Extension Queries in Strings over General Alphabets. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2016.5,
  author =	{Gawrychowski, Pawel and Kociumaka, Tomasz and Rytter, Wojciech and Walen, Tomasz},
  title =	{{Faster Longest Common Extension Queries in Strings over General Alphabets}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{5:1--5:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.5},
  URN =		{urn:nbn:de:0030-drops-60810},
  doi =		{10.4230/LIPIcs.CPM.2016.5},
  annote =	{Keywords: longest common extension, longest common prefix, maximal repetitions, difference cover}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.28
Minimal Suffix and Rotation of a Substring in Optimal Time

Authors: Tomasz Kociumaka

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
For a text of length $n$ given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering such queries optimally: in constant time after linear-time preprocessing. This improves upon the results of Babenko et al. (CPM 2014), whose trade-off solution is characterized by Theta(n log n) product of these time complexities. Next, we extend our queries to support concatenations of O(1) substrings, for which the construction and query time is preserved. We apply these generalized queries to compute lexicographically minimal and maximal rotations of a given substring in constant time after linear-time preprocessing. Our data structures mainly rely on properties of Lyndon words and Lyndon factorizations. We combine them with further algorithmic and combinatorial tools, such as fusion trees and the notion of order isomorphism of strings.
Cite as

Tomasz Kociumaka. Minimal Suffix and Rotation of a Substring in Optimal Time. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 28:1-28:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{kociumaka:LIPIcs.CPM.2016.28,
  author =	{Kociumaka, Tomasz},
  title =	{{Minimal Suffix and Rotation of a Substring in Optimal Time}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{28:1--28:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.28},
  URN =		{urn:nbn:de:0030-drops-60626},
  doi =		{10.4230/LIPIcs.CPM.2016.28},
  annote =	{Keywords: minimal suffix, minimal rotation, Lyndon factorization, substring canon- ization, substring queries}
}
Document
DOI: 10.4230/LIPIcs.APPROX-RANDOM.2015.212
Approximating Upper Degree-Constrained Partial Orientations

Authors: Marek Cygan and Tomasz Kociumaka

Published in: LIPIcs, Volume 40, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)

Abstract
In the Upper Degree-Constrained Partial Orientation (UDPO) problem we are given an undirected graph G=(V,E), together with two degree constraint functions d^-,d^+:V -> N. The goal is to orient as many edges as possible, in such a way that for each vertex v in V the number of arcs entering v is at most d^-(v), whereas the number of arcs leaving v is at most d^+(v). This problem was introduced by Gabow [SODA'06], who proved it to be MAXSNP-hard (and thus APX-hard). In the same paper Gabow presented an LP-based iterative rounding 4/3-approximation algorithm. As already observed by Gabow, the problem in question is a special case of the classic 3-Dimensional Matching, which in turn is a special case of the k-Set Packing problem. Back in 2006 the best known polynomial time approximation algorithm for 3-Dimensional Matching was a simple local search by Hurkens and Schrijver [SIDMA'89], the approximation ratio of which is (3+epsilon)/2; hence the algorithm of Gabow was an improvement over the approach brought from the more general problems. In this paper we show that the UDPO problem when cast as 3-Dimensional Matching admits a special structure, which is obliviously exploited by the known approximation algorithms for k-Set Packing. In fact, we show that already the local-search routine of Hurkens and Schrijver gives (4+epsilon)/3-approximation when used for the instances coming from UDPO. Moreover, the recent approximation algorithm for 3-Set Packing [Cygan, FOCS'13] turns out to be a (5+epsilon)/4-approximation for UDPO. This improves over 4/3 as the best ratio known up to date for UDPO.
Cite as

Marek Cygan and Tomasz Kociumaka. Approximating Upper Degree-Constrained Partial Orientations. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 40, pp. 212-224, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{cygan_et_al:LIPIcs.APPROX-RANDOM.2015.212,
  author =	{Cygan, Marek and Kociumaka, Tomasz},
  title =	{{Approximating Upper Degree-Constrained Partial Orientations}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)},
  pages =	{212--224},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-89-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{40},
  editor =	{Garg, Naveen and Jansen, Klaus and Rao, Anup and Rolim, Jos\'{e} D. P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2015.212},
  URN =		{urn:nbn:de:0030-drops-53040},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2015.212},
  annote =	{Keywords: graph orientations, degree-constrained orientations, approximation algorithm, local search}
}
Document
DOI: 10.4230/LIPIcs.STACS.2014.251
Constant Factor Approximation for Capacitated k-Center with Outliers

