197 Search Results for "F�hndrich, Manuel"


Document
Synergizing Theory and Practice of Automated Algorithm Design for Optimization (Dagstuhl Seminar 23332)

Authors: Diederick Vermetten, Martin S. Krejca, Marius Lindauer, Manuel López-Ibáñez, and Katherine M. Malan

Published in: Dagstuhl Reports, Volume 13, Issue 8 (2024)


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 23332, which focused on automated algorithm design (AAD) for optimization. AAD aims to propose good algorithms and/or parameters thereof for optimization problems in an automated fashion, instead of forcing this decision on the user. As such, AAD is applicable in a variety of domains. The seminar brought together a diverse, international set of researchers from AAD and closely related fields. Especially, we invited people from both the empirical and the theoretical domain. A main goal of the seminar was to enable vivid discussions between these two groups in order to synergize the knowledge from either domain, thus advancing the area of AAD as a whole, and to reduce the gap between theory and practice. Over the course of the seminar, a good mix of breakout sessions and talks took place, which were very well received and which we detail in this report. Efforts to synergize theory and practice bore some fruit, and other important aspects of AAD were highlighted and discussed. Overall, the seminar was a huge success.

Cite as

Diederick Vermetten, Martin S. Krejca, Marius Lindauer, Manuel López-Ibáñez, and Katherine M. Malan. Synergizing Theory and Practice of Automated Algorithm Design for Optimization (Dagstuhl Seminar 23332). In Dagstuhl Reports, Volume 13, Issue 8, pp. 46-70, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@Article{vermetten_et_al:DagRep.13.8.46,
  author =	{Vermetten, Diederick and Krejca, Martin S. and Lindauer, Marius and L\'{o}pez-Ib\'{a}\~{n}ez, Manuel and Malan, Katherine M.},
  title =	{{Synergizing Theory and Practice of Automated Algorithm Design for Optimization (Dagstuhl Seminar 23332)}},
  pages =	{46--70},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2024},
  volume =	{13},
  number =	{8},
  editor =	{Vermetten, Diederick and Krejca, Martin S. and Lindauer, Marius and L\'{o}pez-Ib\'{a}\~{n}ez, Manuel and Malan, Katherine M.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.13.8.46},
  URN =		{urn:nbn:de:0030-drops-198128},
  doi =		{10.4230/DagRep.13.8.46},
  annote =	{Keywords: automated algorithm design, hyper-parameter tuning, parameter control, heuristic optimization, black-box optimization}
}
Document
An FPT Algorithm for Temporal Graph Untangling

Authors: Riccardo Dondi and Manuel Lafond

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)


Abstract
Several classical combinatorial problems have been considered and analysed on temporal graphs. Recently, a variant of Vertex Cover on temporal graphs, called MinTimelineCover, has been introduced to summarize timeline activities in social networks. The problem asks to cover every temporal edge while minimizing the total span of the vertices (where the span of a vertex is the length of the timestamp interval it must remain active in). While the problem has been shown to be NP-hard even in very restricted cases, its parameterized complexity has not been fully understood. The problem is known to be in FPT under the span parameter only for graphs with two timestamps, but the parameterized complexity for the general case is open. We settle this open problem by giving an FPT algorithm that is based on a combination of iterative compression and a reduction to the Digraph Pair Cut problem, a powerful problem that has received significant attention recently.

Cite as

Riccardo Dondi and Manuel Lafond. An FPT Algorithm for Temporal Graph Untangling. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{dondi_et_al:LIPIcs.IPEC.2023.12,
  author =	{Dondi, Riccardo and Lafond, Manuel},
  title =	{{An FPT Algorithm for Temporal Graph Untangling}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.12},
  URN =		{urn:nbn:de:0030-drops-194311},
  doi =		{10.4230/LIPIcs.IPEC.2023.12},
  annote =	{Keywords: Temporal Graphs, Vertex Cover, Graph Algorithms, Parameterized Complexity}
}
Document
PACE Solver Description
PACE Solver Description: Exact (GUTHMI) and Heuristic (GUTHM)

Authors: Alexander Leonhardt, Holger Dell, Anselm Haak, Frank Kammer, Johannes Meintrup, Ulrich Meyer, and Manuel Penschuck

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)


