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} }
Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)
Veli Mäkinen and Kristoffer Sahlin. Chaining with Overlaps Revisited. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 25:1-25:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{makinen_et_al:LIPIcs.CPM.2020.25, author = {M\"{a}kinen, Veli and Sahlin, Kristoffer}, title = {{Chaining with Overlaps Revisited}}, booktitle = {31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)}, pages = {25:1--25:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-149-8}, ISSN = {1868-8969}, year = {2020}, volume = {161}, editor = {G{\o}rtz, Inge Li and Weimann, Oren}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.25}, URN = {urn:nbn:de:0030-drops-121500}, doi = {10.4230/LIPIcs.CPM.2020.25}, annote = {Keywords: Sparse Dynamic Programming, Chaining, Maximal Exact Matches, Longest Common Subsequence} }
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