40 Search Results for "Bulteau, Laurent"


Volume

LIPIcs, Volume 259

34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

CPM 2023, June 26-28, 2023, Marne-la-Vallée, France

Editors: Laurent Bulteau and Zsuzsanna Lipták

Document
Track A: Algorithms, Complexity and Games
Breaking a Barrier in Constructing Compact Indexes for Parameterized Pattern Matching

Authors: Kento Iseri, Tomohiro I, Diptarama Hendrian, Dominik Köppl, Ryo Yoshinaka, and Ayumi Shinohara

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
A parameterized string (p-string) is a string over an alphabet (Σ_s ∪ Σ_p), where Σ_s and Σ_p are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively. Two p-strings x and y are said to parameterized match (p-match) if and only if x can be transformed into y by applying a bijection on Σ_p to every occurrence of p-symbols in x. The indexing problem for p-matching is to preprocess a p-string T of length n so that we can efficiently find the occurrences of substrings of T that p-match with a given pattern. Let σ_s and respectively σ_p be the numbers of distinct s-symbols and p-symbols that appear in T and σ = σ_s + σ_p. Extending the Burrows-Wheeler Transform (BWT) based index for exact string pattern matching, Ganguly et al. [SODA 2017] proposed parameterized BWTs (pBWTs) to design the first compact index for p-matching, and posed an open problem on how to construct the pBWT-based index in compact space, i.e., in O(n lg |Σ_s ∪ Σ_p|) bits of space. Hashimoto et al. [SPIRE 2022] showed how to construct the pBWT for T, under the assumption that Σ_s ∪ Σ_p = [0..O(σ)], in O(n lg σ) bits of space and O(n (σ_p lg n)/(lg lg n)) time in an online manner while reading the symbols of T from right to left. In this paper, we refine Hashimoto et al.’s algorithm to work in O(n lg σ) bits of space and O(n (lg σ_p lg n)/(lg lg n)) time in a more general assumption that Σ_s ∪ Σ_p = [0..n^{O(1)}]. Our result has an immediate application to constructing parameterized suffix arrays in O(n (lg σ_p lg n)/(lg lg n)) time and O(n lg σ) bits of working space. We also show that our data structure can support backward search, a core procedure of BWT-based indexes, at any stage of the online construction, making it the first compact index for p-matching that can be constructed in compact space and even in an online manner.

Cite as

Kento Iseri, Tomohiro I, Diptarama Hendrian, Dominik Köppl, Ryo Yoshinaka, and Ayumi Shinohara. Breaking a Barrier in Constructing Compact Indexes for Parameterized Pattern Matching. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 89:1-89:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{iseri_et_al:LIPIcs.ICALP.2024.89,
  author =	{Iseri, Kento and I, Tomohiro and Hendrian, Diptarama and K\"{o}ppl, Dominik and Yoshinaka, Ryo and Shinohara, Ayumi},
  title =	{{Breaking a Barrier in Constructing Compact Indexes for Parameterized Pattern Matching}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{89:1--89:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.89},
  URN =		{urn:nbn:de:0030-drops-202324},
  doi =		{10.4230/LIPIcs.ICALP.2024.89},
  annote =	{Keywords: Index for parameterized pattern matching, Parameterized Burrows-Wheeler Transform, Online construction}
}
Document
Complete Volume
LIPIcs, Volume 259, CPM 2023, Complete Volume

Authors: Laurent Bulteau and Zsuzsanna Lipták

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


Abstract
LIPIcs, Volume 259, CPM 2023, Complete Volume

Cite as

34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 1-472, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@Proceedings{bulteau_et_al:LIPIcs.CPM.2023,
  title =	{{LIPIcs, Volume 259, CPM 2023, Complete Volume}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{1--472},
  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},
  URN =		{urn:nbn:de:0030-drops-179536},
  doi =		{10.4230/LIPIcs.CPM.2023},
  annote =	{Keywords: LIPIcs, Volume 259, CPM 2023, Complete Volume}
}
Document
Front Matter
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Laurent Bulteau and Zsuzsanna Lipták

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


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

Cite as

34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{bulteau_et_al:LIPIcs.CPM.2023.0,
  author =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{0:i--0:xvi},
  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.2023.0},
  URN =		{urn:nbn:de:0030-drops-179542},
  doi =		{10.4230/LIPIcs.CPM.2023.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
Trie-Compressed Adaptive Set Intersection

Authors: Diego Arroyuelo and Juan Pablo Castillo

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


Abstract
We introduce space- and time-efficient algorithms and data structures for the offline set intersection problem. We show that a sorted integer set S ⊆ [0..u) of n elements can be represented using compressed space while supporting k-way intersections in adaptive O(kδlg(u/δ)) time, δ being the alternation measure introduced by Barbay and Kenyon. Our experimental results suggest that our approaches are competitive in practice, outperforming the most efficient alternatives (Partitioned Elias-Fano indexes, Roaring Bitmaps, and Recursive Universe Partitioning (RUP)) in several scenarios, offering in general relevant space-time trade-offs.

