LIPIcs, Volume 244
ESA 2022, September 5-9, 2022, Berlin/Potsdam, Germany
Editors: Shiri Chechik, Gonzalo Navarro, Eva Rotenberg, and Grzegorz Herman
LIPIcs, Volume 105
CPM 2018, July 2-4, 2018, Qingdao, China
Editors: Gonzalo Navarro, David Sankoff, and Binhai Zhu
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)
Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17, author = {Groot Koerkamp, Ragnar}, title = {{A*PA2: Up to 19× Faster Exact Global Alignment}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {17:1--17:25}, 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.2024.17}, URN = {urn:nbn:de:0030-drops-206610}, doi = {10.4230/LIPIcs.WABI.2024.17}, annote = {Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Jesse Beisegel, Ekkehard Köhler, Fabienne Ratajczak, Robert Scheffler, and Martin Strehler. Graph Search Trees and the Intermezzo Problem. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{beisegel_et_al:LIPIcs.MFCS.2024.22, author = {Beisegel, Jesse and K\"{o}hler, Ekkehard and Ratajczak, Fabienne and Scheffler, Robert and Strehler, Martin}, title = {{Graph Search Trees and the Intermezzo Problem}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {22:1--22:18}, 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.2024.22}, URN = {urn:nbn:de:0030-drops-205781}, doi = {10.4230/LIPIcs.MFCS.2024.22}, annote = {Keywords: graph search trees, intermezzo problem, algorithm, parameterized complexity} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai. Edit and Alphabet-Ordering Sensitivity of Lex-Parse. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 75:1-75:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{nakashima_et_al:LIPIcs.MFCS.2024.75, author = {Nakashima, Yuto and K\"{o}ppl, Dominik and Funakoshi, Mitsuru and Inenaga, Shunsuke and Bannai, Hideo}, title = {{Edit and Alphabet-Ordering Sensitivity of Lex-Parse}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {75:1--75:15}, 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.2024.75}, URN = {urn:nbn:de:0030-drops-206314}, doi = {10.4230/LIPIcs.MFCS.2024.75}, annote = {Keywords: Compression sensitivity, Lex-parse, Fibonacci words} }
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 302, 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)
Jeremy Chizewer, Stephen Melczer, J. Ian Munro, and Ava Pun. Enumeration and Succinct Encoding of AVL Trees. In 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 302, pp. 2:1-2:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{chizewer_et_al:LIPIcs.AofA.2024.2, author = {Chizewer, Jeremy and Melczer, Stephen and Munro, J. Ian and Pun, Ava}, title = {{Enumeration and Succinct Encoding of AVL Trees}}, booktitle = {35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)}, pages = {2:1--2:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-329-4}, ISSN = {1868-8969}, year = {2024}, volume = {302}, editor = {Mailler, C\'{e}cile and Wild, Sebastian}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AofA.2024.2}, URN = {urn:nbn:de:0030-drops-204376}, doi = {10.4230/LIPIcs.AofA.2024.2}, annote = {Keywords: AVL trees, analytic combinatorics, succinct data structures, enumeration} }
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)
Paolo Boldi, Stefano Marchini, and Sebastiano Vigna. Engineering Zuffix Arrays. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boldi_et_al:LIPIcs.SEA.2024.2, author = {Boldi, Paolo and Marchini, Stefano and Vigna, Sebastiano}, title = {{Engineering Zuffix Arrays}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {2:1--2:18}, 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.2024.2}, URN = {urn:nbn:de:0030-drops-203677}, doi = {10.4230/LIPIcs.SEA.2024.2}, annote = {Keywords: Suffix trees, suffix arrays, z-fast tries} }
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)
Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, and Alexandru I. Tomescu. Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{grigorjew_et_al:LIPIcs.SEA.2024.14, author = {Grigorjew, Andreas and Dias, Fernando H. C. and Cracco, Andrea and Rizzi, Romeo and Tomescu, Alexandru I.}, title = {{Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {14:1--14:19}, 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.2024.14}, URN = {urn:nbn:de:0030-drops-203792}, doi = {10.4230/LIPIcs.SEA.2024.14}, annote = {Keywords: Flow decomposition, Integer Linear Programming, Safety, RNA-seq, RNA transcript assembly, isoform} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Matthew D. Laws, Jocelyn Bliven, Kit Conklin, Elyes Laalai, Samuel McCauley, and Zach S. Sturdevant. SPIDER: Improved Succinct Rank and Select Performance. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 21:1-21:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{laws_et_al:LIPIcs.SEA.2024.21, author = {Laws, Matthew D. and Bliven, Jocelyn and Conklin, Kit and Laalai, Elyes and McCauley, Samuel and Sturdevant, Zach S.}, title = {{SPIDER: Improved Succinct Rank and Select Performance}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {21:1--21:18}, 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.2024.21}, URN = {urn:nbn:de:0030-drops-203865}, doi = {10.4230/LIPIcs.SEA.2024.21}, annote = {Keywords: Rank and Select, Succinct Data Structures, Data Structres, Cache Performance, Predictions} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Matthew N. Palmer, Simone Faro, and Stefano Scafiti. Efficient Exact Online String Matching Through Linked Weak Factors. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{palmer_et_al:LIPIcs.SEA.2024.24, author = {Palmer, Matthew N. and Faro, Simone and Scafiti, Stefano}, title = {{Efficient Exact Online String Matching Through Linked Weak Factors}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {24:1--24:14}, 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.2024.24}, URN = {urn:nbn:de:0030-drops-203896}, doi = {10.4230/LIPIcs.SEA.2024.24}, annote = {Keywords: String matching, text processing, weak recognition, hashing, experimental algorithms, design and analysis of algorithms} }
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