13 Search Results for "Díaz-Domínguez, Diego"

Document
DOI: 10.4230/LIPIcs.CPM.2026.5
Efficient Grammar Compression via RLZ-Based RePair

Authors: Rahul Varki, Travis Gagie, and Christina Boucher

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Among grammar-based compression techniques, RePair is a notable offline encoding scheme known for its simplicity and powerful combinatorial properties, producing compact grammars by repeatedly replacing the most frequent adjacent pairs of symbols, known as bigrams. However, RePair’s memory usage scales poorly with input size, as it loads the entire text into memory. In contrast, Relative Lempel-Ziv (RLZ) parsing offers a scalable and lightweight online encoding scheme that losslessly represents a text in terms of phrases that refer to a reference string, but it often fails to expose deeper structural patterns. We introduce an algorithm that produces a RePair grammar from the RLZ parse of the input, leveraging the strengths of both methods. Our method, RLZ-RePair, performs bigram replacements systematically, preserving the integrity of the RLZ phrases throughout the RePair iterations. When the reference is well chosen, our method achieves the same grammar as standard RePair while significantly reducing both memory usage and the number of bigram replacements. In particular, we show that RLZ-RePair can reduce memory usage by more than 80% while incurring only a modest runtime increase compared to RePair. To our knowledge, RLZ-RePair is one of the first scalable methods that constructs exact RePair grammars, resulting in a grammar-based compressor that is both practical for large datasets and faithful to the theoretical elegance of RePair.
Cite as

Rahul Varki, Travis Gagie, and Christina Boucher. Efficient Grammar Compression via RLZ-Based RePair. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 5:1-5:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{varki_et_al:LIPIcs.CPM.2026.5,
  author =	{Varki, Rahul and Gagie, Travis and Boucher, Christina},
  title =	{{Efficient Grammar Compression via RLZ-Based RePair}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{5:1--5:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip 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.CPM.2026.5},
  URN =		{urn:nbn:de:0030-drops-259310},
  doi =		{10.4230/LIPIcs.CPM.2026.5},
  annote =	{Keywords: RePair, RLZ, Grammar Compression}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.16
Merging RLBWTs Adaptively

Authors: Travis Gagie

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in O (r) space and O ((r + L) log (m + n)) time, where m and n are the lengths of the uncompressed strings, r is the number of runs in the final eBWT and L is the sum of its irreducible LCP values.
Cite as

Travis Gagie. Merging RLBWTs Adaptively. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 16:1-16:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{gagie:LIPIcs.CPM.2026.16,
  author =	{Gagie, Travis},
  title =	{{Merging RLBWTs Adaptively}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{16:1--16:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip 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.CPM.2026.16},
  URN =		{urn:nbn:de:0030-drops-259420},
  doi =		{10.4230/LIPIcs.CPM.2026.16},
  annote =	{Keywords: Burrows-Wheeler Transform, run-length compression, RLBWT, construction, merging}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.29
The TAG Array of a Multiple Sequence Alignment

Authors: Jannik Olbrich and Enno Ohlebusch

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs, this has the advantage that efficient exact search via indexes based on the Burrows-Wheeler Transform (BWT) is possible, that no chimeric sequences are created, and that the results are not influenced by heuristics. However, such an index may report a match in thousands of positions even if these all correspond to the same locus, making downstream analysis unnecessarily more expensive. For sufficiently similar sequences (e.g. human chromosomes), a multiple sequence alignment (MSA) can be computed. Since an MSA tends to group similar strings in the same columns, it is likely that a string occurring thousands of times in the pangenome can be described by very few columns in the MSA. We describe a method to tag entries in the BWT with the corresponding column in the MSA and develop an index that can map matches in the BWT to columns in the MSA in time proportional to the output. As a by-product, we can project a match to a designated reference genome, a capability that current pangenome aligners lack.
Cite as

