27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@Proceedings{grossi_et_al:LIPIcs.CPM.2016, title = {{LIPIcs, Volume 54, CPM'16, Complete Volume}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016}, URN = {urn:nbn:de:0030-drops-60935}, doi = {10.4230/LIPIcs.CPM.2016}, annote = {Keywords: Data Structures, Data Storage Representations, Coding and Information Theory, Theory of Computation Discrete Mathematics, Information Systems} }
27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{grossi_et_al:LIPIcs.CPM.2016.0, author = {Grossi, Roberto and Lewenstein, Moshe}, title = {{Front Matter, Table of Contents, Preface}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {0:i--0:x}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.0}, URN = {urn:nbn:de:0030-drops-60916}, doi = {10.4230/LIPIcs.CPM.2016.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, List of Authors} }
Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, and Masayuki Takeda. Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 1:1-1:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{tanimura_et_al:LIPIcs.CPM.2016.1, author = {Tanimura, Yuka and I, Tomohiro and Bannai, Hideo and Inenaga, Shunsuke and Puglisi, Simon J. and Takeda, Masayuki}, title = {{Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {1:1--1:10}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.1}, URN = {urn:nbn:de:0030-drops-60655}, doi = {10.4230/LIPIcs.CPM.2016.1}, annote = {Keywords: longest common extension, longest common prefix, sparse suffix array} }
Arnab Ganguly, Wing-Kai Hon, Kunihiko Sadakane, Rahul Shah, Sharma V. Thankachan, and Yilin Yang. Space-Efficient Dictionaries for Parameterized and Order-Preserving Pattern Matching. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 2:1-2:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{ganguly_et_al:LIPIcs.CPM.2016.2, author = {Ganguly, Arnab and Hon, Wing-Kai and Sadakane, Kunihiko and Shah, Rahul and Thankachan, Sharma V. and Yang, Yilin}, title = {{Space-Efficient Dictionaries for Parameterized and Order-Preserving Pattern Matching}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {2:1--2:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.2}, URN = {urn:nbn:de:0030-drops-60736}, doi = {10.4230/LIPIcs.CPM.2016.2}, annote = {Keywords: Parameterized Matching, Order-preserving Matching, Dictionary Indexing, Aho-Corasick Automaton, Sparsification} }
Seungbum Jo, Rahul Lingala, and Srinivasa Rao Satti. Encoding Two-Dimensional Range Top-k Queries. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 3:1-3:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{jo_et_al:LIPIcs.CPM.2016.3, author = {Jo, Seungbum and Lingala, Rahul and Satti, Srinivasa Rao}, title = {{Encoding Two-Dimensional Range Top-k Queries}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {3:1--3:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.3}, URN = {urn:nbn:de:0030-drops-60704}, doi = {10.4230/LIPIcs.CPM.2016.3}, annote = {Keywords: Encoding model, top-k query, range minimum query} }
Carl Barton, Tomasz Kociumaka, Solon P. Pissis, and Jakub Radoszewski. Efficient Index for Weighted Sequences. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{barton_et_al:LIPIcs.CPM.2016.4, author = {Barton, Carl and Kociumaka, Tomasz and Pissis, Solon P. and Radoszewski, Jakub}, title = {{Efficient Index for Weighted Sequences}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {4:1--4:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.4}, URN = {urn:nbn:de:0030-drops-60807}, doi = {10.4230/LIPIcs.CPM.2016.4}, annote = {Keywords: weighted sequence, position weight matrix, indexing, weighted suffix tree} }
Pawel Gawrychowski, Tomasz Kociumaka, Wojciech Rytter, and Tomasz Walen. Faster Longest Common Extension Queries in Strings over General Alphabets. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2016.5, author = {Gawrychowski, Pawel and Kociumaka, Tomasz and Rytter, Wojciech and Walen, Tomasz}, title = {{Faster Longest Common Extension Queries in Strings over General Alphabets}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {5:1--5:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.5}, URN = {urn:nbn:de:0030-drops-60810}, doi = {10.4230/LIPIcs.CPM.2016.5}, annote = {Keywords: longest common extension, longest common prefix, maximal repetitions, difference cover} }
Tsvi Kopelowitz, Ely Porat, and Yaron Rozen. Succinct Online Dictionary Matching with Improved Worst-Case Guarantees. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{kopelowitz_et_al:LIPIcs.CPM.2016.6, author = {Kopelowitz, Tsvi and Porat, Ely and Rozen, Yaron}, title = {{Succinct Online Dictionary Matching with Improved Worst-Case Guarantees}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {6:1--6:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.6}, URN = {urn:nbn:de:0030-drops-60825}, doi = {10.4230/LIPIcs.CPM.2016.6}, annote = {Keywords: Succinct indexing, dictionary matching, Aho-Corasick, labeled trees} }
