LIPIcs, Volume 113
WABI 2018, August 20-22, 2018, Helsinki, Finland
Editors: Laxmi Parida and Esko Ukkonen
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Aranya Banerjee, Daniel Gibney, and Sharma V. Thankachan. Longest Common Substring with Gaps and Related Problems. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{banerjee_et_al:LIPIcs.ESA.2024.16, author = {Banerjee, Aranya and Gibney, Daniel and Thankachan, Sharma V.}, title = {{Longest Common Substring with Gaps and Related Problems}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {16:1--16:18}, 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.2024.16}, URN = {urn:nbn:de:0030-drops-210877}, doi = {10.4230/LIPIcs.ESA.2024.16}, annote = {Keywords: Pattern Matching, Longest Common Subsequence, Episode Matching} }
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, and Simon J. Puglisi. Height-Bounded Lempel-Ziv Encodings. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 18:1-18:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bannai_et_al:LIPIcs.ESA.2024.18, author = {Bannai, Hideo and Funakoshi, Mitsuru and Hendrian, Diptarama and Matsuda, Myuji and Puglisi, Simon J.}, title = {{Height-Bounded Lempel-Ziv Encodings}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {18:1--18:18}, 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.2024.18}, URN = {urn:nbn:de:0030-drops-210899}, doi = {10.4230/LIPIcs.ESA.2024.18}, annote = {Keywords: Lempel-Ziv parsing, data compression} }
Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)
Nader H. Bshouty and George Haddad. Approximating the Number of Relevant Variables in a Parity Implies Proper Learning. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 38:1-38:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bshouty_et_al:LIPIcs.APPROX/RANDOM.2024.38, author = {Bshouty, Nader H. and Haddad, George}, title = {{Approximating the Number of Relevant Variables in a Parity Implies Proper Learning}}, booktitle = {Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)}, pages = {38:1--38:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-348-5}, ISSN = {1868-8969}, year = {2024}, volume = {317}, editor = {Kumar, Amit and Ron-Zewi, Noga}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.38}, URN = {urn:nbn:de:0030-drops-210316}, doi = {10.4230/LIPIcs.APPROX/RANDOM.2024.38}, annote = {Keywords: PAC Learning, Random Classification Noise, Uniform Distribution, Parity, Sparcity Approximation} }
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)
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 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)
Itai Boneh, Shay Golan, Shay Mozes, and Oren Weimann. Õptimal Dynamic Time Warping on Run-Length Encoded Strings. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 30:1-30:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boneh_et_al:LIPIcs.ICALP.2024.30, author = {Boneh, Itai and Golan, Shay and Mozes, Shay and Weimann, Oren}, title = {{\~{O}ptimal Dynamic Time Warping on Run-Length Encoded Strings}}, booktitle = {51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)}, pages = {30:1--30:17}, 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.2024.30}, URN = {urn:nbn:de:0030-drops-201730}, doi = {10.4230/LIPIcs.ICALP.2024.30}, annote = {Keywords: Dynamic time warping, Fr\'{e}chet distance, edit distance, run-length encoding} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@Proceedings{parida_et_al:LIPIcs.WABI.2018, title = {{LIPIcs, Volume 113, WABI'18, Complete Volume}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018}, URN = {urn:nbn:de:0030-drops-97246}, doi = {10.4230/LIPIcs.WABI.2018}, annote = {Keywords: Applied computing, Bioinformatics, Theory of computation, Design and analysis of algorithms, Mathematics of computing, Probabilistic inference problem} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{parida_et_al:LIPIcs.WABI.2018.0, author = {Parida, Laxmi and Ukkonen, Esko}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {0:i--0:xvi}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.0}, URN = {urn:nbn:de:0030-drops-93028}, doi = {10.4230/LIPIcs.WABI.2018.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch. A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 1:1-1:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{zabeti_et_al:LIPIcs.WABI.2018.1, author = {Zabeti, Hooman and Stephen, Tamon and Berger, Bonnie and Chindelevitch, Leonid}, title = {{A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {1:1--1:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.1}, URN = {urn:nbn:de:0030-drops-93034}, doi = {10.4230/LIPIcs.WABI.2018.1}, annote = {Keywords: Metabolic network analysis, elemental imbalance, linear programming, model verification} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2, author = {Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni}, title = {{Prefix-Free Parsing for Building Big BWTs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {2:1--2:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2}, URN = {urn:nbn:de:0030-drops-93044}, doi = {10.4230/LIPIcs.WABI.2018.2}, annote = {Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone. Detecting Mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{prezza_et_al:LIPIcs.WABI.2018.3, author = {Prezza, Nicola and Pisanti, Nadia and Sciortino, Marinella and Rosone, Giovanna}, title = {{Detecting Mutations by eBWT}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {3:1--3:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.3}, URN = {urn:nbn:de:0030-drops-93051}, doi = {10.4230/LIPIcs.WABI.2018.3}, annote = {Keywords: BWT, LCP Array, SNPs, Reference-free, Assembly-free} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin. Haplotype-aware graph indexes. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{siren_et_al:LIPIcs.WABI.2018.4, author = {Sir\'{e}n, Jouni and Garrison, Erik and Novak, Adam M. and Paten, Benedict J. and Durbin, Richard}, title = {{Haplotype-aware graph indexes}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {4:1--4:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4}, URN = {urn:nbn:de:0030-drops-93060}, doi = {10.4230/LIPIcs.WABI.2018.4}, annote = {Keywords: FM-indexes, variation graphs, haplotypes} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{dondi_et_al:LIPIcs.WABI.2018.5, author = {Dondi, Riccardo and Lafond, Manuel and Scornavacca, Celine}, title = {{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {5:1--5:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5}, URN = {urn:nbn:de:0030-drops-93079}, doi = {10.4230/LIPIcs.WABI.2018.5}, annote = {Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms} }
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