42 Search Results for "Georgiadis, Loukas"

Volume

LIPIcs, Volume 265

21st International Symposium on Experimental Algorithms (SEA 2023)

SEA 2023, July 24-26, 2023, Barcelona, Spain

Editors: Loukas Georgiadis

Document
DOI: 10.4230/LIPIcs.WABI.2024.8
Applying the Safe-And-Complete Framework to Practical Genome Assembly

Authors: Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu

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

Abstract
Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.
Cite as

Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8,
  author =	{Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.},
  title =	{{Applying the Safe-And-Complete Framework to Practical Genome Assembly}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{8:1--8:16},
  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.2024.8},
  URN =		{urn:nbn:de:0030-drops-206520},
  doi =		{10.4230/LIPIcs.WABI.2024.8},
  annote =	{Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.5
Buffered Streaming Edge Partitioning

Authors: Adil Chhabra, Marcelo Fonseca Faraj, Christian Schulz, and Daniel Seemaier

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
Addressing the challenges of processing massive graphs, which are prevalent in diverse fields such as social, biological, and technical networks, we introduce HeiStreamE and FreightE, two innovative (buffered) streaming algorithms designed for efficient edge partitioning of large-scale graphs. HeiStreamE utilizes an adapted Split-and-Connect graph model and a Fennel-based multilevel partitioning scheme, while FreightE partitions a hypergraph representation of the input graph. Besides ensuring superior solution quality, these approaches also overcome the limitations of existing algorithms by maintaining linear dependency on the graph size in both time and memory complexity with no dependence on the number of blocks of partition. Our comprehensive experimental analysis demonstrates that HeiStreamE outperforms current streaming algorithms and the re-streaming algorithm 2PS in partitioning quality (replication factor), and is more memory-efficient for real-world networks where the number of edges is far greater than the number of vertices. Further, FreightE is shown to produce fast and efficient partitions, particularly for higher numbers of partition blocks.
Cite as

Adil Chhabra, Marcelo Fonseca Faraj, Christian Schulz, and Daniel Seemaier. Buffered Streaming Edge Partitioning. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 5:1-5:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chhabra_et_al:LIPIcs.SEA.2024.5,
  author =	{Chhabra, Adil and Fonseca Faraj, Marcelo and Schulz, Christian and Seemaier, Daniel},
  title =	{{Buffered Streaming Edge Partitioning}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{5:1--5:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.5},
  URN =		{urn:nbn:de:0030-drops-203701},
  doi =		{10.4230/LIPIcs.SEA.2024.5},
  annote =	{Keywords: graph partitioning, edge partitioning, streaming, online, buffered partitioning}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.17
Vital Edges for (s,t)-Mincut: Efficient Algorithms, Compact Structures, & Optimal Sensitivity Oracles

Authors: Surender Baswana and Koustav Bhanja

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

Abstract
Let G be a directed weighted graph on n vertices and m edges with designated source and sink vertices s and t. An edge in G is vital if its removal reduces the capacity of (s,t)-mincut. Since the seminal work of Ford and Fulkerson [CJM 1956], a long line of work has been done on computing the most vital edge and all vital edges of G. However, even after 60 years, the existing results are for either undirected or unweighted graphs. We present the following result for directed weighted graphs that also solves an open problem by Ausiello, Franciosa, Lari, and Ribichini [NETWORKS 2019]. 1. Algorithmic Results: There is an algorithm that computes all vital edges as well as the most vital edge of G using {O}(n) maximum (s,t)-flow computations. Vital edges play a crucial role in the design of sensitivity oracle for (s,t)-mincut - a compact data structure for reporting (s,t)-mincut after insertion/failure of any edge. For directed graphs, the only existing sensitivity oracle is for unweighted graphs by Picard and Queyranne [MPS 1982]. We present the first and optimal sensitivity oracle for directed weighted graphs as follows. 2. Sensitivity Oracles: a) There is an optimal O(n²) space data structure that can report an (s,t)-mincut C in O(|C|) time after the failure/insertion of any edge. b) There is an O(n) space data structure that can report the capacity of (s,t)-mincut after failure or insertion of any edge e in O(1) time if the capacity of edge e is known. A mincut for a vital edge e is an (s,t)-cut of the least capacity in which edge e is outgoing. For unweighted graphs, in a classical work, Picard and Queyranne [MPS 1982] designed an O(m) space directed acyclic graph (DAG) that stores and characterizes all mincuts for all vital edges. Conversely, there is a set containing at most n-1 (s,t)-cuts such that at least one mincut for every vital edge belongs to the set. We generalize these results for directed weighted graphs as follows. 3. Structural & Combinatorial Results: a) There is a set M containing at most n-1 (s,t)-cuts such that at least one mincut for every vital edge belongs to the set. This bound is tight as well. We also show that set M can be computed using O(n) maximum (s,t)-flow computations. b) We design two compact structures for storing and characterizing all mincuts for all vital edges - (i) an O(m) space DAG for partial and (ii) an O(mn) space structure for complete characterization. To arrive at our results, we develop new techniques, especially a generalization of maxflow-mincut Theorem by Ford and Fulkerson [CJM 1956], which might be of independent interest.
Cite as

