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)
Shimon Kogan and Merav Parter. Giving Some Slack: Shortcuts and Transitive Closure Compressions. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 79:1-79:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{kogan_et_al:LIPIcs.ESA.2024.79, author = {Kogan, Shimon and Parter, Merav}, title = {{Giving Some Slack: Shortcuts and Transitive Closure Compressions}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {79:1--79:15}, 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.2024.79}, URN = {urn:nbn:de:0030-drops-211509}, doi = {10.4230/LIPIcs.ESA.2024.79}, annote = {Keywords: Reachability Shortcuts, Width, DAG} }
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Shimon Kogan and Merav Parter. The Algorithmic Power of the Greene-Kleitman Theorem. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 80:1-80:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{kogan_et_al:LIPIcs.ESA.2024.80, author = {Kogan, Shimon and Parter, Merav}, title = {{The Algorithmic Power of the Greene-Kleitman Theorem}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {80:1--80:14}, 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.2024.80}, URN = {urn:nbn:de:0030-drops-211512}, doi = {10.4230/LIPIcs.ESA.2024.80}, annote = {Keywords: Chains, Antichains, DAG} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Dibyayan Chakraborty, Antoine Dailly, Florent Foucaud, and Ralf Klasing. Algorithms and Complexity for Path Covers of Temporal DAGs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 38:1-38:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{chakraborty_et_al:LIPIcs.MFCS.2024.38, author = {Chakraborty, Dibyayan and Dailly, Antoine and Foucaud, Florent and Klasing, Ralf}, title = {{Algorithms and Complexity for Path Covers of Temporal DAGs}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {38:1--38:17}, 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.2024.38}, URN = {urn:nbn:de:0030-drops-205940}, doi = {10.4230/LIPIcs.MFCS.2024.38}, annote = {Keywords: Temporal Graphs, Dilworth’s Theorem, DAGs, Path Cover, Temporally Disjoint Paths, Algorithms, Oriented Trees, Treewidth} }
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)
Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu. Practical Minimum Path Cover. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{caceres_et_al:LIPIcs.SEA.2024.3, author = {C\'{a}ceres, Manuel and Mumey, Brendan and Toivonen, Santeri and Tomescu, Alexandru I.}, title = {{Practical Minimum Path Cover}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {3:1--3:19}, 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.2024.3}, URN = {urn:nbn:de:0030-drops-203687}, doi = {10.4230/LIPIcs.SEA.2024.3}, annote = {Keywords: minimum path cover, directed acyclic graph, maximum flow, parameterized algorithms, edge sparsification, algorithm engineering} }
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 274, 31st Annual European Symposium on Algorithms (ESA 2023)
Ruben Becker, Manuel Cáceres, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Francisco Olivares, and Nicola Prezza. Sorting Finite Automata via Partition Refinement. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{becker_et_al:LIPIcs.ESA.2023.15, author = {Becker, Ruben and C\'{a}ceres, Manuel and Cenzato, Davide and Kim, Sung-Hwan and Kodric, Bojana and Olivares, Francisco and Prezza, Nicola}, title = {{Sorting Finite Automata via Partition Refinement}}, booktitle = {31st Annual European Symposium on Algorithms (ESA 2023)}, pages = {15:1--15:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-295-2}, ISSN = {1868-8969}, year = {2023}, volume = {274}, editor = {G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. 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.2023.15}, URN = {urn:nbn:de:0030-drops-186684}, doi = {10.4230/LIPIcs.ESA.2023.15}, annote = {Keywords: Wheeler automata, prefix sorting, pattern matching, graph compression, sorting, partition refinement} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen. Finding Maximal Exact Matches in Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rizzo_et_al:LIPIcs.WABI.2023.10, author = {Rizzo, Nicola and C\'{a}ceres, Manuel and M\"{a}kinen, Veli}, title = {{Finding Maximal Exact Matches in Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {10:1--10:17}, 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.2023.10}, URN = {urn:nbn:de:0030-drops-186364}, doi = {10.4230/LIPIcs.WABI.2023.10}, annote = {Keywords: Sequence to graph alignment, bidirectional BWT, r-index, suffix tree, founder graphs} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Jyotshna Rajput, Ghanshyam Chandra, and Chirag Jain. Co-Linear Chaining on Pangenome Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 12:1-12:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rajput_et_al:LIPIcs.WABI.2023.12, author = {Rajput, Jyotshna and Chandra, Ghanshyam and Jain, Chirag}, title = {{Co-Linear Chaining on Pangenome Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {12:1--12:18}, 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.2023.12}, URN = {urn:nbn:de:0030-drops-186389}, doi = {10.4230/LIPIcs.WABI.2023.12}, annote = {Keywords: Sequence alignment, variation graph, genome sequencing, path cover} }
Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)
Manuel Cáceres. Minimum Chain Cover in Almost Linear Time. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 31:1-31:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{caceres:LIPIcs.ICALP.2023.31, author = {C\'{a}ceres, Manuel}, title = {{Minimum Chain Cover in Almost Linear Time}}, booktitle = {50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)}, pages = {31:1--31:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-278-5}, ISSN = {1868-8969}, year = {2023}, volume = {261}, editor = {Etessami, Kousha and Feige, Uriel and Puppis, Gabriele}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.31}, URN = {urn:nbn:de:0030-drops-180834}, doi = {10.4230/LIPIcs.ICALP.2023.31}, annote = {Keywords: Minimum chain cover, directed acyclic graph, minimum flow, flow decomposition, mergeable dictionaries, amortized running time} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Manuel Cáceres. Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{caceres:LIPIcs.CPM.2023.7, author = {C\'{a}ceres, Manuel}, title = {{Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {7:1--7:19}, 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.2023.7}, URN = {urn:nbn:de:0030-drops-179619}, doi = {10.4230/LIPIcs.CPM.2023.7}, annote = {Keywords: string matching, parameterized algorithms, FPT inside P, string algorithms, graph algorithms, directed acyclic graphs, labeled graphs, funnels} }
Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)
Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, and Lucia Williams. Width Helps and Hinders Splitting Flows. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{caceres_et_al:LIPIcs.ESA.2022.31, author = {C\'{a}ceres, Manuel and Cairo, Massimo and Grigorjew, Andreas and Khan, Shahbaz and Mumey, Brendan and Rizzi, Romeo and Tomescu, Alexandru I. and Williams, Lucia}, title = {{Width Helps and Hinders Splitting Flows}}, booktitle = {30th Annual European Symposium on Algorithms (ESA 2022)}, pages = {31:1--31:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-247-1}, ISSN = {1868-8969}, year = {2022}, volume = {244}, editor = {Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva 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.2022.31}, URN = {urn:nbn:de:0030-drops-169695}, doi = {10.4230/LIPIcs.ESA.2022.31}, annote = {Keywords: Flow decomposition, approximation algorithms, graph width} }
Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)
Shahbaz Khan and Alexandru I. Tomescu. Optimizing Safe Flow Decompositions in DAGs. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 72:1-72:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{khan_et_al:LIPIcs.ESA.2022.72, author = {Khan, Shahbaz and Tomescu, Alexandru I.}, title = {{Optimizing Safe Flow Decompositions in DAGs}}, booktitle = {30th Annual European Symposium on Algorithms (ESA 2022)}, pages = {72:1--72:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-247-1}, ISSN = {1868-8969}, year = {2022}, volume = {244}, editor = {Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva 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.2022.72}, URN = {urn:nbn:de:0030-drops-170101}, doi = {10.4230/LIPIcs.ESA.2022.72}, annote = {Keywords: safety, flows, networks, directed acyclic graphs} }
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