Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)
Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{angrick_et_al:LIPIcs.SEA.2023.10, author = {Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo}, title = {{Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover}}, booktitle = {21st International Symposium on Experimental Algorithms (SEA 2023)}, pages = {10:1--10:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-279-2}, ISSN = {1868-8969}, year = {2023}, volume = {265}, editor = {Georgiadis, Loukas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.10}, URN = {urn:nbn:de:0030-drops-183602}, doi = {10.4230/LIPIcs.SEA.2023.10}, annote = {Keywords: directed feedback vertex set, vertex cover, reduction rules} }
Published in: LIPIcs, Volume 258, 39th International Symposium on Computational Geometry (SoCG 2023)
Luis Scoccola, Hitesh Gakhar, Johnathan Bush, Nikolas Schonsheck, Tatum Rask, Ling Zhou, and Jose A. Perea. Toroidal Coordinates: Decorrelating Circular Coordinates with Lattice Reduction. In 39th International Symposium on Computational Geometry (SoCG 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 258, pp. 57:1-57:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{scoccola_et_al:LIPIcs.SoCG.2023.57, author = {Scoccola, Luis and Gakhar, Hitesh and Bush, Johnathan and Schonsheck, Nikolas and Rask, Tatum and Zhou, Ling and Perea, Jose A.}, title = {{Toroidal Coordinates: Decorrelating Circular Coordinates with Lattice Reduction}}, booktitle = {39th International Symposium on Computational Geometry (SoCG 2023)}, pages = {57:1--57:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-273-0}, ISSN = {1868-8969}, year = {2023}, volume = {258}, editor = {Chambers, Erin W. and Gudmundsson, Joachim}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2023.57}, URN = {urn:nbn:de:0030-drops-179073}, doi = {10.4230/LIPIcs.SoCG.2023.57}, annote = {Keywords: dimensionality reduction, lattice reduction, Dirichlet energy, harmonic, cocycle} }
Published in: LIPIcs, Volume 256, 4th Symposium on Foundations of Responsible Computing (FORC 2023)
Milan Mossé. Multiplicative Metric Fairness Under Composition. In 4th Symposium on Foundations of Responsible Computing (FORC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 256, pp. 4:1-4:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{mosse:LIPIcs.FORC.2023.4, author = {Moss\'{e}, Milan}, title = {{Multiplicative Metric Fairness Under Composition}}, booktitle = {4th Symposium on Foundations of Responsible Computing (FORC 2023)}, pages = {4:1--4:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-272-3}, ISSN = {1868-8969}, year = {2023}, volume = {256}, editor = {Talwar, Kunal}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2023.4}, URN = {urn:nbn:de:0030-drops-179250}, doi = {10.4230/LIPIcs.FORC.2023.4}, annote = {Keywords: algorithmic fairness, metric fairness, fairness under composition} }
Published in: LIPIcs, Volume 249, 17th International Symposium on Parameterized and Exact Computation (IPEC 2022)
Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set. In 17th International Symposium on Parameterized and Exact Computation (IPEC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 249, pp. 28:1-28:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{angrick_et_al:LIPIcs.IPEC.2022.28, author = {Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo}, title = {{PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set}}, booktitle = {17th International Symposium on Parameterized and Exact Computation (IPEC 2022)}, pages = {28:1--28:4}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-260-0}, ISSN = {1868-8969}, year = {2022}, volume = {249}, editor = {Dell, Holger and Nederlof, Jesper}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2022.28}, URN = {urn:nbn:de:0030-drops-173847}, doi = {10.4230/LIPIcs.IPEC.2022.28}, annote = {Keywords: directed feedback vertex set, vertex cover, reduction rules} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang. The Bourque Distances for Mutation Trees of Cancers. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 14:1-14:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{jahn_et_al:LIPIcs.WABI.2020.14, author = {Jahn, Katharina and Beerenwinkel, Niko and Zhang, Louxin}, title = {{The Bourque Distances for Mutation Trees of Cancers}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {14:1--14:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.14}, URN = {urn:nbn:de:0030-drops-128039}, doi = {10.4230/LIPIcs.WABI.2020.14}, annote = {Keywords: mutation trees, clonal trees, tree distance, phylogenetic trees, tree metric, Robinson - Foulds distance, Bourque distance} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Niko Kiirala, Leena Salmela, and Alexandru I. Tomescu. Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{kiirala_et_al:LIPIcs.CPM.2019.8, author = {Kiirala, Niko and Salmela, Leena and Tomescu, Alexandru I.}, title = {{Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {8:1--8:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-103-0}, ISSN = {1868-8969}, year = {2019}, volume = {128}, editor = {Pisanti, Nadia and P. Pissis, Solon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.8}, URN = {urn:nbn:de:0030-drops-104794}, doi = {10.4230/LIPIcs.CPM.2019.8}, annote = {Keywords: RNA secondary structure, RNA folding, Safe solution, Safe and complete algorithm, Counting problem} }
Published in: OASIcs, Volume 70, 2nd Conference on Language, Data and Knowledge (LDK 2019)
Christian Chiarcos and Niko Schenk. CoNLL-Merge: Efficient Harmonization of Concurrent Tokenization and Textual Variation. In 2nd Conference on Language, Data and Knowledge (LDK 2019). Open Access Series in Informatics (OASIcs), Volume 70, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{chiarcos_et_al:OASIcs.LDK.2019.7, author = {Chiarcos, Christian and Schenk, Niko}, title = {{CoNLL-Merge: Efficient Harmonization of Concurrent Tokenization and Textual Variation}}, booktitle = {2nd Conference on Language, Data and Knowledge (LDK 2019)}, pages = {7:1--7:14}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-95977-105-4}, ISSN = {2190-6807}, year = {2019}, volume = {70}, editor = {Eskevich, Maria and de Melo, Gerard and F\"{a}th, Christian and McCrae, John P. and Buitelaar, Paul and Chiarcos, Christian and Klimek, Bettina and Dojchinovski, Milan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.LDK.2019.7}, URN = {urn:nbn:de:0030-drops-103717}, doi = {10.4230/OASIcs.LDK.2019.7}, annote = {Keywords: data heterogeneity, tokenization, tab-separated values (TSV) format, linguistic annotation, merging} }
Published in: Dagstuhl Reports, Volume 7, Issue 11 (2018)
Niko Beerenwinkel, Holger Fröhlich, and Susan A. Murphy. Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). In Dagstuhl Reports, Volume 7, Issue 11, pp. 130-141, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@Article{beerenwinkel_et_al:DagRep.7.11.130, author = {Beerenwinkel, Niko and Fr\"{o}hlich, Holger and Murphy, Susan A.}, title = {{Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472)}}, pages = {130--141}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2018}, volume = {7}, number = {11}, editor = {Beerenwinkel, Niko and Fr\"{o}hlich, Holger and Murphy, Susan A.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.7.11.130}, URN = {urn:nbn:de:0030-drops-86730}, doi = {10.4230/DagRep.7.11.130}, annote = {Keywords: data science, machine learning, computational modeling, bioinformatics, systems biology} }
Published in: Dagstuhl Seminar Proceedings, Volume 8261, Structure-Based Compression of Complex Massive Data (2008)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, and Niko Välimäki. Storage and Retrieval of Individual Genomes. In Structure-Based Compression of Complex Massive Data. Dagstuhl Seminar Proceedings, Volume 8261, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)
@InProceedings{makinen_et_al:DagSemProc.08261.10, author = {M\"{a}kinen, Veli and Navarro, Gonzalo and Sir\'{e}n, Jouni and V\"{a}lim\"{a}ki, Niko}, title = {{Storage and Retrieval of Individual Genomes}}, booktitle = {Structure-Based Compression of Complex Massive Data}, pages = {1--14}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2008}, volume = {8261}, editor = {Stefan B\"{o}ttcher and Markus Lohrey and Sebastian Maneth and Wojcieh Rytter}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.08261.10}, URN = {urn:nbn:de:0030-drops-16743}, doi = {10.4230/DagSemProc.08261.10}, annote = {Keywords: Pattern matching, text indexing, compressed data structures, comparative genomics} }
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