Jannik Olbrich and Enno Ohlebusch. The TAG Array of a Multiple Sequence Alignment. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 29:1-29:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{olbrich_et_al:LIPIcs.CPM.2026.29,
  author =	{Olbrich, Jannik and Ohlebusch, Enno},
  title =	{{The TAG Array of a Multiple Sequence Alignment}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{29:1--29:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip 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.CPM.2026.29},
  URN =		{urn:nbn:de:0030-drops-259555},
  doi =		{10.4230/LIPIcs.CPM.2026.29},
  annote =	{Keywords: Burrows-Wheeler Transform, pattern matching, index data structure, pangenomics}
}
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
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.6
Optimizing the Performance of the FM-Index for Large-Scale Data

Authors: Eddie Ferro and Christina Boucher

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

Abstract
The FM-index is a fundamental data structure used in bioinformatics to efficiently search for strings and index genomes. However, the FM-index can pose computational challenges, particularly in the context of large-scale genomic datasets, due to the complexity of its underlying components and data encodings. In this paper, we present a comprehensive review of efficient variants of the FM-index and the encoding strategies used to improve performance. We examine hardware-accelerated techniques, such as memory-efficient data layouts and cache-aware structures, as well as software-level innovations, including algorithmic refinements and compact representations. The reviewed work demonstrates substantial gains in both speed and scalability, making methods that use the FM-index more practical for high-throughput genomic applications. By analyzing the trade-offs and design choices of these variants, we highlight how combining hardware-aware and software-centric strategies enables more efficient FM-index construction and usage across a range of bioinformatics tasks.
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Eddie Ferro and Christina Boucher. Optimizing the Performance of the FM-Index for Large-Scale Data. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ferro_et_al:OASIcs.Manzini.6,
  author =	{Ferro, Eddie and Boucher, Christina},
  title =	{{Optimizing the Performance of the FM-Index for Large-Scale Data}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{6:1--6:21},
  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.6},
  URN =		{urn:nbn:de:0030-drops-239140},
  doi =		{10.4230/OASIcs.Manzini.6},
  annote =	{Keywords: FM-Index Acceleration, Run-Length Encoding, Suffix Array Optimization, Burrows-Wheeler Transform, Efficient Backward Search}
}
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.
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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/LIPIcs.SEA.2025.14
Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing

Authors: Diego Díaz-Domínguez

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

Abstract
We present compression algorithms designed to process terabyte-sized datasets in parallel. Our approach builds on locally consistent grammars, a lightweight form of compression, combined with simple post-processing techniques to achieve further space reductions. Locally consistent grammar algorithms are suitable for scaling as they need minimal satellite information to compact the text, but they are not inherently parallel. To enable parallelisation, we introduce a novel concept that we call stable local consistency. A grammar algorithm ALG is stable if for any pattern P occurring in a collection 𝒯 = {T_1, T_2, …, T_k}, instances ALG(T_1), ALG(T_2), …, ALG(T_k) independently produce cores for P with the same topology. In a locally consistent grammar, the core of P is a subset of nodes and edges in the parse tree of 𝒯 that remains the same in all the occurrences of P. This feature enables compression, but it only holds if ALG defines a common set of nonterminal symbols for the strings. Stability removes this restriction, allowing us to run ALG(T_1), ALG(T_2), …, ALG(T_k) in parallel and subsequently merge their grammars into a single output equivalent to that of ALG(𝒯). We implemented our ideas and tested them on massive datasets. Our experiments showed that our method could process 7.9 TB of bacterial genomes in around nine hours, using 16 threads and 0.43 bits/symbol of working memory, achieving a compression ratio of 85x.
Cite as

Diego Díaz-Domínguez. Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 14:1-14:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{diazdominguez:LIPIcs.SEA.2025.14,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego},
  title =	{{Efficient Terabyte-Scale Text Compression via Stable Local Consistency and Parallel Grammar Processing}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{14:1--14:20},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-232525},
  doi =		{10.4230/LIPIcs.SEA.2025.14},
  annote =	{Keywords: Grammar compression, locally consistent parsing, hashing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.2
IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data