Abstract
Twin-width (tww) is a parameter measuring the similarity of an undirected graph to a co-graph [Édouard Bonnet et al., 2022]. It is useful to analyze the parameterized complexity of various graph problems. This paper presents two algorithms to compute the twin-width and to provide a contraction sequence as witness. The two algorithms are motivated by the PACE 2023 challenge, one for the exact track and one for the heuristic track. Each algorithm produces a contraction sequence witnessing (i) the minimal twin-width admissible by the graph in the exact track (ii) an upper bound on the twin-width as tight as possible in the heuristic track. Our heuristic algorithm relies on several greedy approaches with different performance characteristics to find and improve solutions. For large graphs we use locality sensitive hashing to approximately identify suitable contraction candidates. The exact solver follows a branch-and-bound design. It relies on the heuristic algorithm to provide initial upper bounds, and uses lower bounds via contraction sequences to show the optimality of a heuristic solution found in some branch.

Cite as

Alexander Leonhardt, Holger Dell, Anselm Haak, Frank Kammer, Johannes Meintrup, Ulrich Meyer, and Manuel Penschuck. PACE Solver Description: Exact (GUTHMI) and Heuristic (GUTHM). In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 37:1-37:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{leonhardt_et_al:LIPIcs.IPEC.2023.37,
  author =	{Leonhardt, Alexander and Dell, Holger and Haak, Anselm and Kammer, Frank and Meintrup, Johannes and Meyer, Ulrich and Penschuck, Manuel},
  title =	{{PACE Solver Description: Exact (GUTHMI) and Heuristic (GUTHM)}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{37:1--37:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.37},
  URN =		{urn:nbn:de:0030-drops-194563},
  doi =		{10.4230/LIPIcs.IPEC.2023.37},
  annote =	{Keywords: PACE 2023 Challenge, Heuristic, Exact, Twin-Width}
}
Document
Every Bit Counts in Consensus

Authors: Pierre Civit, Seth Gilbert, Rachid Guerraoui, Jovan Komatovic, Matteo Monti, and Manuel Vidigueira

Published in: LIPIcs, Volume 281, 37th International Symposium on Distributed Computing (DISC 2023)


Abstract
Consensus enables n processes to agree on a common valid L-bit value, despite t < n/3 processes being faulty and acting arbitrarily. A long line of work has been dedicated to improving the worst-case communication complexity of consensus in partial synchrony. This has recently culminated in the worst-case word complexity of O(n²). However, the worst-case bit complexity of the best solution is still O(n²L + n²κ) (where κ is the security parameter), far from the Ω(nL + n²) lower bound. The gap is significant given the practical use of consensus primitives, where values typically consist of batches of large size (L > n). This paper shows how to narrow the aforementioned gap. Namely, we present a new algorithm, DARE (Disperse, Agree, REtrieve), that improves upon the O(n²L) term via a novel dispersal primitive. DARE achieves O(n^{1.5}L + n^{2.5}κ) bit complexity, an effective √n-factor improvement over the state-of-the-art (when L > nκ). Moreover, we show that employing heavier cryptographic primitives, namely STARK proofs, allows us to devise DARE-Stark, a version of DARE which achieves the near-optimal bit complexity of O(nL + n²poly(κ)). Both DARE and DARE-Stark achieve optimal O(n) worst-case latency.

Cite as

Pierre Civit, Seth Gilbert, Rachid Guerraoui, Jovan Komatovic, Matteo Monti, and Manuel Vidigueira. Every Bit Counts in Consensus. In 37th International Symposium on Distributed Computing (DISC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 281, pp. 13:1-13:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{civit_et_al:LIPIcs.DISC.2023.13,
  author =	{Civit, Pierre and Gilbert, Seth and Guerraoui, Rachid and Komatovic, Jovan and Monti, Matteo and Vidigueira, Manuel},
  title =	{{Every Bit Counts in Consensus}},
  booktitle =	{37th International Symposium on Distributed Computing (DISC 2023)},
  pages =	{13:1--13:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-301-0},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{281},
  editor =	{Oshman, Rotem},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2023.13},
  URN =		{urn:nbn:de:0030-drops-191399},
  doi =		{10.4230/LIPIcs.DISC.2023.13},
  annote =	{Keywords: Byzantine consensus, Bit complexity, Latency}
}
Document
Short Paper
Constraint Model for the Satellite Image Mosaic Selection Problem (Short Paper)

Authors: Manuel Combarro Simón, Pierre Talbot, Grégoire Danoy, Jedrzej Musial, Mohammed Alswaitti, and Pascal Bouvry

