49 Search Results for "Liberti, Leo"

Volume

LIPIcs, Volume 301

22nd International Symposium on Experimental Algorithms (SEA 2024)

SEA 2024, July 23-26, 2024, Vienna, Austria

Editors: Leo Liberti

Volume

OASIcs, Volume 25

12th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems

ATMOS 2012, September 13, 2012, Ljubljana, Slovenia

Editors: Daniel Delling and Leo Liberti

Document
Complete Volume
DOI: 10.4230/LIPIcs.SEA.2024
LIPIcs, Volume 301, SEA 2024, Complete Volume

Authors: Leo Liberti

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

Abstract
LIPIcs, Volume 301, SEA 2024, Complete Volume
Cite as

22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1-548, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Proceedings{liberti:LIPIcs.SEA.2024,
  title =	{{LIPIcs, Volume 301, SEA 2024, Complete Volume}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{1--548},
  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},
  URN =		{urn:nbn:de:0030-drops-203649},
  doi =		{10.4230/LIPIcs.SEA.2024},
  annote =	{Keywords: LIPIcs, Volume 301, SEA 2024, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SEA.2024.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Leo Liberti

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

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

22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 0:i-0:xviii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{liberti:LIPIcs.SEA.2024.0,
  author =	{Liberti, Leo},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{0:i--0:xviii},
  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.2024.0},
  URN =		{urn:nbn:de:0030-drops-203658},
  doi =		{10.4230/LIPIcs.SEA.2024.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.1
Move-r: Optimizing the r-index

Authors: Nico Bertram, Johannes Fischer, and Lukas Nalbach

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

Abstract
We present a static text index called Move-r, which is a highly optimized version of the r-index ([Travis Gagie et al., 2020] Gagie et al., 2020) that encorporates recent theoretical developments of the move data structure ([Takaaki Nishimoto and Yasuo Tabei, 2021] Nishimoto and Tabei, 2021). The r-index is the method of choice for indexing highly repetitive texts, such as different versions of a text document or DNA from the same species, as it exploits the compressibilty of the underlying data. With Move-r, we can answer count- and locate queries 2-35 (typically 15) times as fast as with any other r-index supporting locate queries while being 0.8-2.5 (typically 2) times as large. A Move-r index can be constructed 0.9-2 (typically 2) times as fast while using 1/3-1 (typically 1/2) times as much space.
Cite as

Nico Bertram, Johannes Fischer, and Lukas Nalbach. Move-r: Optimizing the r-index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bertram_et_al:LIPIcs.SEA.2024.1,
  author =	{Bertram, Nico and Fischer, Johannes and Nalbach, Lukas},
  title =	{{Move-r: Optimizing the r-index}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{1:1--1:19},
  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.2024.1},
  URN =		{urn:nbn:de:0030-drops-203662},
  doi =		{10.4230/LIPIcs.SEA.2024.1},
  annote =	{Keywords: Compressed Text Index, Burrows-Wheeler Transform}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.2
Engineering Zuffix Arrays

Authors: Paolo Boldi, Stefano Marchini, and Sebastiano Vigna

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

Abstract
Searching patterns in long strings is a classical algorithmic problem with countless practical applications. Suffix trees and suffix arrays (and their variants) are a long-established solution that yields linear-time search (in the size of the pattern). In [Paolo Boldi and Sebastiano Vigna, 2018] it is shown that a z-map gadget can be attached to (enhanced) suffix arrays to improve their theoretical query time, obtaining a data structure called zuffix array. The main contribution of this paper is to show that a carefully engineered implementation of the z-map gadget does provide significant speedups with respect to enhanced suffix arrays on real-world datasets, albeit doubling the required space. In particular, for large alphabets we observe a sevenfold improvement in query time with respect to enhanced suffix arrays; even in the worst case (small alphabets), the query time is almost halved. Thus, zuffix arrays provide a very interesting new point in the space-time tradeoff spectrum.
Cite as

Paolo Boldi, Stefano Marchini, and Sebastiano Vigna. Engineering Zuffix Arrays. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boldi_et_al:LIPIcs.SEA.2024.2,
  author =	{Boldi, Paolo and Marchini, Stefano and Vigna, Sebastiano},
  title =	{{Engineering Zuffix Arrays}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{2:1--2:18},
  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.2024.2},
  URN =		{urn:nbn:de:0030-drops-203677},
  doi =		{10.4230/LIPIcs.SEA.2024.2},
  annote =	{Keywords: Suffix trees, suffix arrays, z-fast tries}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.3
Practical Minimum Path Cover

