59 Search Results for "Gawrychowski, Pawel"

Volume

LIPIcs, Volume 191

32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)

CPM 2021, July 5-7, 2021, Wrocław, Poland

Editors: Paweł Gawrychowski and Tatiana Starikovskaya

Document
DOI: 10.4230/LIPIcs.ISAAC.2023.12
Substring Complexity in Sublinear Space

Authors: Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis

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

Abstract
Shannon’s entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of strings, e.g., the size z of the Lempel–Ziv parse or the number r of equal-letter runs of the Burrows-Wheeler transform. A more recent one is the size γ of a smallest string attractor. Let T be a string of length n. A string attractor of T is a set of positions of T capturing the occurrences of all the substrings of T. Unfortunately, Kempa and Prezza [STOC 2018] showed that computing γ is NP-hard. Kociumaka et al. [LATIN 2020] considered a new measure of compressibility that is based on the function S_T(k) counting the number of distinct substrings of length k of T, also known as the substring complexity of T. This new measure is defined as δ = sup{S_T(k)/k, k ≥ 1} and lower bounds all the relevant ad hoc measures previously considered. In particular, δ ≤ γ always holds and δ can be computed in 𝒪(n) time using Θ(n) working space. Kociumaka et al. showed that one can construct an 𝒪(δ log n/(δ))-sized representation of T supporting efficient direct access and efficient pattern matching queries on T. Given that for highly compressible strings, δ is significantly smaller than n, it is natural to pose the following question: Can we compute δ efficiently using sublinear working space? It is straightforward to show that in the comparison model, any algorithm computing δ using 𝒪(b) space requires Ω(n^{2-o(1)}/b) time through a reduction from the element distinctness problem [Yao, SIAM J. Comput. 1994]. We thus wanted to investigate whether we can indeed match this lower bound. We address this algorithmic challenge by showing the following bounds to compute δ: - 𝒪((n³log b)/b²) time using 𝒪(b) space, for any b ∈ [1,n], in the comparison model. - 𝒪̃(n²/b) time using 𝒪̃(b) space, for any b ∈ [√n,n], in the word RAM model. This gives an 𝒪̃(n^{1+ε})-time and 𝒪̃(n^{1-ε})-space algorithm to compute δ, for any 0 < ε ≤ 1/2. Let us remark that our algorithms compute S_T(k), for all k, within the same complexities.
Cite as

Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis. Substring Complexity in Sublinear Space. In 34th International Symposium on Algorithms and Computation (ISAAC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 283, pp. 12:1-12:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bernardini_et_al:LIPIcs.ISAAC.2023.12,
  author =	{Bernardini, Giulia and Fici, Gabriele and Gawrychowski, Pawe{\l} and Pissis, Solon P.},
  title =	{{Substring Complexity in Sublinear Space}},
  booktitle =	{34th International Symposium on Algorithms and Computation (ISAAC 2023)},
  pages =	{12:1--12:19},
  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.2023.12},
  URN =		{urn:nbn:de:0030-drops-193143},
  doi =		{10.4230/LIPIcs.ISAAC.2023.12},
  annote =	{Keywords: sublinear-space algorithm, string algorithm, substring complexity}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.18
Hierarchical Relative Lempel-Ziv Compression

Authors: Philip Bille, Inge Li Gørtz, Simon J. Puglisi, and Simon R. Tarnow

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)