Authors: Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger

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

Abstract
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the BWT in terms of time and memory usage is key to these applications. We present a novel external-memory algorithm called Improved-Bucket Burrows-Wheeler transform (IBB) for constructing the BWT of DNA datasets with highly diverse sequence lengths. IBB uses a right-aligned approach to efficiently handle sequences of varying lengths, a tree-based data structure to manage relative insert positions and ranks, and fine buckets to reduce the necessary amount of input and output to external memory. Our experiments demonstrate that IBB is 10% to 40% faster than the best existing state-of-the-art BWT construction algorithms on most datasets while maintaining competitive memory consumption.
Cite as

Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger. IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{adler_et_al:LIPIcs.SEA.2025.2,
  author =	{Adler, Enno and B\"{o}ttcher, Stefan and Hartel, Rita and Steininger, Cederic Alexander},
  title =	{{IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{2:1--2:18},
  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.2025.2},
  URN =		{urn:nbn:de:0030-drops-232402},
  doi =		{10.4230/LIPIcs.SEA.2025.2},
  annote =	{Keywords: burrows-wheeler transform, self-indexes, external-memory}
}
Document
Position
DOI: 10.4230/TGDK.2.1.2
Grounding Stream Reasoning Research

Authors: Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
In the last decade, there has been a growing interest in applying AI technologies to implement complex data analytics over data streams. To this end, researchers in various fields have been organising a yearly event called the "Stream Reasoning Workshop" to share perspectives, challenges, and experiences around this topic. In this paper, the previous organisers of the workshops and other community members provide a summary of the main research results that have been discussed during the first six editions of the event. These results can be categorised into four main research areas: The first is concerned with the technological challenges related to handling large data streams. The second area aims at adapting and extending existing semantic technologies to data streams. The third and fourth areas focus on how to implement reasoning techniques, either considering deductive or inductive techniques, to extract new and valuable knowledge from the data in the stream. This summary is written not only to provide a crystallisation of the field, but also to point out distinctive traits of the stream reasoning community. Moreover, it also provides a foundation for future research by enumerating a list of use cases and open challenges, to stimulate others to join this exciting research area.
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Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer. Grounding Stream Reasoning Research. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 2:1-2:47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.7
Simple Runs-Bounded FM-Index Designs Are Fast

Authors: Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)

Abstract
Given a string X of length n on alphabet σ, the FM-index data structure allows counting all occurrences of a pattern P of length m in O(m) time via an algorithm called backward search. An important difficulty when searching with an FM-index is to support queries on L, the Burrows-Wheeler transform of X, while L is in compressed form. This problem has been the subject of intense research for 25 years now. Run-length encoding of L is an effective way to reduce index size, in particular when the data being indexed is highly-repetitive, which is the case in many types of modern data, including those arising from versioned document collections and in pangenomics. This paper takes a back-to-basics look at supporting backward search in FM-indexes, exploring and engineering two simple designs. The first divides the BWT string into blocks containing b symbols each and then run-length compresses each block separately, possibly introducing new runs (compared to applying run-length encoding once, to the whole string). Each block stores counts of each symbol that occurs before the block. This method supports the operation rank_c(L, i) (i.e., count the number of times c occurs in the prefix L[1..i]) by first determining the block i/b in which i falls and scanning the block to the appropriate position counting occurrences of c along the way. This partial answer to rank_c(L, i) is then added to the stored count of c symbols before the block to determine the final answer. Our second design has a similar structure, but instead divides the run-length-encoded version of L into blocks containing an equal number of runs. The trick then is to determine the block in which a query falls, which is achieved via a predecessor query over the block starting positions. We show via extensive experiments on a wide range of repetitive text collections that these FM-indexes are not only easy to implement, but also fast and space efficient in practice.
Cite as

Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela. Simple Runs-Bounded FM-Index Designs Are Fast. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 7:1-7:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{diazdominguez_et_al:LIPIcs.SEA.2023.7,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and D\"{o}nges, Saska and Puglisi, Simon J. and Salmela, Leena},
  title =	{{Simple Runs-Bounded FM-Index Designs Are Fast}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{7:1--7:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.7},
  URN =		{urn:nbn:de:0030-drops-183579},
  doi =		{10.4230/LIPIcs.SEA.2023.7},
  annote =	{Keywords: data structures, efficient algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.29
Efficient Construction of the BWT for Repetitive Text Using String Compression

Authors: Diego Díaz-Domínguez and Gonzalo Navarro

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
We present a new semi-external algorithm that builds the Burrows-Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce the computational costs when the input is massive and repetitive. Concretely, we build on induced suffix sorting (ISS) and resort to run-length and grammar compression to maintain our intermediate results in compact form. Our compression format not only saves space, but it also speeds up the required computations. Our experiments show important savings in both space and computation time when the text is repetitive. On average, we are 3.7x faster than the baseline compressed approach, while maintaining a similar memory consumption. These results make our method stand out as the only one (to our knowledge) that can build the BCR BWT of a collection of 25 human genomes (75 GB) in about 7.3 hours, and using only 27 GB of working memory.
Cite as

Diego Díaz-Domínguez and Gonzalo Navarro. Efficient Construction of the BWT for Repetitive Text Using String Compression. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 29:1-29:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{diazdominguez_et_al:LIPIcs.CPM.2022.29,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and Navarro, Gonzalo},
  title =	{{Efficient Construction of the BWT for Repetitive Text Using String Compression}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{29:1--29:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.29},
  URN =		{urn:nbn:de:0030-drops-161564},
  doi =		{10.4230/LIPIcs.CPM.2022.29},
  annote =	{Keywords: BWT, string compression, repetitive text}
}
Document
DOI: 10.4230/LIPIcs.CPM.2019.26
Simulating the DNA Overlap Graph in Succinct Space

Authors: Diego Díaz-Domínguez, Travis Gagie, and Gonzalo Navarro

Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)

Abstract
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph (dBG) of some order k. Each has advantages over the other depending on the application. Still, the ideal setting would be to have an index of the reads that is easy to build and can be adapted to any type of biological analysis. In this paper we propose rBOSS, a new data structure based on the Burrows-Wheeler Transform (BWT), which gets close to that ideal. Our rBOSS simultaneously encodes all the dBGs of a set of sequencing reads up to some order k, and for any dBG node v, it can compute in O(k) time all the other nodes whose labels have an overlap of at least m characters with the label of v, with m being a parameter. If we choose the parameter k equal to the size of the reads (assuming that all have equal length), then we can simulate the overlap graph of the read set. Instead of storing the edges of this graph explicitly, rBOSS computes them on the fly as we traverse the graph. As most BWT-based structures, rBOSS is unidirectional, meaning that we can retrieve only the suffix overlaps of the nodes. However, we exploit the property of the DNA reverse complements to simulate bi-directionality. We implemented a genome assembler on top of rBOSS to demonstrate its usefulness. The experimental results show that, using k=100, our rBOSS-based assembler can process ~500K reads of 150 characters long each (a FASTQ file of 185 MB) in less than 15 minutes and using 110 MB in total. It produces contigs of mean sizes over 10,000, which is twice the size obtained by using a pure de Bruijn graph of fixed length k.
Cite as

Diego Díaz-Domínguez, Travis Gagie, and Gonzalo Navarro. Simulating the DNA Overlap Graph in Succinct Space. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 26:1-26:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{diazdominguez_et_al:LIPIcs.CPM.2019.26,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and Gagie, Travis and Navarro, Gonzalo},
  title =	{{Simulating the DNA Overlap Graph in Succinct Space}},
  booktitle =	{30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)},
  pages =	{26:1--26:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-103-0},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{128},
  editor =	{Pisanti, Nadia and P. Pissis, Solon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.26},
  URN =		{urn:nbn:de:0030-drops-104978},
  doi =		{10.4230/LIPIcs.CPM.2019.26},
  annote =	{Keywords: Overlap graph, de Bruijn graph, DNA sequencing, Succinct ordinal trees}
}
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