Published in: LIPIcs, Volume 280, 29th International Conference on Principles and Practice of Constraint Programming (CP 2023)


Abstract
Satellite imagery solutions are widely used to study and monitor different regions of the Earth. However, a single satellite image can cover only a limited area. In cases where a larger area of interest is studied, several images must be stitched together to create a single larger image, called a mosaic, that can cover the area. Today, with the increasing number of satellite images available for commercial use, selecting the images to build the mosaic is challenging, especially when the user wants to optimize one or more parameters, such as the total cost and the cloud coverage percentage in the mosaic. More precisely, for this problem the input is an area of interest, several satellite images intersecting the area, a list of requirements relative to the image and the mosaic, such as cloud coverage percentage, image resolution, and a list of objectives to optimize. We contribute to the constraint and mixed integer lineal programming formulation of this new problem, which we call the satellite image mosaic selection problem, which is a multi-objective extension of the polygon cover problem. We propose a dataset of realistic and challenging instances, where the images were captured by the satellite constellations SPOT, Pléiades and Pléiades Neo. We evaluate and compare the two proposed models and show their efficiency for large instances, up to 200 images.

Cite as

Manuel Combarro Simón, Pierre Talbot, Grégoire Danoy, Jedrzej Musial, Mohammed Alswaitti, and Pascal Bouvry. Constraint Model for the Satellite Image Mosaic Selection Problem (Short Paper). In 29th International Conference on Principles and Practice of Constraint Programming (CP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 280, pp. 44:1-44:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{combarrosimon_et_al:LIPIcs.CP.2023.44,
  author =	{Combarro Sim\'{o}n, Manuel and Talbot, Pierre and Danoy, Gr\'{e}goire and Musial, Jedrzej and Alswaitti, Mohammed and Bouvry, Pascal},
  title =	{{Constraint Model for the Satellite Image Mosaic Selection Problem}},
  booktitle =	{29th International Conference on Principles and Practice of Constraint Programming (CP 2023)},
  pages =	{44:1--44:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-300-3},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{280},
  editor =	{Yap, Roland H. C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2023.44},
  URN =		{urn:nbn:de:0030-drops-190815},
  doi =		{10.4230/LIPIcs.CP.2023.44},
  annote =	{Keywords: constraint modeling, satellite imaging, set covering, polygon covering}
}
Document
Sorting Finite Automata via Partition Refinement

Authors: Ruben Becker, Manuel Cáceres, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Francisco Olivares, and Nicola Prezza

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


Abstract
Wheeler nondeterministic finite automata (WNFAs) were introduced in (Gagie et al., TCS 2017) as a powerful generalization of prefix sorting from strings to labeled graphs. WNFAs admit optimal solutions to classic hard problems on labeled graphs and languages such as compression and regular expression matching. The problem of deciding whether a given NFA is Wheeler is known to be NP-complete (Gibney and Thankachan, ESA 2019). Recently, however, Alanko et al. (Information and Computation 2021) showed how to side-step this complexity by switching to preorders: letting Q be the set of states and δ the set of transitions, they provided a O(|δ|⋅|Q|²)-time algorithm computing a totally-ordered partition (i.e. equivalence relation) of the WNFA’s states such that (1) equivalent states recognize the same regular language, and (2) the order of (the classes of) non-equivalent states is consistent with any Wheeler order, when one exists. As a result, the output is a preorder of the states as useful for pattern matching as standard Wheeler orders. Further extensions of this line of work (Cotumaccio et al., SODA 2021 and DCC 2022) generalized these concepts to arbitrary NFAs by introducing co-lex partial preorders: in general, any NFA admits a partial preorder of its states reflecting the co-lexicographic order of their accepted strings; the smaller the width of such preorder is, the faster regular expression matching queries can be performed. To date, the fastest algorithm for computing the smallest-width partial preorder on NFAs runs in O(|δ|² + |Q|^{5/2}) time (Cotumaccio, DCC 2022), while on DFAs the same task can be accomplished in O(min(|Q|²log|Q|, |δ|⋅|Q|)) time (Kim et al., CPM 2023). In this paper, we provide much more efficient solutions to the co-lex order computation problem. Our results are achieved by extending a classic algorithm for the relational coarsest partition refinement problem of Paige and Tarjan to work with ordered partitions. More specifically, we provide a O(|δ|log|Q|)-time algorithm computing a co-lex total preorder when the input is a Wheeler NFA, and an algorithm with the same time complexity computing the smallest-width co-lex partial order of any DFA. In addition, we present implementations of our algorithms and show that they are very efficient also in practice.

