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Documents authored by Faro, Simone

Document
DOI: 10.4230/LIPIcs.SEA.2024.24
Efficient Exact Online String Matching Through Linked Weak Factors

Authors: Matthew N. Palmer, Simone Faro, and Stefano Scafiti

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

Abstract
Online exact string matching is a fundamental computational problem in computer science, involving the sequential search for a pattern within a large text without prior access to the entire text. Its significance is underscored by its diverse applications in data compression, data mining, text editing, and bioinformatics, just to cite a few, where efficient substring matching is crucial. While the problem has been a subject of study for years, recent decades have witnessed a heightened focus on experimental solutions, employing various techniques to achieve superior performance. Notably, approaches centered around weak factor recognition have emerged as leaders in experimental settings, gaining increasing attention. This paper introduces Hash Chain, a novel algorithm founded on a robust weak factor recognition approach that links adjacent factors through hashing. Building upon the efficacy of weak recognition techniques, the proposed algorithm incorporates innovative strategies for organizing data structures and optimizations to enhance performance. Despite its quadratic worst-case time complexity, the new proposed algorithm demonstrates sublinear behavior in practice, outperforming currently known algorithms in the literature.
Cite as

Matthew N. Palmer, Simone Faro, and Stefano Scafiti. Efficient Exact Online String Matching Through Linked Weak Factors. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{palmer_et_al:LIPIcs.SEA.2024.24,
  author =	{Palmer, Matthew N. and Faro, Simone and Scafiti, Stefano},
  title =	{{Efficient Exact Online String Matching Through Linked Weak Factors}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{24:1--24:14},
  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.2024.24},
  URN =		{urn:nbn:de:0030-drops-203896},
  doi =		{10.4230/LIPIcs.SEA.2024.24},
  annote =	{Keywords: String matching, text processing, weak recognition, hashing, experimental algorithms, design and analysis of algorithms}
}
Document
DOI: 10.4230/LIPIcs.FUN.2024.13
The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples

Authors: Simone Faro, Francesco Pio Marino, Andrea Moschetto, Arianna Pavone, and Antonio Scardace

Published in: LIPIcs, Volume 291, 12th International Conference on Fun with Algorithms (FUN 2024)

Abstract
Sampled String Matching is presented as an efficient solution to the string matching problem, aiming to tackle the space constraints of indexed string matching while purportedly reducing search times for online solutions. Despite the problem’s inception dating back to 1991, practical solutions have only recently emerged. These purportedly accelerate online searches by up to 35 times compared to conventional methods, achieved through a partial index occupying a mere 5% of the text size. This paper delves into the intricacies of one of the latest and most effective text sampling techniques, character distance sampling, which revolves around sampling distances between characters of a selected alphabet within the text. Specifically, we introduce fake samples while remaining honest! In other words, the study reveals that, interestingly, strategically introducing fake samples within the sampled sequence slashes the required index space by almost half, just avoid compromising the algorithm’s correctness. Additionally, since efficiency is everything, this approach, in turn, purportedly enhances the algorithm’s efficiency under specific conditions.
Cite as

Simone Faro, Francesco Pio Marino, Andrea Moschetto, Arianna Pavone, and Antonio Scardace. The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples. In 12th International Conference on Fun with Algorithms (FUN 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 291, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{faro_et_al:LIPIcs.FUN.2024.13,
  author =	{Faro, Simone and Marino, Francesco Pio and Moschetto, Andrea and Pavone, Arianna and Scardace, Antonio},
  title =	{{The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples}},
  booktitle =	{12th International Conference on Fun with Algorithms (FUN 2024)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-314-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{291},
  editor =	{Broder, Andrei Z. and Tamir, Tami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2024.13},
  URN =		{urn:nbn:de:0030-drops-199211},
  doi =		{10.4230/LIPIcs.FUN.2024.13},
  annote =	{Keywords: string matching, sampling}
}
Document
DOI: 10.4230/LIPIcs.WABI.2020.19
Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations

Authors: Domenico Cantone, Simone Faro, and Arianna Pavone

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of matching sequences allowing for this kind of chromosomal alteration. In this paper we investigate the approximate string matching problem when the edit operations are non-overlapping unbalanced translocations of adjacent factors. In particular, we first present a 𝒪(nm³)-time and 𝒪(m²)-space algorithm based on the dynamic-programming approach. Then we improve our first result by designing a second solution which makes use of the Directed Acyclic Word Graph of the pattern. In particular, we show that under the assumptions of equiprobability and independence of characters, our algorithm has a 𝒪(nlog²_{σ} m) average time complexity, for an alphabet of size σ, still maintaining the 𝒪(nm³)-time and the 𝒪(m²)-space complexity in the worst case. To the best of our knowledge this is the first solution in literature for the approximate string matching problem allowing for unbalanced translocations of factors.
Cite as

Domenico Cantone, Simone Faro, and Arianna Pavone. Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 19:1-19:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{cantone_et_al:LIPIcs.WABI.2020.19,
  author =	{Cantone, Domenico and Faro, Simone and Pavone, Arianna},
  title =	{{Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{19:1--19:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.19},
  URN =		{urn:nbn:de:0030-drops-128086},
  doi =		{10.4230/LIPIcs.WABI.2020.19},
  annote =	{Keywords: Text processing, approximate matching, inversions, sequence matching}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.SEA.2020
LIPIcs, Volume 160, SEA 2020, Complete Volume

Authors: Simone Faro and Domenico Cantone

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
LIPIcs, Volume 160, SEA 2020, Complete Volume
Cite as

18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 1-366, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@Proceedings{faro_et_al:LIPIcs.SEA.2020,
  title =	{{LIPIcs, Volume 160, SEA 2020, Complete Volume}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{1--366},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020},
  URN =		{urn:nbn:de:0030-drops-120730},
  doi =		{10.4230/LIPIcs.SEA.2020},
  annote =	{Keywords: LIPIcs, Volume 160, SEA 2020, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SEA.2020.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Simone Faro and Domenico Cantone

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

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

18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{faro_et_al:LIPIcs.SEA.2020.0,
  author =	{Faro, Simone and Cantone, Domenico},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{0:i--0:xii},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.0},
  URN =		{urn:nbn:de:0030-drops-120741},
  doi =		{10.4230/LIPIcs.SEA.2020.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
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