Abstract
Relative Lempel-Ziv (RLZ) parsing is a dictionary compression method in which a string S is compressed relative to a second string R (called the reference) by parsing S into a sequence of substrings that occur in R. RLZ is particularly effective at compressing sets of strings that have a high degree of similarity to the reference string, such as a set of genomes of individuals from the same species. With the now cheap cost of DNA sequencing, such datasets have become extremely abundant and are rapidly growing. In this paper, instead of using a single reference string for the entire collection, we investigate the use of different reference strings for subsets of the collection, with the aim of improving compression. In particular, we propose a new compression scheme hierarchical relative Lempel-Ziv (HRLZ) which form a rooted tree (or hierarchy) on the strings and then compress each string using RLZ with parent as reference, storing only the root of the tree in plain text. To decompress, we traverse the tree in BFS order starting at the root, decompressing children with respect to their parent. We show that this approach leads to a twofold improvement in compression on bacterial genome datasets, with negligible effect on decompression time compared to the standard single reference approach. We show that an effective hierarchy for a given set of strings can be constructed by computing the optimal arborescence of a completed weighted digraph of the strings, with weights as the number of phrases in the RLZ parsing of the source and destination vertices. We further show that instead of computing the complete graph, a sparse graph derived using locality-sensitive hashing can significantly reduce the cost of computing a good hierarchy, without adversely effecting compression performance.
Cite as

Philip Bille, Inge Li Gørtz, Simon J. Puglisi, and Simon R. Tarnow. Hierarchical Relative Lempel-Ziv Compression. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 18:1-18:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bille_et_al:LIPIcs.SEA.2023.18,
  author =	{Bille, Philip and G{\o}rtz, Inge Li and Puglisi, Simon J. and Tarnow, Simon R.},
  title =	{{Hierarchical Relative Lempel-Ziv Compression}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{18:1--18:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.18},
  URN =		{urn:nbn:de:0030-drops-183680},
  doi =		{10.4230/LIPIcs.SEA.2023.18},
  annote =	{Keywords: Relative compression, Lempel-Ziv compression, RLZ, LZ77, string collections, compressed representation, data structures, efficient algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.8
Optimal Near-Linear Space Heaviest Induced Ancestors

Authors: Panagiotis Charalampopoulos, Bartłomiej Dudek, Paweł Gawrychowski, and Karol Pokorski

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

Abstract
We revisit the Heaviest Induced Ancestors (HIA) problem that was introduced by Gagie, Gawrychowski, and Nekrich [CCCG 2013] and has a number of applications in string algorithms. Let T₁ and T₂ be two rooted trees whose nodes have weights that are increasing in all root-to-leaf paths, and labels on the leaves, such that no two leaves of a tree have the same label. A pair of nodes (u, v) ∈ T₁ × T₂ is induced if and only if there is a label shared by leaf-descendants of u and v. In an HIA query, given nodes x ∈ T₁ and y ∈ T₂, the goal is to find an induced pair of nodes (u, v) of the maximum total weight such that u is an ancestor of x and v is an ancestor of y. Let n be the upper bound on the sizes of the two trees. It is known that no data structure of size 𝒪̃(n) can answer HIA queries in o(log n / log log n) time [Charalampopoulos, Gawrychowski, Pokorski; ICALP 2020]. This (unconditional) lower bound is a polyloglog n factor away from the query time of the fastest 𝒪̃(n)-size data structure known to date for the HIA problem [Abedin, Hooshmand, Ganguly, Thankachan; Algorithmica 2022]. In this work, we resolve the query-time complexity of the HIA problem for the near-linear space regime by presenting a data structure that can be built in 𝒪̃(n) time and answers HIA queries in 𝒪(log n/log log n) time. As a direct corollary, we obtain an 𝒪̃(n)-size data structure that maintains the LCS of a static string and a dynamic string, both of length at most n, in time optimal for this space regime. The main ingredients of our approach are fractional cascading and the utilization of an 𝒪(log n/ log log n)-depth tree decomposition. The latter allows us to break through the Ω(log n) barrier faced by previous works, due to the depth of the considered heavy-path decompositions.
Cite as