Cite as

Ruben Becker, Manuel Cáceres, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Francisco Olivares, and Nicola Prezza. Sorting Finite Automata via Partition Refinement. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{becker_et_al:LIPIcs.ESA.2023.15,
  author =	{Becker, Ruben and C\'{a}ceres, Manuel and Cenzato, Davide and Kim, Sung-Hwan and Kodric, Bojana and Olivares, Francisco and Prezza, Nicola},
  title =	{{Sorting Finite Automata via Partition Refinement}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{15:1--15:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2023.15},
  URN =		{urn:nbn:de:0030-drops-186684},
  doi =		{10.4230/LIPIcs.ESA.2023.15},
  annote =	{Keywords: Wheeler automata, prefix sorting, pattern matching, graph compression, sorting, partition refinement}
}
Document
Finding Maximal Exact Matches in Graphs

Authors: Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)


Abstract
We study the problem of finding maximal exact matches (MEMs) between a query string Q and a labeled graph G. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their strong connections to classical metrics. A principled way to speed up chaining is to limit the number of MEMs by considering only MEMs of length at least κ (κ-MEMs). However, on arbitrary input graphs, the problem of finding MEMs cannot be solved in truly sub-quadratic time under SETH (Equi et al., ICALP 2019) even on acyclic graphs. In this paper we show an O(n⋅ L ⋅ d^{L-1} + m + M_{κ,L})-time algorithm finding all κ-MEMs between Q and G spanning exactly L nodes in G, where n is the total length of node labels, d is the maximum degree of a node in G, m = |Q|, and M_{κ,L} is the number of output MEMs. We use this algorithm to develop a κ-MEM finding solution on indexable Elastic Founder Graphs (Equi et al., Algorithmica 2022) running in time O(nH² + m + M_κ), where H is the maximum number of nodes in a block, and M_κ is the total number of κ-MEMs. Our results generalize to the analysis of multiple query strings (MEMs between G and any of the strings). Additionally, we provide some preliminary experimental results showing that the number of graph MEMs is an order of magnitude smaller than the number of string MEMs of the corresponding concatenated collection.

Cite as

Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen. Finding Maximal Exact Matches in Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{rizzo_et_al:LIPIcs.WABI.2023.10,
  author =	{Rizzo, Nicola and C\'{a}ceres, Manuel and M\"{a}kinen, Veli},
  title =	{{Finding Maximal Exact Matches in Graphs}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{10:1--10:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.10},
  URN =		{urn:nbn:de:0030-drops-186364},
  doi =		{10.4230/LIPIcs.WABI.2023.10},
  annote =	{Keywords: Sequence to graph alignment, bidirectional BWT, r-index, suffix tree, founder graphs}
}
Document
Co-Linear Chaining on Pangenome Graphs

Authors: Jyotshna Rajput, Ghanshyam Chandra, and Chirag Jain

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)


Abstract
Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width [Makinen et al., TALG'19] and how incorporating gap cost in the scoring function improves alignment accuracy [Chandra and Jain, RECOMB'23]. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy.

Cite as

Jyotshna Rajput, Ghanshyam Chandra, and Chirag Jain. Co-Linear Chaining on Pangenome Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 12:1-12:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{rajput_et_al:LIPIcs.WABI.2023.12,
  author =	{Rajput, Jyotshna and Chandra, Ghanshyam and Jain, Chirag},
  title =	{{Co-Linear Chaining on Pangenome Graphs}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{12:1--12:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.12},
  URN =		{urn:nbn:de:0030-drops-186389},
  doi =		{10.4230/LIPIcs.WABI.2023.12},
  annote =	{Keywords: Sequence alignment, variation graph, genome sequencing, path cover}
}
Document
Parameterized Complexity of Domination Problems Using Restricted Modular Partitions

Authors: Manuel Lafond and Weidong Luo

Published in: LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)