Cite as

Diego Arroyuelo and Juan Pablo Castillo. Trie-Compressed Adaptive Set Intersection. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{arroyuelo_et_al:LIPIcs.CPM.2023.1,
  author =	{Arroyuelo, Diego and Castillo, Juan Pablo},
  title =	{{Trie-Compressed Adaptive Set Intersection}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{1:1--1:19},
  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.2023.1},
  URN =		{urn:nbn:de:0030-drops-179552},
  doi =		{10.4230/LIPIcs.CPM.2023.1},
  annote =	{Keywords: Set intersection problem, Adaptive Algorithms, Compressed and compact data structures}
}
Document
Approximation Algorithms for the Longest Run Subsequence Problem

Authors: Yuichi Asahiro, Hiroshi Eto, Mingyang Gong, Jesper Jansson, Guohui Lin, Eiji Miyano, Hirotaka Ono, and Shunichi Tanaka

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


Abstract
We study the approximability of the Longest Run Subsequence problem (LRS for short). For a string S = s_1 ⋯ s_n over an alphabet Σ, a run of a symbol σ ∈ Σ in S is a maximal substring of consecutive occurrences of σ. A run subsequence S' of S is a sequence in which every symbol σ ∈ Σ occurs in at most one run. Given a string S, the goal of LRS is to find a longest run subsequence S^* of S such that the length |S^*| is maximized over all the run subsequences of S. It is known that LRS is APX-hard even if each symbol has at most two occurrences in the input string, and that LRS admits a polynomial-time k-approximation algorithm if the number of occurrences of every symbol in the input string is bounded by k. In this paper, we design a polynomial-time (k+1)/2-approximation algorithm for LRS under the k-occurrence constraint on input strings. For the case k = 2, we further improve the approximation ratio from 3/2 to 4/3.

Cite as

Yuichi Asahiro, Hiroshi Eto, Mingyang Gong, Jesper Jansson, Guohui Lin, Eiji Miyano, Hirotaka Ono, and Shunichi Tanaka. Approximation Algorithms for the Longest Run Subsequence Problem. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 2:1-2:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{asahiro_et_al:LIPIcs.CPM.2023.2,
  author =	{Asahiro, Yuichi and Eto, Hiroshi and Gong, Mingyang and Jansson, Jesper and Lin, Guohui and Miyano, Eiji and Ono, Hirotaka and Tanaka, Shunichi},
  title =	{{Approximation Algorithms for the Longest Run Subsequence Problem}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{2:1--2:12},
  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.2023.2},
  URN =		{urn:nbn:de:0030-drops-179560},
  doi =		{10.4230/LIPIcs.CPM.2023.2},
  annote =	{Keywords: Longest run subsequence problem, bounded occurrence, approximation algorithm}
}
Document
Optimal LZ-End Parsing Is Hard

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

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


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

Cite as

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


Copy BibTex To Clipboard

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

Authors: Philip Bille, Johannes Fischer, Inge Li Gørtz, Max Rishøj Pedersen, and Tord Joakim Stordalen

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


Abstract
Given a string S over an alphabet Σ, the string indexing problem is to preprocess S to subsequently support efficient pattern matching queries, that is, given a pattern string P report all the occurrences of P in S. In this paper we study the streaming sliding window string indexing problem. Here the string S arrives as a stream, one character at a time, and the goal is to maintain an index of the last w characters, called the window, for a specified parameter w. At any point in time a pattern matching query for a pattern P may arrive, also streamed one character at a time, and all occurrences of P within the current window must be returned. The streaming sliding window string indexing problem naturally captures scenarios where we want to index the most recent data (i.e. the window) of a stream while supporting efficient pattern matching. Our main result is a simple O(w) space data structure that uses O(log w) time with high probability to process each character from both the input string S and any pattern string P. Reporting each occurrence of P uses additional constant time per reported occurrence. Compared to previous work in similar scenarios this result is the first to achieve an efficient worst-case time per character from the input stream with high probability. We also consider a delayed variant of the problem, where a query may be answered at any point within the next δ characters that arrive from either stream. We present an O(w + δ) space data structure for this problem that improves the above time bounds to O(log (w/δ)). In particular, for a delay of δ = ε w we obtain an O(w) space data structure with constant time processing per character. The key idea to achieve our result is a novel and simple hierarchical structure of suffix trees of independent interest, inspired by the classic log-structured merge trees.