Surender Baswana and Koustav Bhanja. Vital Edges for (s,t)-Mincut: Efficient Algorithms, Compact Structures, & Optimal Sensitivity Oracles. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 17:1-17:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{baswana_et_al:LIPIcs.ICALP.2024.17,
  author =	{Baswana, Surender and Bhanja, Koustav},
  title =	{{Vital Edges for (s,t)-Mincut: Efficient Algorithms, Compact Structures, \& Optimal Sensitivity Oracles}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{17:1--17:20},
  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.2024.17},
  URN =		{urn:nbn:de:0030-drops-201601},
  doi =		{10.4230/LIPIcs.ICALP.2024.17},
  annote =	{Keywords: maxflow, vital edges, graph algorithms, structures, st-cuts, sensitivity oracle}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2024.147
Smoothed Analysis of Deterministic Discounted and Mean-Payoff Games

Authors: Bruno Loff and Mateusz Skomra

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

Abstract
We devise a policy-iteration algorithm for deterministic two-player discounted and mean-payoff games, that runs in polynomial time with high probability, on any input where each payoff is chosen independently from a sufficiently random distribution and the underlying graph of the game is ergodic. This includes the case where an arbitrary set of payoffs has been perturbed by a Gaussian, showing for the first time that deterministic two-player games can be solved efficiently, in the sense of smoothed analysis. More generally, we devise a condition number for deterministic discounted and mean-payoff games played on ergodic graphs, and show that our algorithm runs in time polynomial in this condition number. Our result confirms a previous conjecture of Boros et al., which was claimed as a theorem [Boros et al., 2011] and later retracted [Boros et al., 2018]. It stands in contrast with a recent counter-example by Christ and Yannakakis [Christ and Yannakakis, 2023], showing that Howard’s policy-iteration algorithm does not run in smoothed polynomial time on stochastic single-player mean-payoff games. Our approach is inspired by the analysis of random optimal assignment instances by Frieze and Sorkin [Frieze and Sorkin, 2007], and the analysis of bias-induced policies for mean-payoff games by Akian, Gaubert and Hochart [Akian et al., 2018].
Cite as

Bruno Loff and Mateusz Skomra. Smoothed Analysis of Deterministic Discounted and Mean-Payoff Games. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 147:1-147:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{loff_et_al:LIPIcs.ICALP.2024.147,
  author =	{Loff, Bruno and Skomra, Mateusz},
  title =	{{Smoothed Analysis of Deterministic Discounted and Mean-Payoff Games}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{147:1--147:16},
  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.2024.147},
  URN =		{urn:nbn:de:0030-drops-202908},
  doi =		{10.4230/LIPIcs.ICALP.2024.147},
  annote =	{Keywords: Mean-payoff games, discounted games, policy iteration, smoothed analysis}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.75
Connectivity Queries Under Vertex Failures: Not Optimal, but Practical

Authors: Evangelos Kosinas

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

Abstract
We revisit once more the problem of designing an oracle for answering connectivity queries in undirected graphs in the presence of vertex failures. Specifically, given an undirected graph G with n vertices and m edges and an integer d_⋆ ≪ n, the goal is to preprocess the graph in order to construct a data structure 𝒟 such that, given a set of vertices F with |F| = d ≤ d_⋆, we can derive an oracle from 𝒟 that can efficiently answer queries of the form "is x connected with y in G⧵F?". Very recently, Long and Saranurak (FOCS 2022) provided a solution to this problem that is almost optimal with respect to the preprocessing time, the space usage, the update time, and the query time. However, their solution is highly complicated, and it seems very difficult to be implemented efficiently. Furthermore, it does not settle the complexity of the problem in the regime where d_⋆ is a constant. Here, we provide a much simpler solution to this problem, that uses only textbook data structures. Our algorithm is deterministic, it has preprocessing time and space complexity O(d_⋆ m log n), update time O(d⁴ log n), and query time O(d). These bounds compare very well with the previous best, especially considering the simplicity of our approach. In fact, if we assume that d_⋆ is a constant (d_⋆ ≥ 4), then our algorithm provides some trade-offs that improve the state of the art in some respects. Finally, the data structure that we provide is flexible with respect to d_⋆: it can be adapted to increases and decreases, in time and space that are almost proportional to the change in d_⋆ and the size of the graph.
Cite as