Panagiotis Charalampopoulos, Bartłomiej Dudek, Paweł Gawrychowski, and Karol Pokorski. Optimal Near-Linear Space Heaviest Induced Ancestors. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 8:1-8:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{charalampopoulos_et_al:LIPIcs.CPM.2023.8,
  author =	{Charalampopoulos, Panagiotis and Dudek, Bart{\l}omiej and Gawrychowski, Pawe{\l} and Pokorski, Karol},
  title =	{{Optimal Near-Linear Space Heaviest Induced Ancestors}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{8:1--8:18},
  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.2023.8},
  URN =		{urn:nbn:de:0030-drops-179624},
  doi =		{10.4230/LIPIcs.CPM.2023.8},
  annote =	{Keywords: data structures, string algorithms, fractional cascading}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.12
Compressed Indexing for Consecutive Occurrences

Authors: Paweł Gawrychowski, Garance Gourdel, Tatiana Starikovskaya, and Teresa Anna Steiner

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

Abstract
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact occurrence of a given pattern P. However, practical applications motivate the necessity of considering more complex queries, for example concerning near occurrences of two patterns. Recently, Bille et al. [CPM 2021] introduced a variant of such queries, called gapped consecutive occurrences, in which a query consists of two patterns P₁ and P₂ and a range [a,b], and one must find all consecutive occurrences (q₁,q₂) of P₁ and P₂ such that q₂-q₁ ∈ [a,b]. By their results, we cannot hope for a very efficient indexing structure for such queries, even if a = 0 is fixed (although at the same time they provided a non-trivial upper bound). Motivated by this, we focus on a text given as a straight-line program (SLP) and design an index taking space polynomial in the size of the grammar that answers such queries in time optimal up to polylog factors.
Cite as

Paweł Gawrychowski, Garance Gourdel, Tatiana Starikovskaya, and Teresa Anna Steiner. Compressed Indexing for Consecutive Occurrences. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 12:1-12:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2023.12,
  author =	{Gawrychowski, Pawe{\l} and Gourdel, Garance and Starikovskaya, Tatiana and Steiner, Teresa Anna},
  title =	{{Compressed Indexing for Consecutive Occurrences}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{12:1--12:22},
  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.2023.12},
  URN =		{urn:nbn:de:0030-drops-179666},
  doi =		{10.4230/LIPIcs.CPM.2023.12},
  annote =	{Keywords: Compressed indexing, two patterns, consecutive occurrences}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.13
Order-Preserving Squares in Strings

Authors: Paweł Gawrychowski, Samah Ghazawi, and Gad M. Landau

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

Abstract
An order-preserving square in a string is a fragment of the form uv where u ≠ v and u is order-isomorphic to v. We show that a string w of length n over an alphabet of size σ contains 𝒪(σn) order-preserving squares that are distinct as words. This improves the upper bound of 𝒪(σ²n) by Kociumaka, Radoszewski, Rytter, and Waleń [TCS 2016]. Further, for every σ and n we exhibit a string with Ω(σn) order-preserving squares that are distinct as words, thus establishing that our upper bound is asymptotically tight. Finally, we design an 𝒪(σn) time algorithm that outputs all order-preserving squares that occur in a given string and are distinct as words. By our lower bound, this is optimal in the worst case.
Cite as

Paweł Gawrychowski, Samah Ghazawi, and Gad M. Landau. Order-Preserving Squares in Strings. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 13:1-13:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2023.13,
  author =	{Gawrychowski, Pawe{\l} and Ghazawi, Samah and Landau, Gad M.},
  title =	{{Order-Preserving Squares in Strings}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{13:1--13:19},
  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.2023.13},
  URN =		{urn:nbn:de:0030-drops-179676},
  doi =		{10.4230/LIPIcs.CPM.2023.13},
  annote =	{Keywords: repetitions, distinct squares, order-isomorphism}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2022.32
Finding the KT Partition of a Weighted Graph in Near-Linear Time

Authors: Simon Apers, Paweł Gawrychowski, and Troy Lee

Published in: LIPIcs, Volume 245, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022)