Authors: Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu

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

Abstract
Computing a minimum path cover (MPC) of a directed acyclic graph (DAG) is a fundamental problem with a myriad of applications, including reachability. Although it is known how to solve the problem by a simple reduction to minimum flow, recent theoretical advances exploit this idea to obtain algorithms parameterized by the number of paths of an MPC, known as the width. These results obtain fast [Mäkinen et al., TALG 2019] and even linear time [Cáceres et al., SODA 2022] algorithms in the small-width regime. In this paper, we present the first publicly available high-performance implementation of state-of-the-art MPC algorithms, including the parameterized approaches. Our experiments on random DAGs show that parameterized algorithms are orders-of-magnitude faster on dense graphs. Additionally, we present new fast pre-processing heuristics based on transitive edge sparsification. We show that our heuristics improve MPC-solvers by orders of magnitude.
Cite as

Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu. Practical Minimum Path Cover. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{caceres_et_al:LIPIcs.SEA.2024.3,
  author =	{C\'{a}ceres, Manuel and Mumey, Brendan and Toivonen, Santeri and Tomescu, Alexandru I.},
  title =	{{Practical Minimum Path Cover}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{3:1--3:19},
  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.2024.3},
  URN =		{urn:nbn:de:0030-drops-203687},
  doi =		{10.4230/LIPIcs.SEA.2024.3},
  annote =	{Keywords: minimum path cover, directed acyclic graph, maximum flow, parameterized algorithms, edge sparsification, algorithm engineering}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.4
Separator Based Data Reduction for the Maximum Cut Problem

Authors: Jonas Charfreitag, Christine Dahn, Michael Kaibel, Philip Mayer, Petra Mutzel, and Lukas Schürmann

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

Abstract
Preprocessing is an important ingredient for solving the maximum cut problem to optimality on real-world graphs. In our work, we derive a new framework for data reduction rules based on vertex separators. Vertex separators are sets of vertices, whose removal increases the number of connected components of a graph. Certain small separators can be found in linear time, allowing for an efficient combination of our framework with existing data reduction rules. Additionally, we complement known data reduction rules for triangles with a new one. In our computational experiments on established benchmark instances, we clearly show the effectiveness and efficiency of our proposed data reduction techniques. The resulting graphs are significantly smaller than in earlier studies and sometimes no vertex is left, so preprocessing has fully solved the instance to optimality. The introduced techniques are also shown to offer significant speedup potential for an exact state-of-the-art solver and to help a state-of-the-art heuristic to produce solutions of higher quality.
Cite as

Jonas Charfreitag, Christine Dahn, Michael Kaibel, Philip Mayer, Petra Mutzel, and Lukas Schürmann. Separator Based Data Reduction for the Maximum Cut Problem. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 4:1-4:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{charfreitag_et_al:LIPIcs.SEA.2024.4,
  author =	{Charfreitag, Jonas and Dahn, Christine and Kaibel, Michael and Mayer, Philip and Mutzel, Petra and Sch\"{u}rmann, Lukas},
  title =	{{Separator Based Data Reduction for the Maximum Cut Problem}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{4:1--4:21},
  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.2024.4},
  URN =		{urn:nbn:de:0030-drops-203698},
  doi =		{10.4230/LIPIcs.SEA.2024.4},
  annote =	{Keywords: Data Reduction, Maximum Cut, Vertex Separators}
}
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
DOI: 10.4230/LIPIcs.SEA.2024.6
Faster Treewidth-Based Approximations for Wiener Index

Authors: Giovanna Kobus Conrado, Amir Kafshdar Goharshady, Pavel Hudec, Pingjiang Li, and Harshit Jitendra Motwani

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

Abstract
The Wiener index of a graph G is the sum of distances between all pairs of its vertices. It is a widely-used graph property in chemistry, initially introduced to examine the link between boiling points and structural properties of alkanes, which later found notable applications in drug design. Thus, computing or approximating the Wiener index of molecular graphs, i.e. graphs in which every vertex models an atom of a molecule and every edge models a bond, is of significant interest to the computational chemistry community. In this work, we build upon the observation that molecular graphs are sparse and tree-like and focus on developing efficient algorithms parameterized by treewidth to approximate the Wiener index. We present a new randomized approximation algorithm using a combination of tree decompositions and centroid decompositions. Our algorithm approximates the Wiener index within any desired multiplicative factor (1 ± ε) in time O(n ⋅ log n ⋅ k³ + √n ⋅ k/ε²), where n is the number of vertices of the graph and k is the treewidth. This time bound is almost-linear in n. Finally, we provide experimental results over standard benchmark molecules from PubChem and the Protein Data Bank, showcasing the applicability and scalability of our approach on real-world chemical graphs and comparing it with previous methods.
Cite as