Evangelos Kosinas. Connectivity Queries Under Vertex Failures: Not Optimal, but Practical. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 75:1-75:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{kosinas:LIPIcs.ESA.2023.75,
  author =	{Kosinas, Evangelos},
  title =	{{Connectivity Queries Under Vertex Failures: Not Optimal, but Practical}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{75:1--75:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2023.75},
  URN =		{urn:nbn:de:0030-drops-187289},
  doi =		{10.4230/LIPIcs.ESA.2023.75},
  annote =	{Keywords: Graphs, Connectivity, Fault-Tolerant, Oracles}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.SEA.2023
LIPIcs, Volume 265, SEA 2023, Complete Volume

Authors: Loukas Georgiadis

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

Abstract
LIPIcs, Volume 265, SEA 2023, Complete Volume
Cite as

21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 1-390, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Proceedings{georgiadis:LIPIcs.SEA.2023,
  title =	{{LIPIcs, Volume 265, SEA 2023, Complete Volume}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{1--390},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023},
  URN =		{urn:nbn:de:0030-drops-183495},
  doi =		{10.4230/LIPIcs.SEA.2023},
  annote =	{Keywords: LIPIcs, Volume 265, SEA 2023, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SEA.2023.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Loukas Georgiadis

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

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

21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{georgiadis:LIPIcs.SEA.2023.0,
  author =	{Georgiadis, Loukas},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{0:i--0:xii},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.0},
  URN =		{urn:nbn:de:0030-drops-183508},
  doi =		{10.4230/LIPIcs.SEA.2023.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.1
Engineering a Preprocessor for Symmetry Detection

Authors: Markus Anders, Pascal Schweitzer, and Julian Stieß

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

Abstract
State-of-the-art solvers for symmetry detection in combinatorial objects are becoming increasingly sophisticated software libraries. Most of the solvers were initially designed with inputs from combinatorics in mind (nauty, bliss, Traces, dejavu). They excel at dealing with a complicated core of the input. Others focus on practical instances that exhibit sparsity. They excel at dealing with comparatively easy but extremely large substructures of the input (saucy). In practice, these differences manifest in significantly diverging performances on different types of graph classes. We engineer a preprocessor for symmetry detection. The result is a tool designed to shrink sparse, large substructures of the input graph. On most of the practical instances, the preprocessor improves the overall running time significantly for many of the state-of-the-art solvers. At the same time, our benchmarks show that the additional overhead is negligible. Overall we obtain single algorithms with competitive performance across all benchmark graphs. As such, the preprocessor bridges the disparity between solvers that focus on combinatorial graphs and large practical graphs. In fact, on most of the practical instances the combined setup significantly outperforms previous state-of-the-art.
Cite as

Markus Anders, Pascal Schweitzer, and Julian Stieß. Engineering a Preprocessor for Symmetry Detection. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 1:1-1:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{anders_et_al:LIPIcs.SEA.2023.1,
  author =	{Anders, Markus and Schweitzer, Pascal and Stie{\ss}, Julian},
  title =	{{Engineering a Preprocessor for Symmetry Detection}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{1:1--1:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.1},
  URN =		{urn:nbn:de:0030-drops-183511},
  doi =		{10.4230/LIPIcs.SEA.2023.1},
  annote =	{Keywords: graph isomorphism, automorphism groups, symmetry detection, preprocessors}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.2
Fast Reachability Using DAG Decomposition

Authors: Giorgos Kritikakis and Ioannis G. Tollis

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

Abstract
We present a fast and practical algorithm to compute the transitive closure (TC) of a directed graph. It is based on computing a reachability indexing scheme of a directed acyclic graph (DAG), G = (V, E). Given any path/chain decomposition of G we show how to compute in parameterized linear time such a reachability scheme that can answer reachability queries in constant time. The experimental results reveal that our method is significantly faster in practice than the theoretical bounds imply, indicating that path/chain decomposition algorithms can be applied to obtain fast and practical solutions to the transitive closure (TC) problem. Furthermore, we show that the number of non-transitive edges of a DAG G is ≤ width*|V| and that we can find a substantially large subset of the transitive edges of G in linear time using a path/chain decomposition. Our extensive experimental results show the interplay between these concepts in various models of DAGs.
Cite as

