22 Search Results for "Grossi, Davide"

Document
DOI: 10.4230/LIPIcs.ESA.2025.60
Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars

Authors: Jannik Olbrich

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the entire dataset in main memory. Fortunately, such large datasets are often highly repetitive. It can thus be beneficial to compute the BWT from a compressed representation. We propose an algorithm for computing the BWT via the Lyndon straight-line program, a grammar based on the standard factorization of Lyndon words. Our algorithm can also be used to compute the extended BWT (eBWT) of a multiset of sequences. We empirically evaluate our implementation and find that we can compute the BWT and eBWT of very large datasets faster and/or with less memory than competing methods.
Cite as

Jannik Olbrich. Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 60:1-60:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{olbrich:LIPIcs.ESA.2025.60,
  author =	{Olbrich, Jannik},
  title =	{{Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{60:1--60:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.60},
  URN =		{urn:nbn:de:0030-drops-245286},
  doi =		{10.4230/LIPIcs.ESA.2025.60},
  annote =	{Keywords: Burrows-Wheeler Transform, Grammar compression}
}
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
Research
DOI: 10.4230/OASIcs.Grossi.18
DNA Is a Puzzle Enthusiast

Authors: Roberto Marangoni

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

Abstract
This article presents a concise summary of research projects in which Roberto Grossi participated, yielding interesting results that were never previously published in research papers. At the time, these studies were deemed too limited and in need of further extensions and generalizations, which were never realized due to a lack of resources. The researches focused on methods for inferring possible three-dimensional DNA conformations based on nucleotide sequence characteristics. Specifically, two key approaches were investigated: the identification of structured motifs for detecting Transcription Factor Binding Sites (TFBS) and the study of nested permutations using PQ-trees. This article describes the obtained results in selected case studies, their potential implications, and the current state of the art in these research areas.
Cite as

Roberto Marangoni. DNA Is a Puzzle Enthusiast. 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. 18:1-18:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{marangoni:OASIcs.Grossi.18,
  author =	{Marangoni, Roberto},
  title =	{{DNA Is a Puzzle Enthusiast}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{18:1--18:8},
  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.18},
  URN =		{urn:nbn:de:0030-drops-238172},
  doi =		{10.4230/OASIcs.Grossi.18},
  annote =	{Keywords: DNA, 3D structure, PQ trees, structural motifs}
}
Document
DOI: 10.4230/OASIcs.Manzini.3
BWT for String Collections

Authors: Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics.
Cite as

Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino. BWT for String Collections. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 3:1-3:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cenzato_et_al:OASIcs.Manzini.3,
  author =	{Cenzato, Davide and Lipt\'{a}k, Zsuzsanna and Pisanti, Nadia and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT for String Collections}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{3:1--3:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.3},
  URN =		{urn:nbn:de:0030-drops-239113},
  doi =		{10.4230/OASIcs.Manzini.3},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, compressed text indexes, text compression, string collections, bioinformatics}
}
Document
DOI: 10.4230/OASIcs.Manzini.2
A Survey of the Bijective Burrows-Wheeler Transform

Authors: Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Bijective BWT (BBWT), conceived by Scott in 2007, later summarized in a preprint by Gil and Scott in 2009 (arXiv 2012), is a variant of the Burrows-Wheeler Transform which is bijective: every string is the BBWT of some string. Indeed, the BBWT of a string is the extended BWT [Mantaci et al., 2007] of the factors of its Lyndon factorization. The BBWT has been receiving increasing interest in recent years. In this paper, we survey existing research on the BBWT, starting with its history and motivation. We then present algorithmic topics including construction algorithms with various complexities and an index on top of the BBWT for pattern matching. We subsequently address some properties of the BBWT as a compressor, discussing robustness to operations such as reversal, edits, rotation, as well as compression power. We close with listing other bijective variants of the BWT and open problems concerning the BBWT.
Cite as

Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták. A Survey of the Bijective Burrows-Wheeler Transform. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 2:1-2:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bannai_et_al:OASIcs.Manzini.2,
  author =	{Bannai, Hideo and K\"{o}ppl, Dominik and Lipt\'{a}k, Zsuzsanna},
  title =	{{A Survey of the Bijective Burrows-Wheeler Transform}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{2:1--2:26},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.2},
  URN =		{urn:nbn:de:0030-drops-239100},
  doi =		{10.4230/OASIcs.Manzini.2},
  annote =	{Keywords: Burrows-Wheeler Transform, compression, text indexing, repetitiveness measure, Lyndon words, index construction algorithms, bijective string transformation}
}
Document
DOI: 10.4230/OASIcs.Manzini.5
FM-Adaptive: A Practical Data-Aware FM-Index

Authors: Hongwei Huo, Zongtao He, Pengfei Liu, and Jeffrey Scott Vitter

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The FM-index provides an important solution for efficient retrieval and search in textual big data. Its variants have been widely used in many fields including information retrieval, genome analysis, and web searching. In this paper, we propose improvements via a new compressed representation of the wavelet tree of the Burrows-Wheeler transform of the input text, which incorporates the gap γ-encoding. Our theoretical analysis shows that the new index, called FM-Adaptive, achieves asymptotic space optimality within a factor of 2 in the leading term, but it has a better compression and faster retrieval in practice than the competitive optimal compression boosting used in previous FM-indexes. We present a practical improved locate algorithm that provides substantially faster locating time based upon memoization, which takes advantage of the overlapping subproblems property. We design the lookup table for accelerated decoding to support fast pattern matching in a text. Extensive experiments demonstrate that FM-Adaptive provides faster query performance, often by a considerable amount, and/or comparable or better compression than other state-of-the-art FM-index methods.
Cite as

Hongwei Huo, Zongtao He, Pengfei Liu, and Jeffrey Scott Vitter. FM-Adaptive: A Practical Data-Aware FM-Index. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{huo_et_al:OASIcs.Manzini.5,
  author =	{Huo, Hongwei and He, Zongtao and Liu, Pengfei and Vitter, Jeffrey Scott},
  title =	{{FM-Adaptive: A Practical Data-Aware FM-Index}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{5:1--5:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.5},
  URN =		{urn:nbn:de:0030-drops-239139},
  doi =		{10.4230/OASIcs.Manzini.5},
  annote =	{Keywords: Text indexing, Burrows-Wheeler transform, Compressed wavelet trees, Entropy-compressed, Compressed data structures}
}
Document
DOI: 10.4230/OASIcs.Manzini.11
Circular Dictionary Matching Using Extended BWT

Authors: Wing-Kai Hon, Rahul Shah, and Sharma V. Thankachan

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The dictionary matching problem involves preprocessing a set of strings (patterns) into a data structure that efficiently identifies all occurrences of these patterns within a query string (text). In this work, we investigate a variation of this problem, termed circular dictionary matching, where the patterns are circular, meaning their cyclic shifts are also considered valid patterns. Such patterns naturally occur in areas such as bioinformatics and computational geometry. Based on the extended Burrows-Wheeler Transformation (eBWT), we design a space-efficient solution for this problem. Specifically, we show that a dictionary of d circular patterns of total length n can be indexed in nlog σ + O(n+dlog n+σ log n) bits of space and support circular dictionary matching on a query text T in O((|T|+occ)log n) time, where σ represents the size of the underlying alphabet and occ represents the output size.
Cite as

Wing-Kai Hon, Rahul Shah, and Sharma V. Thankachan. Circular Dictionary Matching Using Extended BWT. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 11:1-11:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hon_et_al:OASIcs.Manzini.11,
  author =	{Hon, Wing-Kai and Shah, Rahul and Thankachan, Sharma V.},
  title =	{{Circular Dictionary Matching Using Extended BWT}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{11:1--11:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.11},
  URN =		{urn:nbn:de:0030-drops-239195},
  doi =		{10.4230/OASIcs.Manzini.11},
  annote =	{Keywords: String algorithms, Burrows-Wheeler transformation, suffix trees, succinct data structures}
}
Document
DOI: 10.4230/OASIcs.Manzini.7
Algorithms for Computing Very Large BWTs: a Short Survey