Cite as

Philip Bille, Johannes Fischer, Inge Li Gørtz, Max Rishøj Pedersen, and Tord Joakim Stordalen. Sliding Window String Indexing in Streams. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{bille_et_al:LIPIcs.CPM.2023.4,
  author =	{Bille, Philip and Fischer, Johannes and G{\o}rtz, Inge Li and Pedersen, Max Rish{\o}j and Stordalen, Tord Joakim},
  title =	{{Sliding Window String Indexing in Streams}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{4:1--4:18},
  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.2023.4},
  URN =		{urn:nbn:de:0030-drops-179587},
  doi =		{10.4230/LIPIcs.CPM.2023.4},
  annote =	{Keywords: String indexing, pattern matching, sliding window, streaming}
}
Document
Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor

Authors: Itai Boneh, Dvir Fried, Adrian Miclăuş, and Alexandru Popa

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


Abstract
Hairpin completion is an operation on formal languages that has been inspired by hairpin formation in DNA biochemistry and has many applications especially in DNA computing. Consider s to be a string over the alphabet {A, C, G, T} such that a prefix/suffix of it matches the reversed complement of a substring of s. Then, in a hairpin completion operation the reversed complement of this prefix/suffix is added to the start/end of s forming a new string. In this paper we study two problems related to the hairpin completion. The first problem asks the minimum number of hairpin operations necessary to transform one string into another, number that is called the hairpin completion distance. For this problem we show an algorithm of running time O(n²), where n is the maximum length of the two strings. Our algorithm improves on the algorithm of Manea (TCS 2010), that has running time O(n² log n). In the minimum distance common hairpin completion ancestor problem we want to find, for two input strings x and y, a string w that minimizes the sum of the hairpin completion distances to x and y. Similarly, we present an algorithm with running time O(n²) that improves by a O(log n) factor the algorithm of Manea (TCS 2010).

Cite as

Itai Boneh, Dvir Fried, Adrian Miclăuş, and Alexandru Popa. Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 5:1-5:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{boneh_et_al:LIPIcs.CPM.2023.5,
  author =	{Boneh, Itai and Fried, Dvir and Micl\u{a}u\c{s}, Adrian and Popa, Alexandru},
  title =	{{Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{5:1--5:18},
  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.2023.5},
  URN =		{urn:nbn:de:0030-drops-179592},
  doi =		{10.4230/LIPIcs.CPM.2023.5},
  annote =	{Keywords: dynamic programming, incremental trees, exact algorithm}
}
Document
On Distances Between Words with Parameters

Authors: Pierre Bourhis, Aaron Boussidan, and Philippe Gambette

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


Abstract
The edit distance between parameterized words is a generalization of the classical edit distance where it is allowed to map particular letters of the first word, called parameters, to parameters of the second word before computing the distance. This problem has been introduced in particular for detection of code duplication, and the notion of words with parameters has also been used with different semantics in other fields. The complexity of several variants of edit distances between parameterized words has been studied, however, the complexity of the most natural one, the Levenshtein distance, remained open. In this paper, we solve this open question and close the exhaustive analysis of all cases of parameterized word matching and function matching, showing that these problems are np-complete. To this aim, we also provide a comparison of the different problems, exhibiting several equivalences between them. We also provide and implement a MaxSAT encoding of the problem, as well as a simple FPT algorithm in the alphabet size, and study their efficiency on real data in the context of theater play structure comparison.

Cite as

Pierre Bourhis, Aaron Boussidan, and Philippe Gambette. On Distances Between Words with Parameters. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{bourhis_et_al:LIPIcs.CPM.2023.6,
  author =	{Bourhis, Pierre and Boussidan, Aaron and Gambette, Philippe},
  title =	{{On Distances Between Words with Parameters}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{6:1--6:23},
  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.2023.6},
  URN =		{urn:nbn:de:0030-drops-179602},
  doi =		{10.4230/LIPIcs.CPM.2023.6},
  annote =	{Keywords: String matching, edit distance, Levenshtein, parameterized matching, parameterized words, parameter words, instantiable words, NP-completeness, MAX-SAT}
}
Document
Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond

