LIPIcs, Volume 242
WABI 2022, September 5-7, 2022, Potsdam, Germany
Editors: Christina Boucher and Sven Rahmann
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Stefan Hermann, Hans-Peter Lehmann, Giulio Ermanno Pibiri, Peter Sanders, and Stefan Walzer. PHOBIC: Perfect Hashing With Optimized Bucket Sizes and Interleaved Coding. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 69:1-69:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hermann_et_al:LIPIcs.ESA.2024.69, author = {Hermann, Stefan and Lehmann, Hans-Peter and Pibiri, Giulio Ermanno and Sanders, Peter and Walzer, Stefan}, title = {{PHOBIC: Perfect Hashing With Optimized Bucket Sizes and Interleaved Coding}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {69:1--69:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-338-6}, ISSN = {1868-8969}, year = {2024}, volume = {308}, editor = {Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.69}, URN = {urn:nbn:de:0030-drops-211405}, doi = {10.4230/LIPIcs.ESA.2024.69}, annote = {Keywords: Compressed Data Structures, Minimal Perfect Hashing, GPU} }
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Justin Kim, Rahul Varki, Marco Oliva, and Christina Boucher. Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 78:1-78:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{kim_et_al:LIPIcs.ESA.2024.78, author = {Kim, Justin and Varki, Rahul and Oliva, Marco and Boucher, Christina}, title = {{Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {78:1--78:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-338-6}, ISSN = {1868-8969}, year = {2024}, volume = {308}, editor = {Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.78}, URN = {urn:nbn:de:0030-drops-211496}, doi = {10.4230/LIPIcs.ESA.2024.78}, annote = {Keywords: RePair, Compressed Data Structures, Prefix-free Parsing} }
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Zsuzsanna Lipták, Francesco Masillo, and Gonzalo Navarro. A Textbook Solution for Dynamic Strings. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 86:1-86:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{liptak_et_al:LIPIcs.ESA.2024.86, author = {Lipt\'{a}k, Zsuzsanna and Masillo, Francesco and Navarro, Gonzalo}, title = {{A Textbook Solution for Dynamic Strings}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {86:1--86:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-338-6}, ISSN = {1868-8969}, year = {2024}, volume = {308}, editor = {Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.86}, URN = {urn:nbn:de:0030-drops-211576}, doi = {10.4230/LIPIcs.ESA.2024.86}, annote = {Keywords: dynamic strings, splay trees, dynamic data structures, LCP, circular strings} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, and Ben Langmead. MEM-Based Pangenome Indexing for k-mer Queries. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 4:1-4:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hwang_et_al:LIPIcs.WABI.2024.4, author = {Hwang, Stephen and Brown, Nathaniel K. and Ahmed, Omar Y. and Jenike, Katharine M. and Kovaka, Sam and Schatz, Michael C. and Langmead, Ben}, title = {{MEM-Based Pangenome Indexing for k-mer Queries}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {4:1--4:17}, 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.2024.4}, URN = {urn:nbn:de:0030-drops-206482}, doi = {10.4230/LIPIcs.WABI.2024.4}, annote = {Keywords: Pangenomics, Comparative genomics, Compressed indexing} }
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 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Md. Hasin Abrar and Paul Medvedev. PLA-index: A k-mer Index Exploiting Rank Curve Linearity. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{abrar_et_al:LIPIcs.WABI.2024.13, author = {Abrar, Md. Hasin and Medvedev, Paul}, title = {{PLA-index: A k-mer Index Exploiting Rank Curve Linearity}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {13:1--13:18}, 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.2024.13}, URN = {urn:nbn:de:0030-drops-206578}, doi = {10.4230/LIPIcs.WABI.2024.13}, annote = {Keywords: K-mer index, Piece-wise linear approximation, Learned index} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti. A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{ascone_et_al:LIPIcs.WABI.2024.14, author = {Ascone, Rocco and Bernardini, Giulia and Conte, Alessio and Equi, Massimo and Gabory, Esteban and Grossi, Roberto and Pisanti, Nadia}, title = {{A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {14:1--14:21}, 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.2024.14}, URN = {urn:nbn:de:0030-drops-206586}, doi = {10.4230/LIPIcs.WABI.2024.14}, annote = {Keywords: Pangenomics, pattern matching, degenerate string, founder graph, fine-grained complexity} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Jens Zentgraf and Sven Rahmann. Swiftly Identifying Strongly Unique k-Mers. