43 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

Artifact
Software
DOI: 10.4230/artifacts.22511
LinearBPDesign

Authors: Théo Boury, Laurent Bulteau, and Yann Ponty

Abstract
Cite as

Théo Boury, Laurent Bulteau, Yann Ponty. LinearBPDesign (Software, Source code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22511,
   title = {{LinearBPDesign}}, 
   author = {Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann},
   note = {Software, version 1.0., swhId: \href{https://archive.softwareheritage.org/swh:1:dir:73673b14e891528ae11d29515662b482f730be12;origin=https://gitlab.inria.fr/amibio/linearbpdesign;visit=swh:1:snp:c8ad7229d32bb5e86b05dda530f3280ae4d87608;anchor=swh:1:rev:c4ba4998d0790a1fc14115c33d500a7e22e5fe9b}{\texttt{swh:1:dir:73673b14e891528ae11d29515662b482f730be12}} (visited on 2024-11-28)},
   url = {https://gitlab.inria.fr/amibio/linearbpdesign},
   doi = {10.4230/artifacts.22511},
}
Document
DOI: 10.4230/LIPIcs.GD.2024.26
Storylines with a Protagonist

Authors: Tim Hegemann and Alexander Wolff

Published in: LIPIcs, Volume 320, 32nd International Symposium on Graph Drawing and Network Visualization (GD 2024)

Abstract
Storyline visualizations show interactions between a given set of characters over time. Each character is represented by an x-monotone curve. A meeting is represented by a vertical bar that is crossed by the curves of exactly those characters that participate in the meeting. Therefore, character curves may have to cross each other. In the context of publication networks, we consider storylines where the characters are authors and the meetings are joint publications. We are especially interested in visualizing a group of colleagues centered around an author, the protagonist, who participates in all selected publications. For such instances, we propose a drawing style where the protagonist’s curve is drawn at a prominent position and never crossed by any other author’s curve. We consider two variants of storylines with a protagonist. In the one-sided variant, the protagonist is required to be drawn at the top position. In this restricted setting, we can efficiently compute a drawing with the minimum number of pairwise crossings, whereas we show that it is NP-hard to minimize the number of block crossings (i.e., pairs of blocks of parallel curves that intersect each other). In the two-sided variant, the task is to split the set of co-authors of the protagonist into two groups, and to place the curves of one group above and the curves of the other group below the protagonist’s curve such that the total number of (block) crossings is minimized. As our main result, we present an algorithm for bundling a sequence of pairwise crossings into a sequence of few block crossings (in the absence of meetings). It exploits a connection to a rectangle dissection problem. In the presence of meetings, it yields results that are very close to a lower bound. Based on this bundling algorithm and our exact algorithm for the one-sided variant, we present a new heuristic for computing two-sided storylines with few block crossings. We perform an extensive experimental study using publication data of 81 protagonists from GD 2023 and their most frequent collaborators over the last ten years. Our study shows that, for two-sided storylines with a protagonist, our new heuristic uses fewer block crossings (and fewer pairwise crossings) than two heuristics for block crossing minimization in general storylines.
Cite as

Tim Hegemann and Alexander Wolff. Storylines with a Protagonist. In 32nd International Symposium on Graph Drawing and Network Visualization (GD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 320, pp. 26:1-26:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hegemann_et_al:LIPIcs.GD.2024.26,
  author =	{Hegemann, Tim and Wolff, Alexander},
  title =	{{Storylines with a Protagonist}},
  booktitle =	{32nd International Symposium on Graph Drawing and Network Visualization (GD 2024)},
  pages =	{26:1--26:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-343-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{320},
  editor =	{Felsner, Stefan and Klein, Karsten},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2024.26},
  URN =		{urn:nbn:de:0030-drops-213109},
  doi =		{10.4230/LIPIcs.GD.2024.26},
  annote =	{Keywords: Storyline visualization, storyline with a protagonist, crossing minimization, block crossings}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.9
Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation

Authors: Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The 𝒞-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired class 𝒞, and to find such an orientation if one exists. The problem can arise when visualising evolutionary data, for example, because popular phylogenetic network reconstruction methods such as Neighbor-Net are distance-based and thus inevitably produce undirected graphs. The complexity of 𝒞-Orientation remains open for many classes 𝒞, including binary tree-child networks, and practical methods are still lacking. In this paper, we propose an exponential but practically efficient FPT algorithm for 𝒞-Orientation, which is parameterised by the reticulation number and the maximum size of minimal basic cycles used in the computation. We also present a very fast heuristic for Tree-Child Orientation. To evaluate the empirical performance of the proposed methods, we compared their accuracy and execution time for Tree-Child Orientation with those of an exponential time 𝒞-orientation algorithm from the literature. Our experiments show that the proposed exact algorithm is significantly faster than the state-of-the-art exponential time algorithm. The proposed heuristic runs even faster but the accuracy decreases as the reticulation number increases.
Cite as

Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu. Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{urata_et_al:LIPIcs.WABI.2024.9,
  author =	{Urata, Tsuyoshi and Yokoyama, Manato and Hayamizu, Momoko},
  title =	{{Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.9},
  URN =		{urn:nbn:de:0030-drops-206531},
  doi =		{10.4230/LIPIcs.WABI.2024.9},
  annote =	{Keywords: Phylogenetic Networks, Tree-Child Networks, Graph Orientation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.19
RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs

Authors: Théo Boury, Laurent Bulteau, and Yann Ponty

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Inverse folding is a classic instance of negative RNA design which consists in finding a sequence that uniquely folds into a target secondary structure with respect to energy minimization. A breakthrough result of Bonnet et al. shows that, even in simple base pairs-based (BP) models, the decision version of a mildly constrained version of inverse folding is NP-hard. In this work, we show that inverse folding can be solved in linear time for a large collection of targets, including every structure that contains no isolated BP and no isolated stack (or, equivalently, when all helices consist of 3^{+} base pairs). For structures featuring shorter helices, our linear algorithm is no longer guaranteed to produce a solution, but still does so for a large proportion of instances. Our approach introduces a notion of modulo m-separability, generalizing a property pioneered by Hales et al. Separability is a sufficient condition for the existence of a solution to the inverse folding problem. We show that, for any input secondary structure of length n, a modulo m-separated sequence can be produced in time 𝒪(n 2^m) anytime such a sequence exists. Meanwhile, we show that any structure consisting of 3^{+} base pairs is either trivially non-designable, or always admits a modulo-2 separated solution (m = 2). Solution sequences can thus be produced in linear time, and even be uniformly generated within the set of modulo-2 separable sequences.
Cite as

Théo Boury, Laurent Bulteau, and Yann Ponty. RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boury_et_al:LIPIcs.WABI.2024.19,
  author =	{Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann},
  title =	{{RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{19:1--19:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.19},
  URN =		{urn:nbn:de:0030-drops-206632},
  doi =		{10.4230/LIPIcs.WABI.2024.19},
  annote =	{Keywords: RNA structure, String Design, Parameterized Complexity, Uniform Sampling}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.CPM.2023
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.0
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.1
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.2
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.3
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.4
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.5
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.6
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)

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@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
DOI: 10.4230/LIPIcs.CPM.2023.7
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)

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@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
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}
}
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