Authors: Manuel Cáceres

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


Abstract
The problem of String Matching to Labeled Graphs (SMLG) asks to find all the paths in a labeled graph G = (V, E) whose spellings match that of an input string S ∈ Σ^m. SMLG can be solved in quadratic O(m|E|) time [Amir et al., JALG 2000], which was proven to be optimal by a recent lower bound conditioned on SETH [Equi et al., ICALP 2019]. The lower bound states that no strongly subquadratic time algorithm exists, even if restricted to directed acyclic graphs (DAGs). In this work we present the first parameterized algorithms for SMLG on DAGs. Our parameters capture the topological structure of G. All our results are derived from a generalization of the Knuth-Morris-Pratt algorithm [Park and Kim, CPM 1995] optimized to work in time proportional to the number of prefix-incomparable matches. To obtain the parameterization in the topological structure of G, we first study a special class of DAGs called funnels [Millani et al., JCO 2020] and generalize them to k-funnels and the class ST_k. We present several novel characterizations and algorithmic contributions on both funnels and their generalizations.

Cite as

Manuel Cáceres. Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{caceres:LIPIcs.CPM.2023.7,
  author =	{C\'{a}ceres, Manuel},
  title =	{{Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{7:1--7:19},
  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.2023.7},
  URN =		{urn:nbn:de:0030-drops-179619},
  doi =		{10.4230/LIPIcs.CPM.2023.7},
  annote =	{Keywords: string matching, parameterized algorithms, FPT inside P, string algorithms, graph algorithms, directed acyclic graphs, labeled graphs, funnels}
}
Document
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)


Copy BibTex To Clipboard

@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
From Bit-Parallelism to Quantum String Matching for Labelled Graphs

Authors: Massimo Equi, Arianne Meijer-van de Griend, and Veli Mäkinen

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


Abstract
Many problems that can be solved in quadratic time have bit-parallel speed-ups with factor w, where w is the computer word size. A classic example is computing the edit distance of two strings of length n, which can be solved in O(n²/w) time. In a reasonable classical model of computation, one can assume w = Θ(log n), and obtaining significantly better speed-ups is unlikely in the light of conditional lower bounds obtained for such problems. In this paper, we study the connection of bit-parallelism to quantum computation, aiming to see if a bit-parallel algorithm could be converted to a quantum algorithm with better than logarithmic speed-up. We focus on string matching in labeled graphs, the problem of finding an exact occurrence of a string as the label of a path in a graph. This problem admits a quadratic conditional lower bound under a very restricted class of graphs (Equi et al. ICALP 2019), stating that no algorithm in the classical model of computation can solve the problem in time O(|P||E|^(1-ε)) or O(|P|^(1-ε)|E|). We show that a simple bit-parallel algorithm on such restricted family of graphs (level DAGs) can indeed be converted into a realistic quantum algorithm that attains subquadratic time complexity O(|E|√|P|).

Cite as

Massimo Equi, Arianne Meijer-van de Griend, and Veli Mäkinen. From Bit-Parallelism to Quantum String Matching for Labelled Graphs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{equi_et_al:LIPIcs.CPM.2023.9,
  author =	{Equi, Massimo and Meijer-van de Griend, Arianne and M\"{a}kinen, Veli},
  title =	{{From Bit-Parallelism to Quantum String Matching for Labelled Graphs}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{9:1--9:20},
  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.2023.9},
  URN =		{urn:nbn:de:0030-drops-179637},
  doi =		{10.4230/LIPIcs.CPM.2023.9},
  annote =	{Keywords: Bit-parallelism, quantum computation, string matching, level DAGs}
}
Document
On the Impact of Morphisms on BWT-Runs

Authors: Gabriele Fici, Giuseppe Romana, Marinella Sciortino, and Cristian Urbina

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


Abstract
Morphisms are widely studied combinatorial objects that can be used for generating infinite families of words. In the context of Information theory, injective morphisms are called (variable length) codes. In Data compression, the morphisms, combined with parsing techniques, have been recently used to define new mechanisms to generate repetitive words. Here, we show that the repetitiveness induced by applying a morphism to a word can be captured by a compression scheme based on the Burrows-Wheeler Transform (BWT). In fact, we prove that, differently from other compression-based repetitiveness measures, the measure r_bwt (which counts the number of equal-letter runs produced by applying BWT to a word) strongly depends on the applied morphism. More in detail, we characterize the binary morphisms that preserve the value of r_bwt(w), when applied to any binary word w containing both letters. They are precisely the Sturmian morphisms, which are well-known objects in Combinatorics on words. Moreover, we prove that it is always possible to find a binary morphism that, when applied to any binary word containing both letters, increases the number of BWT-equal letter runs by a given (even) number. In addition, we derive a method for constructing arbitrarily large families of binary words on which BWT produces a given (even) number of new equal-letter runs. Such results are obtained by using a new class of morphisms that we call Thue-Morse-like. Finally, we show that there exist binary morphisms μ for which it is possible to find words w such that the difference r_bwt(μ(w))-r_bwt(w) is arbitrarily large.