Abstract
For a graph class 𝒢, we define the 𝒢-modular cardinality of a graph G as the minimum size of a vertex partition of G into modules that each induces a graph in 𝒢. This generalizes other module-based graph parameters such as neighborhood diversity and iterated type partition. Moreover, if 𝒢 has bounded modular-width, the W[1]-hardness of a problem in 𝒢-modular cardinality implies hardness on modular-width, clique-width, and other related parameters. Several FPT algorithms based on modular partitions compute a solution table in each module, then combine each table into a global solution. This works well when each table has a succinct representation, but as we argue, when no such representation exists, the problem is typically W[1]-hard. We illustrate these ideas on the generic (α, β)-domination problem, which is a generalization of known domination problems such as Bounded Degree Deletion, k-Domination, and α-Domination. We show that for graph classes 𝒢 that require arbitrarily large solution tables, these problems are W[1]-hard in the 𝒢-modular cardinality, whereas they are fixed-parameter tractable when they admit succinct solution tables. This leads to several new positive and negative results for many domination problems parameterized by known and novel structural graph parameters such as clique-width, modular-width, and cluster-modular cardinality.

Cite as

Manuel Lafond and Weidong Luo. Parameterized Complexity of Domination Problems Using Restricted Modular Partitions. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 61:1-61:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{lafond_et_al:LIPIcs.MFCS.2023.61,
  author =	{Lafond, Manuel and Luo, Weidong},
  title =	{{Parameterized Complexity of Domination Problems Using Restricted Modular Partitions}},
  booktitle =	{48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)},
  pages =	{61:1--61:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-292-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{272},
  editor =	{Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.61},
  URN =		{urn:nbn:de:0030-drops-185958},
  doi =		{10.4230/LIPIcs.MFCS.2023.61},
  annote =	{Keywords: modular-width, parameterized algorithms, W-hardness, 𝒢-modular cardinality}
}
Document
Engineering Shared-Memory Parallel Shuffling to Generate Random Permutations In-Place

Authors: Manuel Penschuck

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


Abstract
Shuffling is the process of placing elements into a random order such that any permutation occurs with equal probability. It is an important building block in virtually all scientific areas. We engineer, - to the best of our knowledge - for the first time, a practically fast, parallel shuffling algorithm with O(√n log n) parallel depth that requires only poly-logarithmic auxiliary memory (with high probability). In an empirical evaluation, we compare our implementations with a number of existing solutions on various computer architectures. Our algorithms consistently achieve the highest through-put on all machines. Further, we demonstrate that the runtime of our parallel algorithm is comparable to the time that other algorithms may take to acquire the memory from the operating system to copy the input.

Cite as

Manuel Penschuck. Engineering Shared-Memory Parallel Shuffling to Generate Random Permutations In-Place. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{penschuck:LIPIcs.SEA.2023.5,
  author =	{Penschuck, Manuel},
  title =	{{Engineering Shared-Memory Parallel Shuffling to Generate Random Permutations In-Place}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{5:1--5:20},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.5},
  URN =		{urn:nbn:de:0030-drops-183550},
  doi =		{10.4230/LIPIcs.SEA.2023.5},
  annote =	{Keywords: Shuffling, random permutation, parallelism, in-place, algorithm engineering, practical implementation}
}
Document
Track A: Algorithms, Complexity and Games
Minimum Chain Cover in Almost Linear Time

Authors: Manuel Cáceres

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
A minimum chain cover (MCC) of a k-width directed acyclic graph (DAG) G = (V, E) is a set of k chains (paths in the transitive closure) of G such that every vertex appears in at least one chain in the cover. The state-of-the-art solutions for MCC run in time Õ(k(|V|+|E|)) [Mäkinen et at., TALG], O(T_{MF}(|E|) + k|V|), O(k²|V| + |E|) [Cáceres et al., SODA 2022], Õ(|V|^{3/2} + |E|) [Kogan and Parter, ICALP 2022] and Õ(T_{MCF}(|E|) + √k|V|) [Kogan and Parter, SODA 2023], where T_{MF}(|E|) and T_{MCF}(|E|) are the running times for solving maximum flow (MF) and minimum-cost flow (MCF), respectively. In this work we present an algorithm running in time O(T_{MF}(|E|) + (|V|+|E|)log k). By considering the recent result for solving MF [Chen et al., FOCS 2022] our algorithm is the first running in almost linear time. Moreover, our techniques are deterministic and derive a deterministic near-linear time algorithm for MCC if the same is provided for MF. At the core of our solution we use a modified version of the mergeable dictionaries [Farach and Thorup, Algorithmica], [Iacono and Özkan, ICALP 2010] data structure boosted with the SIZE-SPLIT operation and answering queries in amortized logarithmic time, which can be of independent interest.