Abstract
In a breakthrough work, Kawarabayashi and Thorup (J. ACM'19) gave a near-linear time deterministic algorithm to compute the weight of a minimum cut in a simple graph G = (V,E). A key component of this algorithm is finding the (1+ε)-KT partition of G, the coarsest partition {P_1, …, P_k} of V such that for every non-trivial (1+ε)-near minimum cut with sides {S, ̄{S}} it holds that P_i is contained in either S or ̄{S}, for i = 1, …, k. In this work we give a near-linear time randomized algorithm to find the (1+ε)-KT partition of a weighted graph. Our algorithm is quite different from that of Kawarabayashi and Thorup and builds on Karger’s framework of tree-respecting cuts (J. ACM'00). We describe a number of applications of the algorithm. (i) The algorithm makes progress towards a more efficient algorithm for constructing the polygon representation of the set of near-minimum cuts in a graph. This is a generalization of the cactus representation, and was initially described by Benczúr (FOCS'95). (ii) We improve the time complexity of a recent quantum algorithm for minimum cut in a simple graph in the adjacency list model from Õ(n^{3/2}) to Õ(√{mn}), when the graph has n vertices and m edges. (iii) We describe a new type of randomized algorithm for minimum cut in simple graphs with complexity 𝒪(m + n log⁶ n). For graphs that are not too sparse, this matches the complexity of the current best 𝒪(m + n log² n) algorithm which uses a different approach based on random contractions. The key technical contribution of our work is the following. Given a weighted graph G with m edges and a spanning tree T of G, consider the graph H whose nodes are the edges of T, and where there is an edge between two nodes of H iff the corresponding 2-respecting cut of T is a non-trivial near-minimum cut of G. We give a 𝒪(m log⁴ n) time deterministic algorithm to compute a spanning forest of H.
Cite as

Simon Apers, Paweł Gawrychowski, and Troy Lee. Finding the KT Partition of a Weighted Graph in Near-Linear Time. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 245, pp. 32:1-32:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{apers_et_al:LIPIcs.APPROX/RANDOM.2022.32,
  author =	{Apers, Simon and Gawrychowski, Pawe{\l} and Lee, Troy},
  title =	{{Finding the KT Partition of a Weighted Graph in Near-Linear Time}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022)},
  pages =	{32:1--32:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-249-5},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{245},
  editor =	{Chakrabarti, Amit and Swamy, Chaitanya},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2022.32},
  URN =		{urn:nbn:de:0030-drops-171544},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2022.32},
  annote =	{Keywords: Graph theory}
}
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.2022.67
Sublinear Dynamic Interval Scheduling (On One or Multiple Machines)

Authors: Paweł Gawrychowski and Karol Pokorski

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

Abstract
We revisit the complexity of the classical Interval Scheduling in the dynamic setting. In this problem, the goal is to maintain a set of intervals under insertions and deletions and report the size of the maximum size subset of pairwise disjoint intervals after each update. Nontrivial approximation algorithms are known for this problem, for both the unweighted and weighted versions [Henzinger, Neumann, Wiese, SoCG 2020]. Surprisingly, it was not known if the general exact version admits an exact solution working in sublinear time, that is, without recomputing the answer after each update. Our first contribution is a structure for Dynamic Interval Scheduling with amortized 𝒪̃(n^{1/3}) update time. Then, building on the ideas used for the case of one machine, we design a sublinear solution for any constant number of machines: we describe a structure for Dynamic Interval Scheduling on m ≥ 2 machines with amortized 𝒪̃(n^{1 - 1/m}) update time. We complement the above results by considering Dynamic Weighted Interval Scheduling on one machine, that is maintaining (the weight of) the maximum weight subset of pairwise disjoint intervals. We show an almost linear lower bound (conditioned on the hardness of Minimum Weight k-Clique) for the update/query time of any structure for this problem. Hence, in the weighted case one should indeed seek approximate solutions.
Cite as