Authors: Marek Cygan and Tomasz Kociumaka

Published in: LIPIcs, Volume 25, 31st International Symposium on Theoretical Aspects of Computer Science (STACS 2014)

Abstract
The k-center problem is a classic facility location problem, where given an edge-weighted graph G=(V,E) one is to find a subset of k vertices S, such that each vertex in V is "close" to some vertex in S. The approximation status of this basic problem is well understood, as a simple 2-approximation algorithm is known to be tight. Consequently different extensions were studied. In the capacitated version of the problem each vertex is assigned a capacity, which is a strict upper bound on the number of clients a facility can serve, when located at this vertex. A constant factor approximation for the capacitated k-center was obtained last year in [Cygan, Hajiaghayi and Khuller, FOCS'12], which was recently improved to a 9-approximation in [An, Bhaskara and Svensson, arXiv'13]. In a different generalization of the problem some clients (denoted as outliers) may be disregarded. Here we are additionally given an integer p and the goal is to serve exactly p clients, which the algorithm is free to choose. In [Charikar et al., SODA'01] the authors presented a 3-approximation for the k-center problem with outliers. In this paper we consider a common generalization of the two extensions previously studied separately, i.e. we work with the capacitated k-center with outliers. We present the first constant factor approximation algorithm with approximation ratio of 25 even for the case of non-uniform hard capacities.
Cite as

Marek Cygan and Tomasz Kociumaka. Constant Factor Approximation for Capacitated k-Center with Outliers. In 31st International Symposium on Theoretical Aspects of Computer Science (STACS 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 25, pp. 251-262, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)

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@InProceedings{cygan_et_al:LIPIcs.STACS.2014.251,
  author =	{Cygan, Marek and Kociumaka, Tomasz},
  title =	{{Constant Factor Approximation for Capacitated k-Center with Outliers}},
  booktitle =	{31st International Symposium on Theoretical Aspects of Computer Science (STACS 2014)},
  pages =	{251--262},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-65-1},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{25},
  editor =	{Mayr, Ernst W. and Portier, Natacha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2014.251},
  URN =		{urn:nbn:de:0030-drops-44625},
  doi =		{10.4230/LIPIcs.STACS.2014.251},
  annote =	{Keywords: approximation algorithms, k-center, capacities, outliers, LP rounding}
}
Document
DOI: 10.4230/LIPIcs.STACS.2013.245
Fast Algorithms for Abelian Periods in Words and Greatest Common Divisor Queries

Authors: Tomasz Kociumaka, Jakub Radoszewski, and Wojciech Rytter

Published in: LIPIcs, Volume 20, 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)

Abstract
We present efficient algorithms computing all Abelian periods of two types in a word. Regular Abelian periods are computed in O(n log log{n}) randomized time which improves over the best previously known algorithm by almost a factor of n. The other algorithm, for full Abelian periods, works in O(n) time. As a tool we develop an O(n) time construction of a data structure that allows O(1) time gcd(i,j) queries for all 1 <= i,j <= n, this is a result of independent interest.
Cite as

Tomasz Kociumaka, Jakub Radoszewski, and Wojciech Rytter. Fast Algorithms for Abelian Periods in Words and Greatest Common Divisor Queries. In 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013). Leibniz International Proceedings in Informatics (LIPIcs), Volume 20, pp. 245-256, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{kociumaka_et_al:LIPIcs.STACS.2013.245,
  author =	{Kociumaka, Tomasz and Radoszewski, Jakub and Rytter, Wojciech},
  title =	{{Fast Algorithms for Abelian Periods in Words and Greatest Common Divisor Queries}},
  booktitle =	{30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)},
  pages =	{245--256},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-50-7},
  ISSN =	{1868-8969},
  year =	{2013},
  volume =	{20},
  editor =	{Portier, Natacha and Wilke, Thomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2013.245},
  URN =		{urn:nbn:de:0030-drops-39387},
  doi =		{10.4230/LIPIcs.STACS.2013.245},
  annote =	{Keywords: Abelian period, greatest common divisor}
}
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