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Documents authored by Riccardi, Brian

Document
DOI: 10.4230/LIPIcs.SEA.2025.13
Pangenome Graph Indexing via the Multidollar-BWT

Authors: Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, and Paola Bonizzoni

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

Abstract
Indexing pangenome graphs is a major algorithmic challenge in computational pangenomics, a recent and active research field that seeks to use graphs as representations of multiple genomes. Since these graphs are constructed from whole genome sequences of a species population, they can become very large, making indexing one of the most challenging problems. In this paper, we propose gindex, a novel indexing approach to solve the Graph Pattern Matching Problem based on the multidollar-BWT. Specifically, gindex aims to find all occurrences of a pattern in a sequence-labeled graph by overcoming two main limitations of GCSA2, one of the most widely used graph indexes: handling queries of arbitrary length and scaling to large graphs without pruning any complex regions. Moreover, we show how a smart preprocessing step can optimize the use of multidollar-BWT to skip small redundant sub-patterns and enhance gindex’s querying capabilities. We demonstrate the effectiveness of our approach by comparing it to GCSA2 in terms of index construction and query time, using different preprocessing modes on three pangenome graphs: one built from Drosophila genomes and two produced by the Human Pangenome Reference Consortium. The results show that gindex can scale on human pangenome graphs - which GCSA2 cannot index using large amounts of RAM - with acceptable memory and time requirements. Moreover, gindex achieves fast query times, although not as fast as GCSA2, which may produce false positives.
Cite as

Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, and Paola Bonizzoni. Pangenome Graph Indexing via the Multidollar-BWT. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cozzi_et_al:LIPIcs.SEA.2025.13,
  author =	{Cozzi, Davide and Riccardi, Brian and Denti, Luca and Ciccolella, Simone and Sadakane, Kunihiko and Bonizzoni, Paola},
  title =	{{Pangenome Graph Indexing via the Multidollar-BWT}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{13:1--13:17},
  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.2025.13},
  URN =		{urn:nbn:de:0030-drops-232515},
  doi =		{10.4230/LIPIcs.SEA.2025.13},
  annote =	{Keywords: Multidollar-BWT, Graph Index, Graph Pattern Matching, Pangenome Graph}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.31
Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property

Authors: Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, and Rosalba Zizza

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
The notion of Lyndon word and Lyndon factorization has shown to have unexpected applications in theory as well as in developing novel algorithms on words. A counterpart to these notions are those of inverse Lyndon word and inverse Lyndon factorization. Differently from the Lyndon words, the inverse Lyndon words may be bordered. The relationship between the two factorizations is related to the inverse lexicographic ordering, and has only been recently explored. More precisely, a main open question is how to get an inverse Lyndon factorization from a classical Lyndon factorization under the inverse lexicographic ordering, named CFL_in. In this paper we reveal a strong connection between these two factorizations where the border plays a relevant role. More precisely, we show two main results. We say that a factorization has the border property if a nonempty border of a factor cannot be a prefix of the next factor. First we show that there exists a unique inverse Lyndon factorization having the border property. Then we show that this unique factorization with the border property is the so-called canonical inverse Lyndon factorization, named ICFL. By showing that ICFL is obtained by compacting factors of the Lyndon factorization over the inverse lexicographic ordering, we provide a linear time algorithm for computing ICFL from CFL_in.
Cite as

Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, and Rosalba Zizza. Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bonizzoni_et_al:LIPIcs.MFCS.2024.31,
  author =	{Bonizzoni, Paola and De Felice, Clelia and Riccardi, Brian and Zaccagnino, Rocco and Zizza, Rosalba},
  title =	{{Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{31:1--31:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.31},
  URN =		{urn:nbn:de:0030-drops-205879},
  doi =		{10.4230/LIPIcs.MFCS.2024.31},
  annote =	{Keywords: Lyndon words, Lyndon factorization, Combinatorial algorithms on words}
}
Document
DOI: 10.4230/LIPIcs.CPM.2024.23
The Rational Construction of a Wheeler DFA

Authors: Giovanni Manzini, Alberto Policriti, Nicola Prezza, and Brian Riccardi

Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)

Abstract
Deterministic Finite Wheeler Automata are a natural generalisation to regular languages of the theory of compressed data structures originated by the introduction of the Burrows-Wheeler transform. Indeed, if we can find a Wheeler automaton recognizing a given language L, such automaton can be used to design time and space efficient algorithms for representing and searching L. In this paper we introduce an alternative representation of Deterministic Wheeler Automata by showing that a natural map between strings and rational numbers in ℚ [0,1) can be extended to represent the automaton’s states as intervals in ℚ [0,1). Using this representation it emerges a natural relationship between automata properties and some properties of real numbers. In addition, such representation enables us to formulate problems related to automata in a numerical setting. Although at the moment the numerical approach does not lead to time efficient algorithms, we believe this new perspective deserves further consideration. As a further demonstration of the convenience of this new representation, we use it to provide a simple proof of an unexpected result on regular languages. More precisely, we compare the size of the smallest Wheeler automaton recognizing a given language L with respect to the size of the smallest automaton, possibly non-Wheeler, recognizing the same language. We show settings in which there can be an exponential gap between the two sizes, and we discuss the implications of this result on the problem of representing regular languages.
Cite as

Giovanni Manzini, Alberto Policriti, Nicola Prezza, and Brian Riccardi. The Rational Construction of a Wheeler DFA. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 23:1-23:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{manzini_et_al:LIPIcs.CPM.2024.23,
  author =	{Manzini, Giovanni and Policriti, Alberto and Prezza, Nicola and Riccardi, Brian},
  title =	{{The Rational Construction of a Wheeler DFA}},
  booktitle =	{35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)},
  pages =	{23:1--23:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-326-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{296},
  editor =	{Inenaga, Shunsuke and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.23},
  URN =		{urn:nbn:de:0030-drops-201336},
  doi =		{10.4230/LIPIcs.CPM.2024.23},
  annote =	{Keywords: String Matching, Deterministic Finite Automata, Wheeler languages, Graph Indexing, Co-lexicographical Sorting}
}
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