Paweł Gawrychowski and Karol Pokorski. Sublinear Dynamic Interval Scheduling (On One or Multiple Machines). In 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 229, pp. 67:1-67:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{gawrychowski_et_al:LIPIcs.ICALP.2022.67,
  author =	{Gawrychowski, Pawe{\l} and Pokorski, Karol},
  title =	{{Sublinear Dynamic Interval Scheduling (On One or Multiple Machines)}},
  booktitle =	{49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)},
  pages =	{67:1--67:19},
  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.2022.67},
  URN =		{urn:nbn:de:0030-drops-164086},
  doi =		{10.4230/LIPIcs.ICALP.2022.67},
  annote =	{Keywords: interval scheduling, dynamic problems, data structures, greedy algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.14
Cartesian Tree Subsequence Matching

Authors: Tsubasa Oizumi, Takeshi Kai, Takuya Mieno, Shunsuke Inenaga, and Hiroki Arimura

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

Abstract
Park et al. [TCS 2020] observed that the similarity between two (numerical) strings can be captured by the Cartesian trees: The Cartesian tree of a string is a binary tree recursively constructed by picking up the smallest value of the string as the root of the tree. Two strings of equal length are said to Cartesian-tree match if their Cartesian trees are isomorphic. Park et al. [TCS 2020] introduced the following Cartesian tree substring matching (CTMStr) problem: Given a text string T of length n and a pattern string of length m, find every consecutive substring S = T[i..j] of a text string T such that S and P Cartesian-tree match. They showed how to solve this problem in Õ(n+m) time. In this paper, we introduce the Cartesian tree subsequence matching (CTMSeq) problem, that asks to find every minimal substring S = T[i..j] of T such that S contains a subsequence S' which Cartesian-tree matches P. We prove that the CTMSeq problem can be solved efficiently, in O(m n p(n)) time, where p(n) denotes the update/query time for dynamic predecessor queries. By using a suitable dynamic predecessor data structure, we obtain O(mn log log n)-time and O(n log m)-space solution for CTMSeq. This contrasts CTMSeq with closely related order-preserving subsequence matching (OPMSeq) which was shown to be NP-hard by Bose et al. [IPL 1998].
Cite as

Tsubasa Oizumi, Takeshi Kai, Takuya Mieno, Shunsuke Inenaga, and Hiroki Arimura. Cartesian Tree Subsequence Matching. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 14:1-14:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{oizumi_et_al:LIPIcs.CPM.2022.14,
  author =	{Oizumi, Tsubasa and Kai, Takeshi and Mieno, Takuya and Inenaga, Shunsuke and Arimura, Hiroki},
  title =	{{Cartesian Tree Subsequence Matching}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{14:1--14:18},
  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.2022.14},
  URN =		{urn:nbn:de:0030-drops-161414},
  doi =		{10.4230/LIPIcs.CPM.2022.14},
  annote =	{Keywords: string algorithms, pattern matching, Cartesian tree subsequence matching, order preserving matching, episode matching}
}
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.2021.45
Compression by Contracting Straight-Line Programs

Authors: Moses Ganardi

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

Abstract
In grammar-based compression a string is represented by a context-free grammar, also called a straight-line program (SLP), that generates only that string. We refine a recent balancing result stating that one can transform an SLP of size g in linear time into an equivalent SLP of size 𝒪(g) so that the height of the unique derivation tree is 𝒪(log N) where N is the length of the represented string (FOCS 2019). We introduce a new class of balanced SLPs, called contracting SLPs, where for every rule A → β₁ … β_k the string length of every variable β_i on the right-hand side is smaller by a constant factor than the string length of A. In particular, the derivation tree of a contracting SLP has the property that every subtree has logarithmic height in its leaf size. We show that a given SLP of size g can be transformed in linear time into an equivalent contracting SLP of size 𝒪(g) with rules of constant length. This result is complemented by a lower bound, proving that converting SLPs into so called α-balanced SLPs or AVL-grammars can incur an increase by a factor of Ω(log N). We present an application to the navigation problem in compressed unranked trees, represented by forest straight-line programs (FSLPs). A linear space data structure by Reh and Sieber (2020) supports navigation steps such as going to the parent, left/right sibling, or to the first/last child in constant time. We extend their solution by the operation of moving to the i-th child in time 𝒪(log d) where d is the degree of the current node. Contracting SLPs are also applied to the finger search problem over SLP-compressed strings where one wants to access positions near to a pre-specified finger position, ideally in 𝒪(log d) time where d is the distance between the accessed position and the finger. We give a linear space solution for the dynamic variant where one can set the finger in 𝒪(log N) time, and then access symbols or move the finger in time 𝒪(log d + log^(t) N) for any constant t where log^(t) N is the t-fold logarithm of N. This improves a previous solution by Bille, Christiansen, Cording, and Gørtz (2018) with access/move time 𝒪(log d + log log N).
Cite as