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2024.15, author = {Zentgraf, Jens and Rahmann, Sven}, title = {{Swiftly Identifying Strongly Unique k-Mers}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {15:1--15:15}, 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.2024.15}, URN = {urn:nbn:de:0030-drops-206593}, doi = {10.4230/LIPIcs.WABI.2024.15}, annote = {Keywords: k-mer, Hamming distance, strong uniqueness, parallelization, algorithm engineering} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23, author = {Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert}, title = {{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {23:1--23:18}, 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.2024.23}, URN = {urn:nbn:de:0030-drops-206673}, doi = {10.4230/LIPIcs.WABI.2024.23}, annote = {Keywords: pangenome, variation graph, genome alignment, population genomics} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Nico Bertram, Johannes Fischer, and Lukas Nalbach. Move-r: Optimizing the r-index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bertram_et_al:LIPIcs.SEA.2024.1, author = {Bertram, Nico and Fischer, Johannes and Nalbach, Lukas}, title = {{Move-r: Optimizing the r-index}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {1:1--1:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-325-6}, ISSN = {1868-8969}, year = {2024}, volume = {301}, editor = {Liberti, Leo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.1}, URN = {urn:nbn:de:0030-drops-203662}, doi = {10.4230/LIPIcs.SEA.2024.1}, annote = {Keywords: Compressed Text Index, Burrows-Wheeler Transform} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro. Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{draesslerova_et_al:LIPIcs.SEA.2024.10, author = {Draesslerov\'{a}, Dominika and Ahmed, Omar and Gagie, Travis and Holub, Jan and Langmead, Ben and Manzini, Giovanni and Navarro, Gonzalo}, title = {{Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {10:1--10:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-325-6}, ISSN = {1868-8969}, year = {2024}, volume = {301}, editor = {Liberti, Leo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.10}, URN = {urn:nbn:de:0030-drops-203756}, doi = {10.4230/LIPIcs.SEA.2024.10}, annote = {Keywords: Taxonomic classification, metagenomics, KATKA, maximal exact matches, string kernels, minimizer digests} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Patrick Dinklage, Johannes Fischer, and Nicola Prezza. Top-k Frequent Patterns in Streams and Parameterized-Space LZ Compression. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{dinklage_et_al:LIPIcs.SEA.2024.9, author = {Dinklage, Patrick and Fischer, Johannes and Prezza, Nicola}, title = {{Top-k Frequent Patterns in Streams and Parameterized-Space LZ Compression}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {9:1--9:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-325-6}, ISSN = {1868-8969}, year = {2024}, volume = {301}, editor = {Liberti, Leo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.9}, URN = {urn:nbn:de:0030-drops-203748}, doi = {10.4230/LIPIcs.SEA.2024.9}, annote = {Keywords: compression, streaming, heavy hitters, algorithm engineering} }
Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, and Yuri Pirola. Solving the Minimal Positional Substring Cover Problem in Sublinear Space. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bonizzoni_et_al:LIPIcs.CPM.2024.12, author = {Bonizzoni, Paola and Boucher, Christina and Cozzi, Davide and Gagie, Travis and Pirola, Yuri}, title = {{Solving the Minimal Positional Substring Cover Problem in Sublinear Space}}, booktitle = {35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-326-3}, ISSN = {1868-8969}, year = {2024}, volume = {296}, editor = {Inenaga, Shunsuke and Puglisi, Simon J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.12}, URN = {urn:nbn:de:0030-drops-201225}, doi = {10.4230/LIPIcs.CPM.2024.12}, annote = {Keywords: Positional Burrows-Wheeler Transform, r-index, minimal position substring cover, set-maximal exact matches} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie. Acceleration of FM-Index Queries Through Prefix-Free Parsing. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{hong_et_al:LIPIcs.WABI.2023.13, author = {Hong, Aaron and Oliva, Marco and K\"{o}ppl, Dominik and Bannai, Hideo and Boucher, Christina and Gagie, Travis}, title = {{Acceleration of FM-Index Queries Through Prefix-Free Parsing}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {13:1--13:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.13}, URN = {urn:nbn:de:0030-drops-186390}, doi = {10.4230/LIPIcs.WABI.2023.13}, annote = {Keywords: FM-index, pangenomics, scalability, word-based indexing, random access} }
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