Cite as

Manuel Cáceres. Minimum Chain Cover in Almost Linear Time. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 31:1-31:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{caceres:LIPIcs.ICALP.2023.31,
  author =	{C\'{a}ceres, Manuel},
  title =	{{Minimum Chain Cover in Almost Linear Time}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{31:1--31:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.31},
  URN =		{urn:nbn:de:0030-drops-180834},
  doi =		{10.4230/LIPIcs.ICALP.2023.31},
  annote =	{Keywords: Minimum chain cover, directed acyclic graph, minimum flow, flow decomposition, mergeable dictionaries, amortized running time}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
Population Protocols with Unordered Data

Authors: Michael Blondin and François Ladouceur

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
Population protocols form a well-established model of computation of passively mobile anonymous agents with constant-size memory. It is well known that population protocols compute Presburger-definable predicates, such as absolute majority and counting predicates. In this work, we initiate the study of population protocols operating over arbitrarily large data domains. More precisely, we introduce population protocols with unordered data as a formalism to reason about anonymous crowd computing over unordered sequences of data. We first show that it is possible to determine whether an unordered sequence from an infinite data domain has a datum with absolute majority. We then establish the expressive power of the "immediate observation" restriction of our model, namely where, in each interaction, an agent observes another agent who is unaware of the interaction.

Cite as

Michael Blondin and François Ladouceur. Population Protocols with Unordered Data. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 115:1-115:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{blondin_et_al:LIPIcs.ICALP.2023.115,
  author =	{Blondin, Michael and Ladouceur, Fran\c{c}ois},
  title =	{{Population Protocols with Unordered Data}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{115:1--115:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.115},
  URN =		{urn:nbn:de:0030-drops-181673},
  doi =		{10.4230/LIPIcs.ICALP.2023.115},
  annote =	{Keywords: Population protocols, unordered data, colored Petri nets}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
Network Satisfaction Problems Solved by k-Consistency

Authors: Manuel Bodirsky and Simon Knäuer

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
We show that the problem of deciding for a given finite relation algebra A whether the network satisfaction problem for A can be solved by the k-consistency procedure, for some k ∈ ℕ, is undecidable. For the important class of finite relation algebras A with a normal representation, however, the decidability of this problem remains open. We show that if A is symmetric and has a flexible atom, then the question whether NSP(A) can be solved by k-consistency, for some k ∈ ℕ, is decidable (even in polynomial time in the number of atoms of A). This result follows from a more general sufficient condition for the correctness of the k-consistency procedure for finite symmetric relation algebras. In our proof we make use of a result of Alexandr Kazda about finite binary conservative structures.

Cite as

Manuel Bodirsky and Simon Knäuer. Network Satisfaction Problems Solved by k-Consistency. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 116:1-116:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{bodirsky_et_al:LIPIcs.ICALP.2023.116,
  author =	{Bodirsky, Manuel and Kn\"{a}uer, Simon},
  title =	{{Network Satisfaction Problems Solved by k-Consistency}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{116:1--116:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.116},
  URN =		{urn:nbn:de:0030-drops-181680},
  doi =		{10.4230/LIPIcs.ICALP.2023.116},
  annote =	{Keywords: Constraint Satisfaction, Computational Complexity, Relation Algebras, Network Satisfaction, Qualitative Reasoning, k-Consistency, Datalog}
}
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)


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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-dev.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
MONI Can Find k-MEMs

Authors: Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, and Travis Gagie

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


Abstract
Suppose we are asked to index a text T [0..n - 1] such that, given a pattern P [0..m - 1], we can quickly report the maximal substrings of P that each occur in T at least k times. We first show how we can add O (r log n) bits to Rossi et al.’s recent MONI index, where r is the number of runs in the Burrows-Wheeler Transform of T, such that it supports such queries in O (k m log n) time. We then show how, if we are given k at construction time, we can reduce the query time to O (m log n).

Cite as

Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, and Travis Gagie. MONI Can Find k-MEMs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 26:1-26:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{tatarnikov_et_al:LIPIcs.CPM.2023.26,
  author =	{Tatarnikov, Igor and Shahrabi Farahani, Ardavan and Kashgouli, Sana and Gagie, Travis},
  title =	{{MONI Can Find k-MEMs}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{26:1--26:14},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.26},
  URN =		{urn:nbn:de:0030-drops-179802},
  doi =		{10.4230/LIPIcs.CPM.2023.26},
  annote =	{Keywords: Compact data structures, Burrows-Wheeler Transform, run-length compression, maximal exact matches}
}
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