Moses Ganardi. Compression by Contracting Straight-Line Programs. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 45:1-45:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)

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@InProceedings{ganardi:LIPIcs.ESA.2021.45,
  author =	{Ganardi, Moses},
  title =	{{Compression by Contracting Straight-Line Programs}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{45:1--45:16},
  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.2021.45},
  URN =		{urn:nbn:de:0030-drops-146263},
  doi =		{10.4230/LIPIcs.ESA.2021.45},
  annote =	{Keywords: grammar-based compression, balancing, finger search}
}
Document
DOI: 10.4230/LIPIcs.ESA.2021.77
Hardness of Detecting Abelian and Additive Square Factors in Strings

Authors: Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, and Wiktor Zuba

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

Abstract
We prove 3SUM-hardness (no strongly subquadratic-time algorithm, assuming the 3SUM conjecture) of several problems related to finding Abelian square and additive square factors in a string. In particular, we conclude conditional optimality of the state-of-the-art algorithms for finding such factors. Overall, we show 3SUM-hardness of (a) detecting an Abelian square factor of an odd half-length, (b) computing centers of all Abelian square factors, (c) detecting an additive square factor in a length-n string of integers of magnitude n^{𝒪(1)}, and (d) a problem of computing a double 3-term arithmetic progression (i.e., finding indices i ≠ j such that (x_i+x_j)/2 = x_{(i+j)/2}) in a sequence of integers x₁,… ,x_n of magnitude n^{𝒪(1)}. Problem (d) is essentially a convolution version of the AVERAGE problem that was proposed in a manuscript of Erickson. We obtain a conditional lower bound for it with the aid of techniques recently developed by Dudek et al. [STOC 2020]. Problem (d) immediately reduces to problem (c) and is a step in reductions to problems (a) and (b). In conditional lower bounds for problems (a) and (b) we apply an encoding of Amir et al. [ICALP 2014] and extend it using several string gadgets that include arbitrarily long Abelian-square-free strings. Our reductions also imply conditional lower bounds for detecting Abelian squares in strings over a constant-sized alphabet. We also show a subquadratic upper bound in this case, applying a result of Chan and Lewenstein [STOC 2015].
Cite as

Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, and Wiktor Zuba. Hardness of Detecting Abelian and Additive Square Factors in Strings. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 77:1-77:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)

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@InProceedings{radoszewski_et_al:LIPIcs.ESA.2021.77,
  author =	{Radoszewski, Jakub and Rytter, Wojciech and Straszy\'{n}ski, Juliusz and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Hardness of Detecting Abelian and Additive Square Factors in Strings}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{77:1--77:19},
  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.2021.77},
  URN =		{urn:nbn:de:0030-drops-146581},
  doi =		{10.4230/LIPIcs.ESA.2021.77},
  annote =	{Keywords: Abelian square, additive square, 3SUM problem}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2021.48
Matching Patterns with Variables Under Hamming Distance

Authors: Paweł Gawrychowski, Florin Manea, and Stefan Siemer

Published in: LIPIcs, Volume 202, 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021)

