4 Search Results for "Foley, James"

Document
Research
DOI: 10.4230/OASIcs.Grossi.20
Subsequence-Based Indices for Genome Sequence Analysis

Authors: Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
Compact indices are a fundamental tool in string analysis, even more so in bioinformatics, where genomic sequences can reach billions in length. This paper presents some recent results in which Roberto Grossi has been involved, showing how some of these indices do more than just efficiently represent data, but rather are able to bring out salient information within it, which can be exploited for their downstream analysis. Specifically, we first review a recently-introduced method [Guerrini et al., 2023] that employs the Burrows-Wheeler Transform to build reasonably accurate phylogenetic trees in an assembly-free scenario. We then describe a recent practical tool [Buzzega et al., 2025] for indexing Maximal Common Subsequences between strings, which can enable analysis of genomic sequence similarity. Experimentally, we show that the results produced by the one index are consistent with the expectations about the results of the other index.
Cite as

Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini. Subsequence-Based Indices for Genome Sequence Analysis. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buzzega_et_al:OASIcs.Grossi.20,
  author =	{Buzzega, Giovanni and Conte, Alessio and Guerrini, Veronica and Punzi, Giulia and Rosone, Giovanna and Tattini, Lorenzo},
  title =	{{Subsequence-Based Indices for Genome Sequence Analysis}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{20:1--20:21},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.20},
  URN =		{urn:nbn:de:0030-drops-238199},
  doi =		{10.4230/OASIcs.Grossi.20},
  annote =	{Keywords: String Indices, Burrows-Wheeler Transform, Maximal Common Subsequences, Sequence Analysis, Phylogeny}
}
Document
Replication Paper
DOI: 10.4230/LIPIcs.ECOOP.2025.40
Scaling Up: Revisiting Mining Android Sandboxes at Scale for Malware Classification (Replication Paper)

Authors: Francisco Handrick Tomaz da Costa, Ismael Medeiros, Leandro Oliveira, João Calássio, Rodrigo Bonifácio, Krishna Narasimhan, Mira Mezini, and Márcio Ribeiro

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
The widespread use of smartphones in daily life has raised concerns about privacy and security among researchers and practitioners. Privacy issues are generally highly prevalent in mobile applications, particularly targeting the Android platform - the most popular mobile operating system. For this reason, several techniques have been proposed to identify malicious behavior in Android applications, including the Mining Android Sandbox approach (MAS approach), which aims to identify malicious behavior in repackaged Android applications (apps). However, previous empirical studies evaluated the MAS approach using a small dataset consisting of only 102 pairs of original and repackaged apps. This limitation raises questions about the external validity of their findings and whether the MAS approach can be generalized to larger datasets. To address these concerns, this paper presents the results of a replication study focused on evaluating the performance of the MAS approach regarding its capabilities of correctly classifying malware from different families. Unlike previous studies, our research employs a dataset that is an order of magnitude larger, comprising 4,076 pairs of apps covering a more diverse range of Android malware families. Surprisingly, our findings indicate a poor performance of the MAS approach for identifying malware, with the F1-score decreasing from 0.90 for the small dataset used in the previous studies to 0.54 in our more extensive dataset. Upon closer examination, we discovered that certain malware families partially account for the low accuracy of the MAS approach, which fails to classify a repackaged version of an app as malware correctly. Our findings highlight the limitations of the MAS approach, particularly when scaled, and underscore the importance of complementing it with other techniques to detect a broader range of malware effectively. This opens avenues for further discussion on addressing the blind spots that affect the accuracy of the MAS approach.
Cite as

Francisco Handrick Tomaz da Costa, Ismael Medeiros, Leandro Oliveira, João Calássio, Rodrigo Bonifácio, Krishna Narasimhan, Mira Mezini, and Márcio Ribeiro. Scaling Up: Revisiting Mining Android Sandboxes at Scale for Malware Classification (Replication Paper). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 40:1-40:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{handricktomazdacosta_et_al:LIPIcs.ECOOP.2025.40,
  author =	{Handrick Tomaz da Costa, Francisco and Medeiros, Ismael and Oliveira, Leandro and Cal\'{a}ssio, Jo\~{a}o and Bonif\'{a}cio, Rodrigo and Narasimhan, Krishna and Mezini, Mira and Ribeiro, M\'{a}rcio},
  title =	{{Scaling Up: Revisiting Mining Android Sandboxes at Scale for Malware Classification}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{40:1--40:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.40},
  URN =		{urn:nbn:de:0030-drops-233320},
  doi =		{10.4230/LIPIcs.ECOOP.2025.40},
  annote =	{Keywords: Android Malware Detection, Dynamic Analysis, Mining Android Sandboxes}
}
Document
DOI: 10.4230/DagSemRep.92
Fundamentals and Perspectives of Multimedia Systems (Dagstuhl Seminar 9427)

Authors: José Encarnação, James Foley, and Ralf Guido Herrtwich

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

José Encarnação, James Foley, and Ralf Guido Herrtwich. Fundamentals and Perspectives of Multimedia Systems (Dagstuhl Seminar 9427). Dagstuhl Seminar Report 92, pp. 1-75, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1994)

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@TechReport{encarnacao_et_al:DagSemRep.92,
  author =	{Encarna\c{c}\~{a}o, Jos\'{e} and Foley, James and Herrtwich, Ralf Guido},
  title =	{{Fundamentals and Perspectives of Multimedia Systems (Dagstuhl Seminar 9427)}},
  pages =	{1--75},
  ISSN =	{1619-0203},
  year =	{1994},
  type = 	{Dagstuhl Seminar Report},
  number =	{92},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.92},
  URN =		{urn:nbn:de:0030-drops-149806},
  doi =		{10.4230/DagSemRep.92},
}
Document
DOI: 10.4230/DagSemRep.51
Multimedia - System Architectures and Applications (Dagstuhl Seminar 9245)

Authors: José Encarnação and James Foley

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

José Encarnação and James Foley. Multimedia - System Architectures and Applications (Dagstuhl Seminar 9245). Dagstuhl Seminar Report 51, pp. 1-87, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1993)

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@TechReport{encarnacao_et_al:DagSemRep.51,
  author =	{Encarna\c{c}\~{a}o, Jos\'{e} and Foley, James},
  title =	{{Multimedia - System Architectures and Applications (Dagstuhl Seminar 9245)}},
  pages =	{1--87},
  ISSN =	{1619-0203},
  year =	{1993},
  type = 	{Dagstuhl Seminar Report},
  number =	{51},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.51},
  URN =		{urn:nbn:de:0030-drops-149396},
  doi =		{10.4230/DagSemRep.51},
}
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