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Documents authored by Cantone, Domenico

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-dev.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-dev.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-dev.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}
}
Document
DOI: 10.4230/LIPIcs.CSL.2011.129
A Decidable Quantified Fragment of Set Theory Involving Ordered Pairs with Applications to Description Logics

Authors: Domenico Cantone, Cristiano Longo, and Marianna Nicolosi Asmundo

Published in: LIPIcs, Volume 12, Computer Science Logic (CSL'11) - 25th International Workshop/20th Annual Conference of the EACSL (2011)

Abstract
We present a decision procedure for a quantified fragment of set theory involving ordered pairs and some operators to manipulate them. When our decision procedure is applied to formulae in this fragment whose quantifier prefixes have length bounded by a fixed constant, it runs in nondeterministic polynomial-time. Related to this fragment, we also introduce a description logic which provides an unusually large set of constructs, such as, for instance, Boolean constructs among roles. The set-theoretic nature of the description logics semantics yields a straightforward reduction of the knowledge base consistency problem to the satisfiability problem for formulae of our fragment with quantifier prefixes of length at most 2, from which the NP-completeness of reasoning in this novel description logic follows. Finally, we extend this reduction to cope also with SWRL rules.
Cite as

Domenico Cantone, Cristiano Longo, and Marianna Nicolosi Asmundo. A Decidable Quantified Fragment of Set Theory Involving Ordered Pairs with Applications to Description Logics. In Computer Science Logic (CSL'11) - 25th International Workshop/20th Annual Conference of the EACSL. Leibniz International Proceedings in Informatics (LIPIcs), Volume 12, pp. 129-143, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{cantone_et_al:LIPIcs.CSL.2011.129,
  author =	{Cantone, Domenico and Longo, Cristiano and Nicolosi Asmundo, Marianna},
  title =	{{A Decidable Quantified Fragment of Set Theory Involving Ordered Pairs with Applications to Description Logics}},
  booktitle =	{Computer Science Logic (CSL'11) - 25th International Workshop/20th Annual Conference of the EACSL},
  pages =	{129--143},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-32-3},
  ISSN =	{1868-8969},
  year =	{2011},
  volume =	{12},
  editor =	{Bezem, Marc},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2011.129},
  URN =		{urn:nbn:de:0030-drops-32278},
  doi =		{10.4230/LIPIcs.CSL.2011.129},
  annote =	{Keywords: NP-complete decision procedures, set theory, description logic}
}
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