Giovanna Kobus Conrado, Amir Kafshdar Goharshady, Pavel Hudec, Pingjiang Li, and Harshit Jitendra Motwani. Faster Treewidth-Based Approximations for Wiener Index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 6:1-6:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{conrado_et_al:LIPIcs.SEA.2024.6,
  author =	{Conrado, Giovanna Kobus and Goharshady, Amir Kafshdar and Hudec, Pavel and Li, Pingjiang and Motwani, Harshit Jitendra},
  title =	{{Faster Treewidth-Based Approximations for Wiener Index}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{6:1--6:19},
  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.2024.6},
  URN =		{urn:nbn:de:0030-drops-203718},
  doi =		{10.4230/LIPIcs.SEA.2024.6},
  annote =	{Keywords: Computational Chemistry, Treewidth, Wiener Index}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.7
Local Search k-means++ with Foresight

Authors: Theo Conrads, Lukas Drexler, Joshua Könen, Daniel R. Schmidt, and Melanie Schmidt

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

Abstract
Since its introduction in 1957, Lloyd’s algorithm for k-means clustering has been extensively studied and has undergone several improvements. While in its original form it does not guarantee any approximation factor at all, Arthur and Vassilvitskii (SODA 2007) proposed k-means++ which enhances Lloyd’s algorithm by a seeding method which guarantees a 𝒪(log k)-approximation in expectation. More recently, Lattanzi and Sohler (ICML 2019) proposed LS++ which further improves the solution quality of k-means++ by local search techniques to obtain a 𝒪(1)-approximation. On the practical side, the greedy variant of k-means++ is often used although its worst-case behaviour is provably worse than for the standard k-means++ variant. We investigate how to improve LS++ further in practice. We study two options for improving the practical performance: (a) Combining LS++ with greedy k-means++ instead of k-means++, and (b) Improving LS++ by better entangling it with Lloyd’s algorithm. Option (a) worsens the theoretical guarantees of k-means++ but improves the practical quality also in combination with LS++ as we confirm in our experiments. Option (b) is our new algorithm, Foresight LS++. We experimentally show that FLS++ improves upon the solution quality of LS++. It retains its asymptotic runtime and its worst-case approximation bounds.
Cite as

Theo Conrads, Lukas Drexler, Joshua Könen, Daniel R. Schmidt, and Melanie Schmidt. Local Search k-means++ with Foresight. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{conrads_et_al:LIPIcs.SEA.2024.7,
  author =	{Conrads, Theo and Drexler, Lukas and K\"{o}nen, Joshua and Schmidt, Daniel R. and Schmidt, Melanie},
  title =	{{Local Search k-means++ with Foresight}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{7:1--7:20},
  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.2024.7},
  URN =		{urn:nbn:de:0030-drops-203727},
  doi =		{10.4230/LIPIcs.SEA.2024.7},
  annote =	{Keywords: k-means clustering, kmeans++, greedy, local search}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.8
Practical Computation of Graph VC-Dimension

Authors: David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot

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

Abstract
For any set system ℋ = (V,ℛ), ℛ ⊆ 2^V, a subset S ⊆ V is called shattered if every S' ⊆ S results from the intersection of S with some set in ℛ. The VC-dimension of ℋ is the size of a largest shattered set in V. In this paper, we focus on the problem of computing the VC-dimension of graphs. In particular, given a graph G = (V,E), the VC-dimension of G is defined as the VC-dimension of (V, N), where N contains each subset of V that can be obtained as the closed neighborhood of some vertex v ∈ V in G. Our main contribution is an algorithm for computing the VC-dimension of any graph, whose effectiveness is shown through experiments on various types of practical graphs, including graphs with millions of vertices. A key aspect of its efficiency resides in the fact that practical graphs have small VC-dimension, up to 8 in our experiments. As a side-product, we present several new bounds relating the graph VC-dimension to other classical graph theoretical notions. We also establish the W[1]-hardness of the graph VC-dimension problem by extending a previous result for arbitrary set systems.
Cite as

David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot. Practical Computation of Graph VC-Dimension. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{coudert_et_al:LIPIcs.SEA.2024.8,
  author =	{Coudert, David and Csik\'{o}s, M\'{o}nika and Ducoffe, Guillaume and Viennot, Laurent},
  title =	{{Practical Computation of Graph VC-Dimension}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{8:1--8:20},
  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.2024.8},
  URN =		{urn:nbn:de:0030-drops-203731},
  doi =		{10.4230/LIPIcs.SEA.2024.8},
  annote =	{Keywords: VC-dimension, graph, algorithm}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.9
Top- k Frequent Patterns in Streams and Parameterized-Space LZ Compression

Authors: Patrick Dinklage, Johnnes Fischer, and Nicola Prezza

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

Abstract
We present novel online approximations of the Lempel-Ziv 77 (LZ77) and Lempel-Ziv 78 (LZ78) compression schemes [Lempel & Ziv, 1977/1978] with parameterizable space usage based on estimating which k patterns occur the most frequently in the streamed input for parameter k. This new approach overcomes the issue of finding only local repetitions, which is a natural limitation of algorithms that compress using a sliding window or by partitioning the input into blocks. For this, we introduce the top-k trie, a summary for maintaining online the top-k frequent consecutive patterns in a stream of characters based on a combination of the Lempel-Ziv 78 compression scheme and the Misra-Gries algorithm for frequent item estimation in streams. Using straightforward encoding, our implementations yield compression ratios (output over input size) competitive with established general-purpose LZ-based compression utilities such as gzip or xz.
Cite as