Giorgos Kritikakis and Ioannis G. Tollis. Fast Reachability Using DAG Decomposition. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 2:1-2:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{kritikakis_et_al:LIPIcs.SEA.2023.2,
  author =	{Kritikakis, Giorgos and Tollis, Ioannis G.},
  title =	{{Fast Reachability Using DAG Decomposition}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{2:1--2:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.2},
  URN =		{urn:nbn:de:0030-drops-183526},
  doi =		{10.4230/LIPIcs.SEA.2023.2},
  annote =	{Keywords: graph algorithms, hierarchy, directed acyclic graphs (DAG), path/chain decomposition, transitive closure, transitive reduction, reachability, reachability indexing scheme}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.3
Partitioning the Bags of a Tree Decomposition into Cliques

Authors: Thomas Bläsius, Maximilian Katzmann, and Marcus Wilhelm

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

Abstract
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With this paper, we take a first step towards computing clique-partitioned tree decompositions. Our focus lies on the subproblem of computing clique partitions, i.e., for each bag of a given tree decomposition, we compute an optimal partition of the induced subgraph into cliques. The goal here is to minimize the product of the clique sizes (plus 1). We show that this problem is NP-hard. We also describe four heuristic approaches as well as an exact branch-and-bound algorithm. Our evaluation shows that the branch-and-bound solver is sufficiently efficient to serve as a good baseline. Moreover, our heuristics yield solutions close to the optimum. As a bonus, our algorithms allow us to compute first upper bounds for the clique-partitioned treewidth of real-world networks. A comparison to traditional treewidth indicates that clique-partitioned treewidth is a promising parameter for graphs with high clustering.
Cite as

Thomas Bläsius, Maximilian Katzmann, and Marcus Wilhelm. Partitioning the Bags of a Tree Decomposition into Cliques. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{blasius_et_al:LIPIcs.SEA.2023.3,
  author =	{Bl\"{a}sius, Thomas and Katzmann, Maximilian and Wilhelm, Marcus},
  title =	{{Partitioning the Bags of a Tree Decomposition into Cliques}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{3:1--3:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.3},
  URN =		{urn:nbn:de:0030-drops-183533},
  doi =		{10.4230/LIPIcs.SEA.2023.3},
  annote =	{Keywords: treewidth, weighted treewidth, algorithm engineering, cliques, clustering, complex networks}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.4
Subset Wavelet Trees

Authors: Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, and Jaakko Vuohtoniemi

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

Abstract
Given an alphabet Σ of σ = |Σ| symbols, a degenerate (or indeterminate) string X is a sequence X = X[0],X[1]…, X[n-1] of n subsets of Σ. Since their introduction in the mid 70s, degenerate strings have been widely studied, with applications driven by their being a natural model for sequences in which there is a degree of uncertainty about the precise symbol at a given position, such as those arising in genomics and proteomics. In this paper we introduce a new data structural tool for degenerate strings, called the subset wavelet tree (SubsetWT). A SubsetWT supports two basic operations on degenerate strings: subset-rank(i,c), which returns the number of subsets up to the i-th subset in the degenerate string that contain the symbol c; and subset-select(i,c), which returns the index in the degenerate string of the i-th subset that contains symbol c. These queries are analogs of rank and select queries that have been widely studied for ordinary strings. Via experiments in a real genomics application in which degenerate strings are fundamental, we show that subset wavelet trees are practical data structures, and in particular offer an attractive space-time tradeoff. Along the way we investigate data structures for supporting (normal) rank queries on base-4 and base-3 sequences, which may be of independent interest. Our C++ implementations of the data structures are available at https://github.com/jnalanko/SubsetWT.
Cite as

Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, and Jaakko Vuohtoniemi. Subset Wavelet Trees. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{alanko_et_al:LIPIcs.SEA.2023.4,
  author =	{Alanko, Jarno N. and Biagi, Elena and Puglisi, Simon J. and Vuohtoniemi, Jaakko},
  title =	{{Subset Wavelet Trees}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{4:1--4:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.4},
  URN =		{urn:nbn:de:0030-drops-183549},
  doi =		{10.4230/LIPIcs.SEA.2023.4},
  annote =	{Keywords: degenerate strings, compressed data structures, succinct data structures, string processing, data structures, efficient algorithms}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.5
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.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
DOI: 10.4230/LIPIcs.SEA.2023.6
Proxying Betweenness Centrality Rankings in Temporal Networks

