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 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 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, and Rosalba Zizza. Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bonizzoni_et_al:LIPIcs.MFCS.2024.31, author = {Bonizzoni, Paola and De Felice, Clelia and Riccardi, Brian and Zaccagnino, Rocco and Zizza, Rosalba}, title = {{Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {31:1--31:14}, 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.2024.31}, URN = {urn:nbn:de:0030-drops-205879}, doi = {10.4230/LIPIcs.MFCS.2024.31}, annote = {Keywords: Lyndon words, Lyndon factorization, Combinatorial algorithms on words} }
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)
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)
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 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 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Philip Bille, Johannes Fischer, Inge Li Gørtz, Max Rishøj Pedersen, and Tord Joakim Stordalen. Sliding Window String Indexing in Streams. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{bille_et_al:LIPIcs.CPM.2023.4, author = {Bille, Philip and Fischer, Johannes and G{\o}rtz, Inge Li and Pedersen, Max Rish{\o}j and Stordalen, Tord Joakim}, title = {{Sliding Window String Indexing in Streams}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {4:1--4:18}, 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.2023.4}, URN = {urn:nbn:de:0030-drops-179587}, doi = {10.4230/LIPIcs.CPM.2023.4}, annote = {Keywords: String indexing, pattern matching, sliding window, streaming} }
Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)
Nico Bertram, Jonas Ellert, and Johannes Fischer. A Parallel Framework for Approximate Max-Dicut in Partitionable Graphs. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 10:1-10:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{bertram_et_al:LIPIcs.SEA.2022.10, author = {Bertram, Nico and Ellert, Jonas and Fischer, Johannes}, title = {{A Parallel Framework for Approximate Max-Dicut in Partitionable Graphs}}, booktitle = {20th International Symposium on Experimental Algorithms (SEA 2022)}, pages = {10:1--10:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-251-8}, ISSN = {1868-8969}, year = {2022}, volume = {233}, editor = {Schulz, Christian and U\c{c}ar, Bora}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.10}, URN = {urn:nbn:de:0030-drops-165441}, doi = {10.4230/LIPIcs.SEA.2022.10}, annote = {Keywords: maximum directed cut, graph partitioning, algorithm engineering, approximation, parallel algorithms} }
Published in: LIPIcs, Volume 216, 30th EACSL Annual Conference on Computer Science Logic (CSL 2022)
Clemens Kupke, Johannes Marti, and Yde Venema. Succinct Graph Representations of μ-Calculus Formulas. In 30th EACSL Annual Conference on Computer Science Logic (CSL 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 216, pp. 29:1-29:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{kupke_et_al:LIPIcs.CSL.2022.29, author = {Kupke, Clemens and Marti, Johannes and Venema, Yde}, title = {{Succinct Graph Representations of \mu-Calculus Formulas}}, booktitle = {30th EACSL Annual Conference on Computer Science Logic (CSL 2022)}, pages = {29:1--29:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-218-1}, ISSN = {1868-8969}, year = {2022}, volume = {216}, editor = {Manea, Florin and Simpson, Alex}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2022.29}, URN = {urn:nbn:de:0030-drops-157491}, doi = {10.4230/LIPIcs.CSL.2022.29}, annote = {Keywords: modal mu-calculus, model checking, alternating tree automata, hierachical equation systems} }
Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)
Nico Bertram, Jonas Ellert, and Johannes Fischer. Lyndon Words Accelerate Suffix Sorting. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{bertram_et_al:LIPIcs.ESA.2021.15, author = {Bertram, Nico and Ellert, Jonas and Fischer, Johannes}, title = {{Lyndon Words Accelerate Suffix Sorting}}, booktitle = {29th Annual European Symposium on Algorithms (ESA 2021)}, pages = {15:1--15:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-204-4}, ISSN = {1868-8969}, year = {2021}, volume = {204}, editor = {Mutzel, Petra and Pagh, Rasmus 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.2021.15}, URN = {urn:nbn:de:0030-drops-145961}, doi = {10.4230/LIPIcs.ESA.2021.15}, annote = {Keywords: Suffix array, suffix sorting, Lyndon words, string algorithms} }
Published in: LIPIcs, Volume 198, 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)
Jonas Ellert and Johannes Fischer. Linear Time Runs Over General Ordered Alphabets. In 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 198, pp. 63:1-63:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{ellert_et_al:LIPIcs.ICALP.2021.63, author = {Ellert, Jonas and Fischer, Johannes}, title = {{Linear Time Runs Over General Ordered Alphabets}}, booktitle = {48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)}, pages = {63:1--63:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-195-5}, ISSN = {1868-8969}, year = {2021}, volume = {198}, editor = {Bansal, Nikhil and Merelli, Emanuela and Worrell, James}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2021.63}, URN = {urn:nbn:de:0030-drops-141322}, doi = {10.4230/LIPIcs.ICALP.2021.63}, annote = {Keywords: String algorithms, Lyndon array, runs, squares, longest common extension, general ordered alphabets, combinatorics on words} }
Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)
Hideo Bannai. Repetitions in Strings: A "Constant" Problem (Invited Talk). In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, p. 1:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{bannai:LIPIcs.CPM.2021.1, author = {Bannai, Hideo}, title = {{Repetitions in Strings: A "Constant" Problem}}, booktitle = {32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)}, pages = {1:1--1:1}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-186-3}, ISSN = {1868-8969}, year = {2021}, volume = {191}, editor = {Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.1}, URN = {urn:nbn:de:0030-drops-139523}, doi = {10.4230/LIPIcs.CPM.2021.1}, annote = {Keywords: Maximal repetitions, Squares, Lyndon words} }
Published in: LIPIcs, Volume 190, 19th International Symposium on Experimental Algorithms (SEA 2021)
Patrick Dinklage, Johannes Fischer, and Alexander Herlez. Engineering Predecessor Data Structures for Dynamic Integer Sets. In 19th International Symposium on Experimental Algorithms (SEA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 190, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{dinklage_et_al:LIPIcs.SEA.2021.7, author = {Dinklage, Patrick and Fischer, Johannes and Herlez, Alexander}, title = {{Engineering Predecessor Data Structures for Dynamic Integer Sets}}, booktitle = {19th International Symposium on Experimental Algorithms (SEA 2021)}, pages = {7:1--7:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-185-6}, ISSN = {1868-8969}, year = {2021}, volume = {190}, editor = {Coudert, David and Natale, Emanuele}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2021.7}, URN = {urn:nbn:de:0030-drops-137799}, doi = {10.4230/LIPIcs.SEA.2021.7}, annote = {Keywords: integer data structures, dynamic data structures, predecessor, universe reduction, y-fast trie, fusion tree, B-tree} }