Compressed Indexes for Regular Languages with Applications to Computational Pan-genomics

Project Information

REGINDEX

Grant agreement ID: 101039208

DOI

10.3030/101039208

EC signature date 28 January 2022

Start date 1 September 2022

End date 31 August 2027

Funded under

• European Research Council (ERC)

Total cost

€ 1 385 743,00

EU contribution

€ 1 385 743,00

Coordinated by

UNIVERSITA CA' FOSCARI VENEZIA
Italy

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (1)

Data management plan

Publications

Conference proceedings (12)

Sorting Finite Automata via Partition Refinement

Author(s): Ruben Becker; Manuel Cáceres; Davide Cenzato; Sung-Hwan Kim; Bojana Kodric; Francisco Olivares; Nicola Prezza
Published in: Proceedings of the 31st Annual European Symposium on Algorithms (ESA 2023), 2023, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.48550/arXiv.2305.05129

Random Wheeler Automata

Author(s): Ruben Becker, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Riccardo Maso, Nicola Prezza
Published in: Proceedings of the 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), 2024, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/LIPIcs.CPM.2024.5

The Rational Construction of a Wheeler DFA

Author(s): Giovanni Manzini, Alberto Policriti, Nicola Prezza, Brian Riccardi
Published in: Proceedings of the 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Issue 35, 2024, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/LIPIcs.CPM.2024.23

Top-k Frequent Patterns in Streams and Parameterized-Space LZ Compression

Author(s): Patrick Dinklage, Johannes Fischer, Nicola Prezza
Published in: Proceedings of the 22nd International Symposium on Experimental Algorithms (SEA 2024), 2024, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/LIPIcs.SEA.2024.9

On Computing the Smallest Suffixient Set

Author(s): Davide Cenzato, Francisco Olivares, Nicola Prezza
Published in: Proceedings of the 31st International Symposium on String Processing and Information Retrieval (SPIRE 2024), 2024, ISSN 1611-3349
Publisher: Springer Cham
DOI: 10.48550/arXiv.2407.18753

Faster Prefix-Sorting Algorithms for Deterministic Finite Automata

Author(s): Sung-Hwan Kim; Francisco Olivares; Nicola Prezza
Published in: Proceedings of the 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), 2023, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.48550/arxiv.2304.10962

Computing matching statistics on Wheeler DFAs

Author(s): Conte A.; Cotumaccio N.; Gagie T.; Manzini G.; Prezza N.; Sciortino M.
Published in: Proceedings of the 2023 Data Compression Conference (DCC), 2023, ISSN 2375-0359
Publisher: IEEE
DOI: 10.48550/arXiv.2301.05338

Optimal Wheeler Language Recognition

Author(s): Ruben Becker; Davide Cenzato; Sung-Hwan Kim; Bojana Kodric; Alberto Policriti; Nicola Prezza
Published in: Proceedings of String Processing and Information Retrieval 2023 ISBN: 9783031439797, 2023, ISSN 1611-3349
Publisher: Springer
DOI: 10.48550/arXiv.2306.04737

Sketching and Streaming for Dictionary Compression

Author(s): Ruben Becker, Matteo Canton, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Nicola Prezza
Published in: Proceedings of the Data Compression Conference 2024, 2024, ISSN 2375-0359
Publisher: IEEE
DOI: 10.48550/arXiv.2310.17980

Computing the LCP Array of a Labeled Graph

Author(s): Jarno N. Alanko, Davide Cenzato, Nicola Cotumaccio, Sung-Hwan Kim, Giovanni Manzini, Nicola Prezza
Published in: Proceedings of the 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), 2024, ISSN 1868-8969
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/LIPIcs.CPM.2024.1

Indexing Finite-State Automata Using Forward-Stable Partitions

Author(s): Ruben Becker, Sung-Hwan Kim, Nicola Prezza, Carlo Tosoni
Published in: Proceedings of the 31st International Symposium on String Processing and Information Retrieval (SPIRE 2024), 2024, ISSN 1611-3349
Publisher: Springer Cham
DOI: 10.48550/arXiv.2406.02763

Space-time Trade-offs for the LCP Array of Wheeler DFAs

Author(s): Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza
Published in: Proceedings of String Processing and Information Retrieval 2023, 2023, ISSN 1611-3349
Publisher: Springer
DOI: 10.48550/arXiv.2306.05684

Peer reviewed articles (3)

A survey of BWT variants for string collections

Author(s): Cenzato, Davide; Lipták, Zsuzsanna
Published in: Bioinformatics, 2024, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.48550/arXiv.2202.13235

Toward a Definitive Compressibility Measure for Repetitive Sequences

Author(s): Tomasz Kociumaka; Gonzalo Navarro; Nicola Prezza
Published in: IEEE Transactions on Information Theory, 2023, ISSN 0018-9448
Publisher: IEEE
DOI: 10.48550/arXiv.1910.02151

Co-lexicographically Ordering Automata and Regular Languages -- Part I

Author(s): Nicola Cotumaccio; Giovanna D’Agostino; Alberto Policriti; Nicola Prezza
Published in: Journal of the ACM, 2023, ISSN 0004-5411
Publisher: Association for Computing Machinery, New York, NY, United States
DOI: 10.1145/3607471