Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, and Jan Fostier. b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{depuydt_et_al:LIPIcs.WABI.2024.10, author = {Depuydt, Lore and Renders, Luca and Van de Vyver, Simon and Veys, Lennart and Gagie, Travis and Fostier, Jan}, title = {{b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {10:1--10:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.10}, URN = {urn:nbn:de:0030-drops-206546}, doi = {10.4230/LIPIcs.WABI.2024.10}, annote = {Keywords: Pan-genomics, FM-index, r-index, Move Structure, Bidirectional Search, Approximate Pattern Matching, Lossless Alignment, Cache Efficiency} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Wiktor Zuba, Grigorios Loukides, Solon P. Pissis, and Sharma V. Thankachan. Approximate Suffix-Prefix Dictionary Queries. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 85:1-85:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zuba_et_al:LIPIcs.MFCS.2024.85, author = {Zuba, Wiktor and Loukides, Grigorios and Pissis, Solon P. and Thankachan, Sharma V.}, title = {{Approximate Suffix-Prefix Dictionary Queries}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {85:1--85:18}, 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.2024.85}, URN = {urn:nbn:de:0030-drops-206416}, doi = {10.4230/LIPIcs.MFCS.2024.85}, annote = {Keywords: all-pairs suffix-prefix, suffix-prefix queries, suffix tree, k-errata tree} }
Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)
Hugo Aaronson, Tom Gur, Ninad Rajgopal, and Ron D. Rothblum. Distribution-Free Proofs of Proximity. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 24:1-24:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{aaronson_et_al:LIPIcs.CCC.2024.24, author = {Aaronson, Hugo and Gur, Tom and Rajgopal, Ninad and Rothblum, Ron D.}, title = {{Distribution-Free Proofs of Proximity}}, booktitle = {39th Computational Complexity Conference (CCC 2024)}, pages = {24:1--24:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-331-7}, ISSN = {1868-8969}, year = {2024}, volume = {300}, editor = {Santhanam, Rahul}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.24}, URN = {urn:nbn:de:0030-drops-204204}, doi = {10.4230/LIPIcs.CCC.2024.24}, annote = {Keywords: Property Testing, Interactive Proofs, Distribution-Free Property Testing} }
Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)
Panagiotis Charalampopoulos, Paweł Gawrychowski, and Samah Ghazawi. Optimal Bounds for Distinct Quartics. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 39:1-39:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{charalampopoulos_et_al:LIPIcs.ICALP.2024.39, author = {Charalampopoulos, Panagiotis and Gawrychowski, Pawe{\l} and Ghazawi, Samah}, title = {{Optimal Bounds for Distinct Quartics}}, booktitle = {51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)}, pages = {39:1--39:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-322-5}, ISSN = {1868-8969}, year = {2024}, volume = {297}, editor = {Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.39}, URN = {urn:nbn:de:0030-drops-201823}, doi = {10.4230/LIPIcs.ICALP.2024.39}, annote = {Keywords: 2D strings, quartics, repetitions, periodicity} }
Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)
Djamal Belazzougui, Gregory Kucherov, and Stefan Walzer. Better Space-Time-Robustness Trade-Offs for Set Reconciliation. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{belazzougui_et_al:LIPIcs.ICALP.2024.20, author = {Belazzougui, Djamal and Kucherov, Gregory and Walzer, Stefan}, title = {{Better Space-Time-Robustness Trade-Offs for Set Reconciliation}}, booktitle = {51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)}, pages = {20:1--20:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-322-5}, ISSN = {1868-8969}, year = {2024}, volume = {297}, editor = {Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.20}, URN = {urn:nbn:de:0030-drops-201639}, doi = {10.4230/LIPIcs.ICALP.2024.20}, annote = {Keywords: data structures, hashing, set reconciliation, invertible Bloom lookup tables, random hypergraphs, BCH codes} }
Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)
