5 Search Results for "Ouangraoua, Aïda"

Volume

LIPIcs, Volume 273

23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

WABI 2023, September 4-6, 2023, Houston, TX, USA

Editors: Djamal Belazzougui and Aïda Ouangraoua

Document
DOI: 10.4230/LIPIcs.SEA.2025.4
U-Index: A Universal Indexing Framework for Matching Long Patterns

Authors: Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Motivation. Text indexing is a fundamental and well-studied problem. Classic solutions to this problem either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index - to accelerate matching, e.g., the suffix array. The former solutions thus retain excellent compressed space, but are practically slow to construct and query. The latter approaches, instead, sacrifice space efficiency but are typically faster; for example, the suffix array takes much more space than the text itself for commonly used alphabets, like ASCII or DNA, but it is very fast to construct and query. Methods. In this paper, we show that efficient text indexing can be achieved using just a small extra space on top of the original text, provided that the query patterns are sufficiently long. More specifically, we develop a new indexing paradigm in which a sketch of a query pattern is first matched against a sketch of the text. Once candidate matches are retrieved, they are verified using the original text. This paradigm is thus universal in the sense that it allows us to use any solution to index the sketched text, like a suffix array, FM-index, or r-index. Results. We explore both the theory and the practice of this universal framework. With an extensive experimental analysis, we show that, surprisingly, universal indexes can be constructed much faster than their unsketched counterparts and take a fraction of the space, as a direct consequence of (i) having a lower bound on the length of patterns and (ii) working in sketch space. Furthermore, these data structures have the potential of retaining or even improving query time, because matching against the sketched text is faster and verifying candidates can be theoretically done in constant time per occurrence (or, in practice, by short and cache-friendly scans of the text). Finally, we discuss some important applications of this novel indexing paradigm to computational biology. We hypothesize that such indexes will be particularly effective when the queries are sufficiently long, and so we demonstrate applications in long-read mapping.
Cite as

Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis. U-Index: A Universal Indexing Framework for Matching Long Patterns. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ayad_et_al:LIPIcs.SEA.2025.4,
  author =	{Ayad, Lorraine A. K. and Fici, Gabriele and Groot Koerkamp, Ragnar and Loukides, Grigorios and Patro, Rob and Pibiri, Giulio Ermanno and Pissis, Solon P.},
  title =	{{U-Index: A Universal Indexing Framework for Matching Long Patterns}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{4:1--4:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.4},
  URN =		{urn:nbn:de:0030-drops-232420},
  doi =		{10.4230/LIPIcs.SEA.2025.4},
  annote =	{Keywords: Text Indexing, Sketching, Minimizers, Hashing}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.WABI.2023
LIPIcs, Volume 273, WABI 2023, Complete Volume

Authors: Djamal Belazzougui and Aïda Ouangraoua

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
LIPIcs, Volume 273, WABI 2023, Complete Volume
Cite as

23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 1-400, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Proceedings{belazzougui_et_al:LIPIcs.WABI.2023,
  title =	{{LIPIcs, Volume 273, WABI 2023, Complete Volume}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{1--400},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023},
  URN =		{urn:nbn:de:0030-drops-186250},
  doi =		{10.4230/LIPIcs.WABI.2023},
  annote =	{Keywords: LIPIcs, Volume 273, WABI 2023, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.WABI.2023.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Djamal Belazzougui and Aïda Ouangraoua

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

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

23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{belazzougui_et_al:LIPIcs.WABI.2023.0,
  author =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.0},
  URN =		{urn:nbn:de:0030-drops-186267},
  doi =		{10.4230/LIPIcs.WABI.2023.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.8
A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation

Authors: Nadia El-Mabrouk and Aïda Ouangraoua

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Due to the key role played by gene trees and species phylogenies in biological studies, it is essential to have as much confidence as possible on the available trees. As phylogenetic tools are error-prone, it is a common task to use a correction method for improving an initial tree. Various correction methods exist. In this paper we focus on those based on the Duplication-Loss reconciliation model. The polytomy resolution approach consists in contracting weakly supported branches and then refining the obtained non-binary tree in a way minimizing a reconciliation distance with the given species tree. On the other hand, the supertree approach takes as input a set of separated subtrees, either obtained for separared orthology groups or by removing the upper branches of an initial tree to a certain level, and amalgamating them in an optimal way preserving the topology of the initial trees. The two classes of problems have always been considered as two separate fields, based on apparently different models. In this paper we give a unifying view showing that these two classes of problems are in fact special cases of a more general problem that we call LabelGTC, whose input includes a 0-1 edge-labelled gene tree to be corrected. Considering a tree as a set of triplets, we also formulate the TripletGTC Problem whose input includes a set of gene triplets that should be preserved in the corrected tree. These two general models allow to unify, understand and compare the principles of the duplication-loss reconciliation-based tree correction approaches. We show that LabelGTC is a special case of TripletGTC. We then develop appropriate algorithms allowing to handle these two general correction problems.
Cite as

Nadia El-Mabrouk and Aïda Ouangraoua. A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 8:1-8:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{elmabrouk_et_al:LIPIcs.WABI.2017.8,
  author =	{El-Mabrouk, Nadia and Ouangraoua, A\"{i}da},
  title =	{{A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{8:1--8:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.8},
  URN =		{urn:nbn:de:0030-drops-76565},
  doi =		{10.4230/LIPIcs.WABI.2017.8},
  annote =	{Keywords: Gene tree correction, Supertree, Polytomy, Reconciliation, Phylogeny}
}
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