7 Search Results for "Rossi, S."

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.2023.3
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.2023.7
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.CPM.2023.26
MONI Can Find k-MEMs

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

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

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

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

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@InProceedings{tatarnikov_et_al:LIPIcs.CPM.2023.26,
  author =	{Tatarnikov, Igor and Shahrabi Farahani, Ardavan and Kashgouli, Sana and Gagie, Travis},
  title =	{{MONI Can Find k-MEMs}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{26:1--26:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.26},
  URN =		{urn:nbn:de:0030-drops-179802},
  doi =		{10.4230/LIPIcs.CPM.2023.26},
  annote =	{Keywords: Compact data structures, Burrows-Wheeler Transform, run-length compression, maximal exact matches}
}
Document
DOI: 10.4230/LIPIcs.SEA.2022.22
Computing Maximal Unique Matches with the r-Index

Authors: Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi

Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)

Abstract
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique Matches (MUMs) have proven themselves to be useful in multiple bioinformatic contexts, for example short-read alignment and multiple-genome alignment. However, standard techniques using suffix trees and FM-indexes do not scale to a pangenomic level. Recently, Gagie et al. [JACM 20] introduced the r-index that is a Burrows-Wheeler Transform (BWT)-based index able to handle hundreds of human genomes. Later, Rossi et al. [JCB 22] enabled the computation of MEMs using the r-index, and Boucher et al. [DCC 21] showed how to compute them in a streaming fashion. In this paper, we show how to augment Boucher et al.’s approach to enable the computation of MUMs on the r-index, while preserving the space and time bounds. We add additional O(r) samples of the longest common prefix (LCP) array, where r is the number of equal-letter runs of the BWT, that permits the computation of the second longest match of the pattern suffix with respect to the input text, which in turn allows the computation of candidate MUMs. We implemented a proof-of-concept of our approach, that we call MUM-PHINDER, and tested on real-world datasets. We compared our approach with competing methods that are able to compute MUMs. We observe that our method is up to 8 times smaller, while up to 19 times slower when the dataset is not highly repetitive, while on highly repetitive data, our method is up to 6.5 times slower and uses up to 25 times less memory.
Cite as

Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi. Computing Maximal Unique Matches with the r-Index. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 22:1-22:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{giuliani_et_al:LIPIcs.SEA.2022.22,
  author =	{Giuliani, Sara and Romana, Giuseppe and Rossi, Massimiliano},
  title =	{{Computing Maximal Unique Matches with the r-Index}},
  booktitle =	{20th International Symposium on Experimental Algorithms (SEA 2022)},
  pages =	{22:1--22:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-251-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{233},
  editor =	{Schulz, Christian and U\c{c}ar, Bora},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.22},
  URN =		{urn:nbn:de:0030-drops-165568},
  doi =		{10.4230/LIPIcs.SEA.2022.22},
  annote =	{Keywords: Burrows-Wheeler Transform, r-index, maximal unique matches, bioinformatics, pangenomics}
}
Document
DOI: 10.4230/LIPIcs.STACS.2022.12
Single-Source Shortest p-Disjoint Paths: Fast Computation and Sparse Preservers

Authors: Davide Bilò, Gianlorenzo D'Angelo, Luciano Gualà, Stefano Leucci, Guido Proietti, and Mirko Rossi

Published in: LIPIcs, Volume 219, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)

Abstract
Let G be a directed graph with n vertices, m edges, and non-negative edge costs. Given G, a fixed source vertex s, and a positive integer p, we consider the problem of computing, for each vertex t≠ s, p edge-disjoint paths of minimum total cost from s to t in G. Suurballe and Tarjan [Networks, 1984] solved the above problem for p = 2 by designing a O(m+nlog n) time algorithm which also computes a sparse single-source 2-multipath preserver, i.e., a subgraph containing 2 edge-disjoint paths of minimum total cost from s to every other vertex of G. The case p ≥ 3 was left as an open problem. We study the general problem (p ≥ 2) and prove that any graph admits a sparse single-source p-multipath preserver with p(n-1) edges. This size is optimal since the in-degree of each non-root vertex v must be at least p. Moreover, we design an algorithm that requires O(pn² (p + log n)) time to compute both p edge-disjoint paths of minimum total cost from the source to all other vertices and an optimal-size single-source p-multipath preserver. The running time of our algorithm outperforms that of a natural approach that solves n-1 single-pair instances using the well-known successive shortest paths algorithm by a factor of Θ(m/(np)) and is asymptotically near optimal if p = O(1) and m = Θ(n²). Our results extend naturally to the case of p vertex-disjoint paths.
Cite as

Davide Bilò, Gianlorenzo D'Angelo, Luciano Gualà, Stefano Leucci, Guido Proietti, and Mirko Rossi. Single-Source Shortest p-Disjoint Paths: Fast Computation and Sparse Preservers. In 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 219, pp. 12:1-12:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bilo_et_al:LIPIcs.STACS.2022.12,
  author =	{Bil\`{o}, Davide and D'Angelo, Gianlorenzo and Gual\`{a}, Luciano and Leucci, Stefano and Proietti, Guido and Rossi, Mirko},
  title =	{{Single-Source Shortest p-Disjoint Paths: Fast Computation and Sparse Preservers}},
  booktitle =	{39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)},
  pages =	{12:1--12:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-222-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{219},
  editor =	{Berenbrink, Petra and Monmege, Benjamin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2022.12},
  URN =		{urn:nbn:de:0030-drops-158221},
  doi =		{10.4230/LIPIcs.STACS.2022.12},
  annote =	{Keywords: multipath spanners, graph sparsification, edge-disjoint paths, min-cost flow}
}
Document
DOI: 10.4230/DagSemProc.10081.4
Attentive Monitoring and Adaptive Control in Cognitive Robotics

Authors: E. Burattini, Alberto Finzi, S. Rossi, and Maria Carla Staffa

Published in: Dagstuhl Seminar Proceedings, Volume 10081, Cognitive Robotics (2010)

Abstract
In this work, we present an attentional system for a robotic agent capable of adapting its emergent behavior to the surrounding environment and to its internal state. In this framework, the agent is endowed with simple attentional mechanisms regulating the frequencies of sensory readings and behavior activations. The process of changing the frequency of sensory readings is interpreted as an increase or decrease of attention towards relevant behaviors and particular aspects of the external environment. In this paper, we present our framework discussing several case studies considering incrementally complex behaviors and tasks.
Cite as

E. Burattini, Alberto Finzi, S. Rossi, and Maria Carla Staffa. Attentive Monitoring and Adaptive Control in Cognitive Robotics. In Cognitive Robotics. Dagstuhl Seminar Proceedings, Volume 10081, pp. 1-8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2010)

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@InProceedings{burattini_et_al:DagSemProc.10081.4,
  author =	{Burattini, E. and Finzi, Alberto and Rossi, S. and Staffa, Maria Carla},
  title =	{{Attentive Monitoring and Adaptive Control in Cognitive Robotics}},
  booktitle =	{Cognitive Robotics},
  pages =	{1--8},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10081},
  editor =	{Gerhard Lakemeyer and Hector J. Levesque and Fiora Pirri},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10081.4},
  URN =		{urn:nbn:de:0030-drops-26322},
  doi =		{10.4230/DagSemProc.10081.4},
  annote =	{Keywords: Attention, behavior-based control, robotics}
}
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