Authors: Ruben Becker, Pierluigi Crescenzi, Antonio Cruciani, and Bojana Kodric

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

Abstract
Identifying influential nodes in a network is arguably one of the most important tasks in graph mining and network analysis. A large variety of centrality measures, all aiming at correctly quantifying a node’s importance in the network, have been formulated in the literature. One of the most cited ones is the betweenness centrality, formally introduced by Freeman (Sociometry, 1977). On the other hand, researchers have recently been very interested in capturing the dynamic nature of real-world networks by studying temporal graphs, rather than static ones. Clearly, centrality measures, including the betweenness centrality, have also been extended to temporal graphs. Buß et al. (KDD, 2020) gave algorithms to compute various notions of temporal betweenness centrality, including the perhaps most natural one - shortest temporal betweenness. Their algorithm computes centrality values of all nodes in time O(n³ T²), where n is the size of the network and T is the total number of time steps. For real-world networks, which easily contain tens of thousands of nodes, this complexity becomes prohibitive. Thus, it is reasonable to consider proxies for shortest temporal betweenness rankings that are more efficiently computed, and, therefore, allow for measuring the relative importance of nodes in very large temporal graphs. In this paper, we compare several such proxies on a diverse set of real-world networks. These proxies can be divided into global and local proxies. The considered global proxies include the exact algorithm for static betweenness (computed on the underlying graph), prefix foremost temporal betweenness of Buß et al., which is more efficiently computable than shortest temporal betweenness, and the recently introduced approximation approach of Santoro and Sarpe (WWW, 2022). As all of these global proxies are still expensive to compute on very large networks, we also turn to more efficiently computable local proxies. Here, we consider temporal versions of the ego-betweenness in the sense of Everett and Borgatti (Social Networks, 2005), standard degree notions, and a novel temporal degree notion termed the pass-through degree, that we introduce in this paper and which we consider to be one of our main contributions. We show that the pass-through degree, which measures the number of pairs of neighbors of a node that are temporally connected through it, can be computed in nearly linear time for all nodes in the network and we experimentally observe that it is surprisingly competitive as a proxy for shortest temporal betweenness.
Cite as

Ruben Becker, Pierluigi Crescenzi, Antonio Cruciani, and Bojana Kodric. Proxying Betweenness Centrality Rankings in Temporal Networks. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 6:1-6:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{becker_et_al:LIPIcs.SEA.2023.6,
  author =	{Becker, Ruben and Crescenzi, Pierluigi and Cruciani, Antonio and Kodric, Bojana},
  title =	{{Proxying Betweenness Centrality Rankings in Temporal Networks}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{6:1--6:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.6},
  URN =		{urn:nbn:de:0030-drops-183568},
  doi =		{10.4230/LIPIcs.SEA.2023.6},
  annote =	{Keywords: node centrality, betweenness, temporal graphs, graph mining}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.7
Simple Runs-Bounded FM-Index Designs Are Fast

Authors: Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela

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

Abstract
Given a string X of length n on alphabet σ, the FM-index data structure allows counting all occurrences of a pattern P of length m in O(m) time via an algorithm called backward search. An important difficulty when searching with an FM-index is to support queries on L, the Burrows-Wheeler transform of X, while L is in compressed form. This problem has been the subject of intense research for 25 years now. Run-length encoding of L is an effective way to reduce index size, in particular when the data being indexed is highly-repetitive, which is the case in many types of modern data, including those arising from versioned document collections and in pangenomics. This paper takes a back-to-basics look at supporting backward search in FM-indexes, exploring and engineering two simple designs. The first divides the BWT string into blocks containing b symbols each and then run-length compresses each block separately, possibly introducing new runs (compared to applying run-length encoding once, to the whole string). Each block stores counts of each symbol that occurs before the block. This method supports the operation rank_c(L, i) (i.e., count the number of times c occurs in the prefix L[1..i]) by first determining the block i/b in which i falls and scanning the block to the appropriate position counting occurrences of c along the way. This partial answer to rank_c(L, i) is then added to the stored count of c symbols before the block to determine the final answer. Our second design has a similar structure, but instead divides the run-length-encoded version of L into blocks containing an equal number of runs. The trick then is to determine the block in which a query falls, which is achieved via a predecessor query over the block starting positions. We show via extensive experiments on a wide range of repetitive text collections that these FM-indexes are not only easy to implement, but also fast and space efficient in practice.
Cite as

Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela. Simple Runs-Bounded FM-Index Designs Are Fast. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 7:1-7:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{diazdominguez_et_al:LIPIcs.SEA.2023.7,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and D\"{o}nges, Saska and Puglisi, Simon J. and Salmela, Leena},
  title =	{{Simple Runs-Bounded FM-Index Designs Are Fast}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{7:1--7:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.7},
  URN =		{urn:nbn:de:0030-drops-183579},
  doi =		{10.4230/LIPIcs.SEA.2023.7},
  annote =	{Keywords: data structures, efficient algorithms}
}
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