Patrick Dinklage, Johnnes Fischer, and Nicola Prezza. Top- k Frequent Patterns in Streams and Parameterized-Space LZ Compression. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dinklage_et_al:LIPIcs.SEA.2024.9,
  author =	{Dinklage, Patrick and Fischer, Johnnes and Prezza, Nicola},
  title =	{{Top- k Frequent Patterns in Streams and Parameterized-Space LZ Compression}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{9:1--9:20},
  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.2024.9},
  URN =		{urn:nbn:de:0030-drops-203748},
  doi =		{10.4230/LIPIcs.SEA.2024.9},
  annote =	{Keywords: compression, streaming, heavy hitters, algorithm engineering}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.10
Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests

Authors: Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro

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

Abstract
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular classifiers such as Kraken use k-mers, recent research indicates that using maximal exact matches (MEMs) can lead to better classifications. For example, we can - build an augmented FM-index over the the genomes in the tree concatenated in left-to-right order; - for each MEM in a read, find the interval in the suffix array containing the starting positions of that MEM’s occurrences in those genomes; - find the minimum and maximum values stored in that interval; - take the lowest common ancestor (LCA) of the genomes containing the characters at those positions. This solution is practical, however, only when the total size of the genomes in the tree is fairly small. In this paper we consider applying the same solution to three lossily compressed representations of the genomes' concatenation: - a KATKA kernel, which discards characters that are not in the first or last occurrence of any k_max-tuple, for a parameter k_max; - a minimizer digest; - a KATKA kernel of a minimizer digest. With a test dataset and these three representations of it, simulated reads and various parameter settings, we checked how many reads' longest MEMs occurred only in the sequences from which those reads were generated ("true positive" reads). For some parameter settings we achieved significant compression while only slightly decreasing the true-positive rate.
Cite as

Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro. Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{draesslerova_et_al:LIPIcs.SEA.2024.10,
  author =	{Draesslerov\'{a}, Dominika and Ahmed, Omar and Gagie, Travis and Holub, Jan and Langmead, Ben and Manzini, Giovanni and Navarro, Gonzalo},
  title =	{{Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{10:1--10:13},
  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.2024.10},
  URN =		{urn:nbn:de:0030-drops-203756},
  doi =		{10.4230/LIPIcs.SEA.2024.10},
  annote =	{Keywords: Taxonomic classification, metagenomics, KATKA, maximal exact matches, string kernels, minimizer digests}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.11
Engineering Weighted Connectivity Augmentation Algorithms

Authors: Marcelo Fonseca Faraj, Ernestine Großmann, Felix Joos, Thomas Möller, and Christian Schulz

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

Abstract
Increasing the connectivity of a graph is a pivotal challenge in robust network design. The weighted connectivity augmentation problem is a common version of the problem that takes link costs into consideration. The problem is then to find a minimum cost subset of a given set of weighted links that increases the connectivity of a graph by one when the links are added to the edge set of the input instance. In this work, we give a first implementation of recently discovered better-than-2 approximations. Furthermore, we propose three new heuristics and one exact approach. These include a greedy algorithm considering link costs and the number of unique cuts covered, an approach based on minimum spanning trees and a local search algorithm that may improve a given solution by swapping links of paths. Our exact approach uses an ILP formulation with efficient cut enumeration as well as a fast initialization routine. We then perform an extensive experimental evaluation which shows that our algorithms are faster and yield the best solutions compared to the current state-of-the-art as well as the recently discovered better-than-2 approximation algorithms. Our novel local search algorithm can improve solution quality even further.
Cite as

Marcelo Fonseca Faraj, Ernestine Großmann, Felix Joos, Thomas Möller, and Christian Schulz. Engineering Weighted Connectivity Augmentation Algorithms. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 11:1-11:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{faraj_et_al:LIPIcs.SEA.2024.11,
  author =	{Faraj, Marcelo Fonseca and Gro{\ss}mann, Ernestine and Joos, Felix and M\"{o}ller, Thomas and Schulz, Christian},
  title =	{{Engineering Weighted Connectivity Augmentation Algorithms}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{11:1--11:22},
  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.2024.11},
  URN =		{urn:nbn:de:0030-drops-203768},
  doi =		{10.4230/LIPIcs.SEA.2024.11},
  annote =	{Keywords: weighted connectivity augmentation, approximation, heuristic, integer linear program, algorithm engineering}
}
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