Abstract
A pattern α is a string of variables and terminal letters. We say that α matches a word w, consisting only of terminal letters, if w can be obtained by replacing the variables of α by terminal words. The matching problem, i.e., deciding whether a given pattern matches a given word, was heavily investigated: it is NP-complete in general, but can be solved efficiently for classes of patterns with restricted structure. In this paper, we approach this problem in a generalized setting, by considering approximate pattern matching under Hamming distance. More precisely, we are interested in what is the minimum Hamming distance between w and any word u obtained by replacing the variables of α by terminal words. Firstly, we address the class of regular patterns (in which no variable occurs twice) and propose efficient algorithms for this problem, as well as matching conditional lower bounds. We show that the problem can still be solved efficiently if we allow repeated variables, but restrict the way the different variables can be interleaved according to a locality parameter. However, as soon as we allow a variable to occur more than once and its occurrences can be interleaved arbitrarily with those of other variables, even if none of them occurs more than once, the problem becomes intractable.
Cite as

Paweł Gawrychowski, Florin Manea, and Stefan Siemer. Matching Patterns with Variables Under Hamming Distance. In 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 202, pp. 48:1-48:24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)

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@InProceedings{gawrychowski_et_al:LIPIcs.MFCS.2021.48,
  author =	{Gawrychowski, Pawe{\l} and Manea, Florin and Siemer, Stefan},
  title =	{{Matching Patterns with Variables Under Hamming Distance}},
  booktitle =	{46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021)},
  pages =	{48:1--48:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-201-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{202},
  editor =	{Bonchi, Filippo and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2021.48},
  URN =		{urn:nbn:de:0030-drops-144886},
  doi =		{10.4230/LIPIcs.MFCS.2021.48},
  annote =	{Keywords: Pattern with variables, Matching algorithms, Hamming distance, Conditional lower bounds, Patterns with structural restrictions}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2021.48
An Almost Optimal Edit Distance Oracle

Authors: Panagiotis Charalampopoulos, Paweł Gawrychowski, Shay Mozes, and Oren Weimann

Published in: LIPIcs, Volume 198, 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)

Abstract
We consider the problem of preprocessing two strings S and T, of lengths m and n, respectively, in order to be able to efficiently answer the following queries: Given positions i,j in S and positions a,b in T, return the optimal alignment score of S[i..j] and T[a..b]. Let N = mn. We present an oracle with preprocessing time N^{1+o(1)} and space N^{1+o(1)} that answers queries in log^{2+o(1)}N time. In other words, we show that we can efficiently query for the alignment score of every pair of substrings after preprocessing the input for almost the same time it takes to compute just the alignment of S and T. Our oracle uses ideas from our distance oracle for planar graphs [STOC 2019] and exploits the special structure of the alignment graph. Conditioned on popular hardness conjectures, this result is optimal up to subpolynomial factors. Our results apply to both edit distance and longest common subsequence (LCS). The best previously known oracle with construction time and size 𝒪(N) has slow Ω(√N) query time [Sakai, TCS 2019], and the one with size N^{1+o(1)} and query time log^{2+o(1)}N (using a planar graph distance oracle) has slow Ω(N^{3/2}) construction time [Long & Pettie, SODA 2021]. We improve both approaches by roughly a √ N factor.
Cite as

Panagiotis Charalampopoulos, Paweł Gawrychowski, Shay Mozes, and Oren Weimann. An Almost Optimal Edit Distance Oracle. In 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 198, pp. 48:1-48:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)

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@InProceedings{charalampopoulos_et_al:LIPIcs.ICALP.2021.48,
  author =	{Charalampopoulos, Panagiotis and Gawrychowski, Pawe{\l} and Mozes, Shay and Weimann, Oren},
  title =	{{An Almost Optimal Edit Distance Oracle}},
  booktitle =	{48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)},
  pages =	{48:1--48:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-195-5},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{198},
  editor =	{Bansal, Nikhil and Merelli, Emanuela and Worrell, James},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2021.48},
  URN =		{urn:nbn:de:0030-drops-141175},
  doi =		{10.4230/LIPIcs.ICALP.2021.48},
  annote =	{Keywords: longest common subsequence, edit distance, planar graphs, Voronoi diagrams}
}
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