2 Search Results for "Nunes, Gabriel H."

Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
Invited Paper
DOI: 10.4230/LIPIcs.CONCUR.2020.1
On Privacy and Accuracy in Data Releases (Invited Paper)

Authors: Mário S. Alvim, Natasha Fernandes, Annabelle McIver, and Gabriel H. Nunes

Published in: LIPIcs, Volume 171, 31st International Conference on Concurrency Theory (CONCUR 2020)

Abstract
In this paper we study the relationship between privacy and accuracy in the context of correlated datasets. We use a model of quantitative information flow to describe the the trade-off between privacy of individuals' data and and the utility of queries to that data by modelling the effectiveness of adversaries attempting to make inferences after a data release. We show that, where correlations exist in datasets, it is not possible to implement optimal noise-adding mechanisms that give the best possible accuracy or the best possible privacy in all situations. Finally we illustrate the trade-off between accuracy and privacy for local and oblivious differentially private mechanisms in terms of inference attacks on medium-scale datasets.
Cite as

Mário S. Alvim, Natasha Fernandes, Annabelle McIver, and Gabriel H. Nunes. On Privacy and Accuracy in Data Releases (Invited Paper). In 31st International Conference on Concurrency Theory (CONCUR 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 171, pp. 1:1-1:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{alvim_et_al:LIPIcs.CONCUR.2020.1,
  author =	{Alvim, M\'{a}rio S. and Fernandes, Natasha and McIver, Annabelle and Nunes, Gabriel H.},
  title =	{{On Privacy and Accuracy in Data Releases}},
  booktitle =	{31st International Conference on Concurrency Theory (CONCUR 2020)},
  pages =	{1:1--1:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-160-3},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{171},
  editor =	{Konnov, Igor and Kov\'{a}cs, Laura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2020.1},
  URN =		{urn:nbn:de:0030-drops-128130},
  doi =		{10.4230/LIPIcs.CONCUR.2020.1},
  annote =	{Keywords: Privacy/utility trade-off, Quantitative Information Flow, inference attacks}
}
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