Authors: Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Burrows-Wheeler Transform (BWT) is a fundamental string transformation that, although initially introduced for data compression, has been extensively utilized across various domains, including text indexing and pattern matching within large datasets. Although the BWT construction is linear, the constants make the task impractical for large datasets, and as highlighted by Ferragina et al. [Paolo Ferragina et al., 2012], "to use it, one must first build it!". Thus, the construction of the BWT remains a significant challenge. For these reasons, during the past three decades there has been a succession of new algorithms for its construction using techniques that work in external memory or that use text compression. In this survey, we revise some of the most important advancements and tools presented in the past years for computing large BWTs exploiting external memory or text compression approaches without using additional information about the data.
Cite as

Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone. Algorithms for Computing Very Large BWTs: a Short Survey. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 7:1-7:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{diazdominguez_et_al:OASIcs.Manzini.7,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and Egidi, Lavinia and Guerrini, Veronica and Louza, Felipe A. and Rosone, Giovanna},
  title =	{{Algorithms for Computing Very Large BWTs: a Short Survey}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{7:1--7:28},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.7},
  URN =		{urn:nbn:de:0030-drops-239151},
  doi =		{10.4230/OASIcs.Manzini.7},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, external memory, text compression, longest common prefix}
}
Document
DOI: 10.4230/OASIcs.Manzini.12
Wheeler Graphs and Wheeler Languages

Authors: Nicola Cotumaccio, Giovanna D'Agostino, Daniel Gibney, Alberto Policriti, Nicola Prezza, and Sharma V. Thankachan

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
Suffix sorting stands at the core of the most efficient solutions for indexed pattern matching: the suffix tree, the suffix array, compressed indexes based on the Burrows-Wheeler transform, and so on. In [Gagie, Manzini, Sirén, TCS 2017] this concept was extended to labeled graphs, obtaining the rich class of Wheeler graphs. This work opened a very fruitful line of research, ultimately generating results able to bridge the fields of compressed data structures, graph theory, and regular language theory. In a Wheeler graph, nodes are sorted according to the alphabetic order of their incoming labels, propagating this order through pairs of equally-labeled edges. This apparently-simple definition makes it possible to solve on Wheeler graphs problems (including, but not limited to: compression, subpath queries, NFA equivalence, determinization, minimization) that on general labeled graphs are extremely hard to solve, and induces a rich structure in the class of regular languages (Wheeler languages) recognized by automata whose state transition is a Wheeler graph. The goal of this survey is to provide a summary of (and intuitions behind) the results on Wheeler graphs that appeared in the literature since their introduction, in addition to a discussion of interesting problems that are still open in the field.
Cite as

Nicola Cotumaccio, Giovanna D'Agostino, Daniel Gibney, Alberto Policriti, Nicola Prezza, and Sharma V. Thankachan. Wheeler Graphs and Wheeler Languages. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 12:1-12:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cotumaccio_et_al:OASIcs.Manzini.12,
  author =	{Cotumaccio, Nicola and D'Agostino, Giovanna and Gibney, Daniel and Policriti, Alberto and Prezza, Nicola and Thankachan, Sharma V.},
  title =	{{Wheeler Graphs and Wheeler Languages}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{12:1--12:28},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.12},
  URN =		{urn:nbn:de:0030-drops-239205},
  doi =		{10.4230/OASIcs.Manzini.12},
  annote =	{Keywords: Wheeler languages, Wheeler graphs, pattern matching, indexing, compressed data structures}
}
Document
DOI: 10.4230/OASIcs.Manzini.14
BWT Indexes for Optimal Joins in Graph Databases