Cite as

Gabriele Fici, Giuseppe Romana, Marinella Sciortino, and Cristian Urbina. On the Impact of Morphisms on BWT-Runs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{fici_et_al:LIPIcs.CPM.2023.10,
  author =	{Fici, Gabriele and Romana, Giuseppe and Sciortino, Marinella and Urbina, Cristian},
  title =	{{On the Impact of Morphisms on BWT-Runs}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{10:1--10:18},
  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.2023.10},
  URN =		{urn:nbn:de:0030-drops-179641},
  doi =		{10.4230/LIPIcs.CPM.2023.10},
  annote =	{Keywords: Morphism, Burrows-Wheeler transform, Sturmian word, Sturmian morphism, Thue-Morse morphism, Repetitiveness measure}
}
Document
Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications

Authors: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, and Wiktor Zuba

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


Abstract
An elastic-degenerate (ED) string T is a sequence of n sets T[1],…,T[n] containing m strings in total whose cumulative length is N. We call n, m, and N the length, the cardinality and the size of T, respectively. The language of T is defined as ℒ(T) = {S_1 ⋯ S_n : S_i ∈ T[i] for all i ∈ [1,n]}. ED strings have been introduced to represent a set of closely-related DNA sequences, also known as a pangenome. The basic question we investigate here is: Given two ED strings, how fast can we check whether the two languages they represent have a nonempty intersection? We call the underlying problem the ED String Intersection (EDSI) problem. For two ED strings T₁ and T₂ of lengths n₁ and n₂, cardinalities m₁ and m₂, and sizes N₁ and N₂, respectively, we show the following: - There is no 𝒪((N₁N₂)^{1-ε})-time algorithm, thus no 𝒪((N₁m₂+N₂m₁)^{1-ε})-time algorithm and no 𝒪((N₁n₂+N₂n₁)^{1-ε})-time algorithm, for any constant ε > 0, for EDSI even when T₁ and T₂ are over a binary alphabet, unless the Strong Exponential-Time Hypothesis is false. - There is no combinatorial 𝒪((N₁+N₂)^{1.2-ε}f(n₁,n₂))-time algorithm, for any constant ε > 0 and any function f, for EDSI even when T₁ and T₂ are over a binary alphabet, unless the Boolean Matrix Multiplication conjecture is false. - An 𝒪(N₁log N₁log n₁+N₂log N₂log n₂)-time algorithm for outputting a compact (RLE) representation of the intersection language of two unary ED strings. In the case when T₁ and T₂ are given in a compact representation, we show that the problem is NP-complete. - An 𝒪(N₁m₂+N₂m₁)-time algorithm for EDSI. - An Õ(N₁^{ω-1}n₂+N₂^{ω-1}n₁)-time algorithm for EDSI, where ω is the exponent of matrix multiplication; the Õ notation suppresses factors that are polylogarithmic in the input size. We also show that the techniques we develop have applications outside of ED string comparison.

Cite as

Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, and Wiktor Zuba. Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{gabory_et_al:LIPIcs.CPM.2023.11,
  author =	{Gabory, Esteban and Mwaniki, Moses Njagi and Pisanti, Nadia and Pissis, Solon P. and Radoszewski, Jakub and Sweering, Michelle and Zuba, Wiktor},
  title =	{{Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{11:1--11:20},
  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.2023.11},
  URN =		{urn:nbn:de:0030-drops-179650},
  doi =		{10.4230/LIPIcs.CPM.2023.11},
  annote =	{Keywords: elastic-degenerate string, sequence comparison, languages intersection, pangenome, acronym identification}
}
  • Refine by Author
  • 12 Bulteau, Laurent
  • 3 Fertin, Guillaume
  • 3 Gawrychowski, Paweł
  • 3 Marchand, Bertrand
  • 3 Ponty, Yann
  • Show More...

  • Refine by Classification
  • 18 Theory of computation → Pattern matching
  • 7 Theory of computation → Data compression
  • 6 Theory of computation → Design and analysis of algorithms
  • 5 Theory of computation → Parameterized complexity and exact algorithms
  • 4 Mathematics of computing → Combinatorics on words
  • Show More...

  • Refine by Keyword
  • 3 treewidth
  • 2 FPT algorithms
  • 2 NP-hard string problems
  • 2 Repetitiveness measures
  • 2 approximation algorithm
  • Show More...

  • Refine by Type
  • 39 document
  • 1 volume

  • Refine by Publication Year
  • 29 2023
  • 4 2022
  • 3 2021
  • 1 2017
  • 1 2018
  • Show More...