Orestis Plevrakis, Seyoon Ragavan, and S. Matthew Weinberg. On the Cut-Query Complexity of Approximating Max-Cut. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 115:1-115:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{plevrakis_et_al:LIPIcs.ICALP.2024.115, author = {Plevrakis, Orestis and Ragavan, Seyoon and Weinberg, S. Matthew}, title = {{On the Cut-Query Complexity of Approximating Max-Cut}}, booktitle = {51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)}, pages = {115:1--115:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-322-5}, ISSN = {1868-8969}, year = {2024}, volume = {297}, editor = {Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.115}, URN = {urn:nbn:de:0030-drops-202587}, doi = {10.4230/LIPIcs.ICALP.2024.115}, annote = {Keywords: query complexity, maximum cut, approximation algorithms, graph sparsification} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Gregory Kucherov and Steven Skiena. Improving the Sensitivity of MinHash Through Hash-Value Analysis. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 20:1-20:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{kucherov_et_al:LIPIcs.CPM.2023.20, author = {Kucherov, Gregory and Skiena, Steven}, title = {{Improving the Sensitivity of MinHash Through Hash-Value Analysis}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {20:1--20:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-276-1}, ISSN = {1868-8969}, year = {2023}, volume = {259}, editor = {Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.20}, URN = {urn:nbn:de:0030-drops-179740}, doi = {10.4230/LIPIcs.CPM.2023.20}, annote = {Keywords: MinHash sketching, sequence similarity, hashing} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov. Efficient Reconciliation of Genomic Datasets of High Similarity. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{shibuya_et_al:LIPIcs.WABI.2022.14, author = {Shibuya, Yoshihiro and Belazzougui, Djamal and Kucherov, Gregory}, title = {{Efficient Reconciliation of Genomic Datasets of High Similarity}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {14:1--14:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.14}, URN = {urn:nbn:de:0030-drops-170481}, doi = {10.4230/LIPIcs.WABI.2022.14}, annote = {Keywords: k-mers, sketching, Invertible Bloom Lookup Tables, IBLT, MinHash, syncmers, minimizers} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov. Space-Efficient Representation of Genomic k-Mer Count Tables. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 8:1-8:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{shibuya_et_al:LIPIcs.WABI.2021.8, author = {Shibuya, Yoshihiro and Belazzougui, Djamal and Kucherov, Gregory}, title = {{Space-Efficient Representation of Genomic k-Mer Count Tables}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {8:1--8:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.8}, URN = {urn:nbn:de:0030-drops-143619}, doi = {10.4230/LIPIcs.WABI.2021.8}, annote = {Keywords: k-mer counting, data structures, compression, minimizers, compressed static function, Bloom filter, empirical entropy} }
Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)
Djamal Belazzougui and Gregory Kucherov. Efficient Tree-Structured Categorical Retrieval. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 4:1-4:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{belazzougui_et_al:LIPIcs.CPM.2020.4, author = {Belazzougui, Djamal and Kucherov, Gregory}, title = {{Efficient Tree-Structured Categorical Retrieval}}, booktitle = {31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)}, pages = {4:1--4:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-149-8}, ISSN = {1868-8969}, year = {2020}, volume = {161}, editor = {G{\o}rtz, Inge Li and Weimann, Oren}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.4}, URN = {urn:nbn:de:0030-drops-121299}, doi = {10.4230/LIPIcs.CPM.2020.4}, annote = {Keywords: pattern matching, document retrieval, category tree, space-efficient data structures} }
Published in: Dagstuhl Reports, Volume 4, Issue 3 (2014)
Maxime Crochemore, James D. Currie, Gregory Kucherov, and Dirk Nowotka. Combinatorics and Algorithmics of Strings (Dagstuhl Seminar 14111). In Dagstuhl Reports, Volume 4, Issue 3, pp. 28-46, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)
@Article{crochemore_et_al:DagRep.4.3.28, author = {Crochemore, Maxime and Currie, James D. and Kucherov, Gregory and Nowotka, Dirk}, title = {{Combinatorics and Algorithmics of Strings (Dagstuhl Seminar 14111)}}, pages = {28--46}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2014}, volume = {4}, number = {3}, editor = {Crochemore, Maxime and Currie, James D. and Kucherov, Gregory and Nowotka, Dirk}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagRep.4.3.28}, URN = {urn:nbn:de:0030-drops-45524}, doi = {10.4230/DagRep.4.3.28}, annote = {Keywords: combinatorics on words, string algorithms, automata} }