Authors: Diego Arroyuelo and Gonzalo Navarro

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
Graph databases represent data as a labeled directed graph, where the labels refer to properties that connect the entities represented by their source and target vertices. Queries feature, most prominently, sets of edges where source, target, and/or label can be variables; each instantiation of the variables where all the edges occur in the graph is a solution to the query. Worst-case-optimal algorithms to solve those queries have been devised, but they pose significant space requirements. This overhead has hindered the adoption of worst-case-optimal algorithms in real systems. We show that a representation of the graph based on the extended BWT (eBWT), where each edge is seen as an independent string of length 3 (source, label, target) supports worst-case-optimal algorithms while using almost no extra space on top of the raw data. We then show how the idea is generalized to the relational model, where the strings can be longer than 3 and several eBWTs are needed to obtain worst-case optimality. The aim to minimize the amount of space in that case leads to consider novel eBWT variants, where columns other than the last can be chosen. Finally, we show how the same graph representation can be used to solve other typical queries, like finding graph paths that match regular expressions.
Cite as

Diego Arroyuelo and Gonzalo Navarro. BWT Indexes for Optimal Joins in Graph Databases. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{arroyuelo_et_al:OASIcs.Manzini.14,
  author =	{Arroyuelo, Diego and Navarro, Gonzalo},
  title =	{{BWT Indexes for Optimal Joins in Graph Databases}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{14:1--14:19},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.14},
  URN =		{urn:nbn:de:0030-drops-239222},
  doi =		{10.4230/OASIcs.Manzini.14},
  annote =	{Keywords: Graph databases, Ring index, extended BWT, compact data structures}
}
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.SAND.2025.9
Spanner Enumeration for Temporal Graphs

Authors: Kazuhiro Kurita, Andrea Marino, Jason Schoeters, and Takeaki Uno

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
A spanner of a temporal graph is a subset of edges that preserves connectivity over time between vertices. A minimal spanner is one in which no additional edges can be removed without breaking this connectivity. Our focus is on enumerating minimal spanners for a given temporal graph. We explore several variations of this problem based on the type of connectivity that must be maintained, ranging from one-to-all connectivity to one-to-all-to-one, many-to-all, and finally all-to-all connectivity. We establish that these problems become progressively harder: (i) We present a polynomial-delay enumeration algorithm for one-to-all connectivity; (ii) We prove Dual-hardness for both one-to-all-to-one and many-to-all connectivity, even in the restricted case of two-to-all; (iii) Finally, for all-to-all connectivity, we show that enumeration cannot be performed in output-polynomial time unless P = NP.
Cite as

Kazuhiro Kurita, Andrea Marino, Jason Schoeters, and Takeaki Uno. Spanner Enumeration for Temporal Graphs. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kurita_et_al:LIPIcs.SAND.2025.9,
  author =	{Kurita, Kazuhiro and Marino, Andrea and Schoeters, Jason and Uno, Takeaki},
  title =	{{Spanner Enumeration for Temporal Graphs}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{9:1--9:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.9},
  URN =		{urn:nbn:de:0030-drops-230621},
  doi =		{10.4230/LIPIcs.SAND.2025.9},
  annote =	{Keywords: temporal graphs, temporal spanners, one-to-all connectivity, all-to-all connectivity enumeration, NP-completeness, Dual-hardness, binary partition tree, flashlight search, polynomial delay}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.3
Knowledge Engineering Using Large Language Models

Authors: Bradley P. Allen, Lise Stork, and Paul Groth

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Knowledge engineering is a discipline that focuses on the creation and maintenance of processes that generate and apply knowledge. Traditionally, knowledge engineering approaches have focused on knowledge expressed in formal languages. The emergence of large language models and their capabilities to effectively work with natural language, in its broadest sense, raises questions about the foundations and practice of knowledge engineering. Here, we outline the potential role of LLMs in knowledge engineering, identifying two central directions: 1) creating hybrid neuro-symbolic knowledge systems; and 2) enabling knowledge engineering in natural language. Additionally, we formulate key open research questions to tackle these directions.
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Bradley P. Allen, Lise Stork, and Paul Groth. Knowledge Engineering Using Large Language Models. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{allen_et_al:TGDK.1.1.3,
  author =	{Allen, Bradley P. and Stork, Lise and Groth, Paul},
  title =	{{Knowledge Engineering Using Large Language Models}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:19},
  ISSN =	{2942-7517},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.3},
  URN =		{urn:nbn:de:0030-drops-194777},
  doi =		{10.4230/TGDK.1.1.3},
  annote =	{Keywords: knowledge engineering, large language models}
}
Document
DOI: 10.4230/OASIcs.Tokenomics.2020.5
Decentralization in Open Quorum Systems: Limitative Results for Ripple and Stellar

