38 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.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}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.8
Noisy Sorting Without Searching: Data Oblivious Sorting with Comparison Errors

Authors: Ramtin Afshar, Michael Dillencourt, Michael T. Goodrich, and Evrim Ozel

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

Abstract
We provide and study several algorithms for sorting an array of n comparable distinct elements subject to probabilistic comparison errors. In this model, the comparison of two elements returns the wrong answer according to a fixed probability, p_e < 1/2, and otherwise returns the correct answer. The dislocation of an element is the distance between its position in a given (current or output) array and its position in a sorted array. There are various algorithms that can be utilized for sorting or near-sorting elements subject to probabilistic comparison errors, but these algorithms are not data oblivious because they all make heavy use of noisy binary searching. In this paper, we provide new methods for sorting with comparison errors that are data oblivious while avoiding the use of noisy binary search methods. In addition, we experimentally compare our algorithms and other sorting algorithms.
Cite as

Ramtin Afshar, Michael Dillencourt, Michael T. Goodrich, and Evrim Ozel. Noisy Sorting Without Searching: Data Oblivious Sorting with Comparison Errors. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 8:1-8:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{afshar_et_al:LIPIcs.SEA.2023.8,
  author =	{Afshar, Ramtin and Dillencourt, Michael and Goodrich, Michael T. and Ozel, Evrim},
  title =	{{Noisy Sorting Without Searching: Data Oblivious Sorting with Comparison Errors}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{8:1--8:18},
  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.2023.8},
  URN =		{urn:nbn:de:0030-drops-183585},
  doi =		{10.4230/LIPIcs.SEA.2023.8},
  annote =	{Keywords: sorting, algorithms, randomization, experimentation}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.9
Optimizing over the Efficient Set of a Multi-Objective Discrete Optimization Problem

Authors: Satya Tamby and Daniel Vanderpooten

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

Abstract
Optimizing over the efficient set of a discrete multi-objective problem is a challenging issue. The main reason is that, unlike when optimizing over the feasible set, the efficient set is implicitly characterized. Therefore, methods designed for this purpose iteratively generate efficient solutions by solving appropriate single-objective problems. However, the number of efficient solutions can be quite large and the problems to be solved can be difficult practically. Thus, the challenge is both to minimize the number of iterations and to reduce the difficulty of the problems to be solved at each iteration. In this paper, a new enumeration scheme is proposed. By introducing some constraints and optimizing over projections of the search region, potentially large parts of the search space can be discarded, drastically reducing the number of iterations. Moreover, the single-objective programs to be solved can be guaranteed to be feasible, and a starting solution can be provided allowing warm start resolutions. This results in a fast algorithm that is simple to implement. Experimental computations on two standard multi-objective instance families show that our approach seems to perform significantly faster than the state of the art algorithm.
Cite as

Satya Tamby and Daniel Vanderpooten. Optimizing over the Efficient Set of a Multi-Objective Discrete Optimization Problem. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 9:1-9:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{tamby_et_al:LIPIcs.SEA.2023.9,
  author =	{Tamby, Satya and Vanderpooten, Daniel},
  title =	{{Optimizing over the Efficient Set of a Multi-Objective Discrete Optimization Problem}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{9:1--9:13},
  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.2023.9},
  URN =		{urn:nbn:de:0030-drops-183599},
  doi =		{10.4230/LIPIcs.SEA.2023.9},
  annote =	{Keywords: discrete optimization, multi-objective optimization, non-dominated set, efficient set}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.10
Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover

Authors: Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt

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

Abstract
In the Directed Feedback Vertex Set (DFVS) problem, one is given a directed graph G = (V,E) and wants to find a minimum cardinality set S ⊆ V such that G-S is acyclic. DFVS is a fundamental problem in computer science and finds applications in areas such as deadlock detection. The problem was the subject of the 2022 PACE coding challenge. We develop a novel exact algorithm for the problem that is tailored to perform well on instances that are mostly bi-directed. For such instances, we adapt techniques from the well-researched vertex cover problem. Our core idea is an iterative reduction to vertex cover. To this end, we also develop a new reduction rule that reduces the number of not bi-directed edges. With the resulting algorithm, we were able to win third place in the exact track of the PACE challenge. We perform computational experiments and compare the running time to other exact algorithms, in particular to the winning algorithm in PACE. Our experiments show that we outpace the other algorithms on instances that have a low density of uni-directed edges.
Cite as

Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 10:1-10:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{angrick_et_al:LIPIcs.SEA.2023.10,
  author =	{Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo},
  title =	{{Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{10:1--10:14},
  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.2023.10},
  URN =		{urn:nbn:de:0030-drops-183602},
  doi =		{10.4230/LIPIcs.SEA.2023.10},
  annote =	{Keywords: directed feedback vertex set, vertex cover, reduction rules}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.11
CompDP: A Framework for Simultaneous Subgraph Counting Under Connectivity Constraints

Authors: Kengo Nakamura, Masaaki Nishino, Norihito Yasuda, and Shin-ichi Minato

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

Abstract
The subgraph counting problem computes the number of subgraphs of a given graph that satisfy some constraints. Among various constraints imposed on a graph, those regarding the connectivity of vertices, such as "these two vertices must be connected," have great importance since they are indispensable for determining various graph substructures, e.g., paths, Steiner trees, and rooted spanning forests. In this view, the subgraph counting problem under connectivity constraints is also important because counting such substructures often corresponds to measuring the importance of a vertex in network infrastructures. However, we must solve the subgraph counting problems multiple times to compute such an importance measure for every vertex. Conventionally, they are solved separately by constructing decision diagrams such as BDD and ZDD for each problem. However, even solving a single subgraph counting is a computationally hard task, preventing us from solving it multiple times in a reasonable time. In this paper, we propose a dynamic programming framework that simultaneously counts subgraphs for every vertex by focusing on similar connectivity constraints. Experimental results show that the proposed method solved multiple subgraph counting problems about 10-20 times faster than the existing approach for many problem settings.
Cite as

Kengo Nakamura, Masaaki Nishino, Norihito Yasuda, and Shin-ichi Minato. CompDP: A Framework for Simultaneous Subgraph Counting Under Connectivity Constraints. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 11:1-11:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{nakamura_et_al:LIPIcs.SEA.2023.11,
  author =	{Nakamura, Kengo and Nishino, Masaaki and Yasuda, Norihito and Minato, Shin-ichi},
  title =	{{CompDP: A Framework for Simultaneous Subgraph Counting Under Connectivity Constraints}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{11:1--11:20},
  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.2023.11},
  URN =		{urn:nbn:de:0030-drops-183613},
  doi =		{10.4230/LIPIcs.SEA.2023.11},
  annote =	{Keywords: Subgraph counting, Connectivity, Zero-suppressed Binary Decision Diagram}
}
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