Authors: Andrea Bracciali, Davide Grossi, and Ronald de Haan

Published in: OASIcs, Volume 82, 2nd International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2020)

Abstract
Decentralisation is one of the promises introduced by blockchain technologies: fair and secure interaction amongst peers with no dominant positions, single points of failure or censorship. Decentralisation, however, appears difficult to be formally defined, possibly a continuum property of systems that can be more or less decentralised, or can tend to decentralisation in their lifetime. In this paper we focus on decentralisation in quorum-based approaches to open (permissionless) consensus as illustrated in influential protocols such as the Ripple and Stellar protocols. Drawing from game theory and computational complexity, we establish limiting results concerning the decentralisation vs. safety trade-off in Ripple and Stellar, and we propose a novel methodology to formalise and quantitatively analyse decentralisation in this type of blockchains.
Cite as

Andrea Bracciali, Davide Grossi, and Ronald de Haan. Decentralization in Open Quorum Systems: Limitative Results for Ripple and Stellar. In 2nd International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2020). Open Access Series in Informatics (OASIcs), Volume 82, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{bracciali_et_al:OASIcs.Tokenomics.2020.5,
  author =	{Bracciali, Andrea and Grossi, Davide and de Haan, Ronald},
  title =	{{Decentralization in Open Quorum Systems: Limitative Results for Ripple and Stellar}},
  booktitle =	{2nd International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2020)},
  pages =	{5:1--5:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-157-3},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{82},
  editor =	{Anceaume, Emmanuelle and Bisi\`{e}re, Christophe and Bouvard, Matthieu and Bramas, Quentin and Casamatta, Catherine},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Tokenomics.2020.5},
  URN =		{urn:nbn:de:0030-drops-135277},
  doi =		{10.4230/OASIcs.Tokenomics.2020.5},
  annote =	{Keywords: Blockchain, decentralization, game theory, computational complexity}
}
Document
DOI: 10.4230/LIPIcs.ICALP.2016.148
Sublinear-Space Bounded-Delay Enumeration for Massive Network Analytics: Maximal Cliques

Authors: Alessio Conte, Roberto Grossi, Andrea Marino, and Luca Versari

Published in: LIPIcs, Volume 55, 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016)

Abstract
Due to the sheer size of real-world networks, delay and space become quite relevant measures for the cost of enumeration in network analytics. This paper presents efficient algorithms for listing maximum cliques in networks, providing the first sublinear-space bounds with guaranteed delay per enumerated clique, thus comparing favorably with the known literature.
Cite as

Alessio Conte, Roberto Grossi, Andrea Marino, and Luca Versari. Sublinear-Space Bounded-Delay Enumeration for Massive Network Analytics: Maximal Cliques. In 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 55, pp. 148:1-148:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{conte_et_al:LIPIcs.ICALP.2016.148,
  author =	{Conte, Alessio and Grossi, Roberto and Marino, Andrea and Versari, Luca},
  title =	{{Sublinear-Space Bounded-Delay Enumeration for Massive Network Analytics: Maximal Cliques}},
  booktitle =	{43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016)},
  pages =	{148:1--148:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-013-2},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{55},
  editor =	{Chatzigiannakis, Ioannis and Mitzenmacher, Michael and Rabani, Yuval and Sangiorgi, Davide},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2016.148},
  URN =		{urn:nbn:de:0030-drops-62927},
  doi =		{10.4230/LIPIcs.ICALP.2016.148},
  annote =	{Keywords: Enumeration algorithms, maximal cliques, network mining and analytics, reverse search, space efficiency}
}
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