Guillaume Fertin and Christian Komusiewicz. Graph Motif Problems Parameterized by Dual. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 7:1-7:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{fertin_et_al:LIPIcs.CPM.2016.7, author = {Fertin, Guillaume and Komusiewicz, Christian}, title = {{Graph Motif Problems Parameterized by Dual}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {7:1--7:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.7}, URN = {urn:nbn:de:0030-drops-60837}, doi = {10.4230/LIPIcs.CPM.2016.7}, annote = {Keywords: NP-hard problem, subgraph problem, fixed-parameter algorithm, lowerbounds, kernelization} }
Costas S. Iliopoulos and Jakub Radoszewski. Truly Subquadratic-Time Extension Queries and Periodicity Detection in Strings with Uncertainties. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 8:1-8:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{iliopoulos_et_al:LIPIcs.CPM.2016.8, author = {Iliopoulos, Costas S. and Radoszewski, Jakub}, title = {{Truly Subquadratic-Time Extension Queries and Periodicity Detection in Strings with Uncertainties}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {8:1--8:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.8}, URN = {urn:nbn:de:0030-drops-60842}, doi = {10.4230/LIPIcs.CPM.2016.8}, annote = {Keywords: string with don’t cares, partial word, indeterminate string, longest common conservative prefix queries, prefix array} }
Cyril Nicaud. Estimating Statistics on Words Using Ambiguous Descriptions. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 9:1-9:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{nicaud:LIPIcs.CPM.2016.9, author = {Nicaud, Cyril}, title = {{Estimating Statistics on Words Using Ambiguous Descriptions}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {9:1--9:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.9}, URN = {urn:nbn:de:0030-drops-60859}, doi = {10.4230/LIPIcs.CPM.2016.9}, annote = {Keywords: random words, runs, symbolic method, analytic combinatorics} }
Dénes Bartha, Peter Burcsi, and Zsuzsanna Lipták. Reconstruction of Trees from Jumbled and Weighted Subtrees. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{bartha_et_al:LIPIcs.CPM.2016.10, author = {Bartha, D\'{e}nes and Burcsi, Peter and Lipt\'{a}k, Zsuzsanna}, title = {{Reconstruction of Trees from Jumbled and Weighted Subtrees}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {10:1--10:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.10}, URN = {urn:nbn:de:0030-drops-60861}, doi = {10.4230/LIPIcs.CPM.2016.10}, annote = {Keywords: trees, paths, Parikh vectors, reconstruction problems, homometric sets, polynomial method, jumbled strings, weighted strings} }
Nicolas Boria, Gianpiero Cabodi, Paolo Camurati, Marco Palena, Paolo Pasini, and Stefano Quer. A 7/2-Approximation Algorithm for the Maximum Duo-Preservation String Mapping Problem. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 11:1-11:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{boria_et_al:LIPIcs.CPM.2016.11, author = {Boria, Nicolas and Cabodi, Gianpiero and Camurati, Paolo and Palena, Marco and Pasini, Paolo and Quer, Stefano}, title = {{A 7/2-Approximation Algorithm for the Maximum Duo-Preservation String Mapping Problem}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {11:1--11:8}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.11}, URN = {urn:nbn:de:0030-drops-60875}, doi = {10.4230/LIPIcs.CPM.2016.11}, annote = {Keywords: Polynomial approximation, Max Duo-Preservation String Mapping Problem, Min Common String Partition Problem, Local Search} }
Yun Deng and David Fernández-Baca. Fast Compatibility Testing for Rooted Phylogenetic Trees. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{deng_et_al:LIPIcs.CPM.2016.12, author = {Deng, Yun and Fern\'{a}ndez-Baca, David}, title = {{Fast Compatibility Testing for Rooted Phylogenetic Trees}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {12:1--12:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.12}, URN = {urn:nbn:de:0030-drops-60884}, doi = {10.4230/LIPIcs.CPM.2016.12}, annote = {Keywords: Algorithms, computational biology, phylogenetics} }
Yi-Jun Chang. Hardness of RNA Folding Problem With Four Symbols. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 13:1-13:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{chang:LIPIcs.CPM.2016.13, author = {Chang, Yi-Jun}, title = {{Hardness of RNA Folding Problem With Four Symbols}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {13:1--13:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.13}, URN = {urn:nbn:de:0030-drops-60894}, doi = {10.4230/LIPIcs.CPM.2016.13}, annote = {Keywords: RNA folding, Dyck edit distance, longest common subsequence, conditional lower bound, clique} }
Manuel Lafond, Emmanuel Noutahi, and Nadia El-Mabrouk. Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 14:1-14:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{lafond_et_al:LIPIcs.CPM.2016.14, author = {Lafond, Manuel and Noutahi, Emmanuel and El-Mabrouk, Nadia}, title = {{Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {14:1--14:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.14}, URN = {urn:nbn:de:0030-drops-60907}, doi = {10.4230/LIPIcs.CPM.2016.14}, annote = {Keywords: gene tree, polytomy, reconciliation, resolution, weighted cost, phylogeny} }
Haitao Jiang, Chenglin Fan, Boting Yang, Farong Zhong, Daming Zhu, and Binhai Zhu. Genomic Scaffold Filling Revisited. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{jiang_et_al:LIPIcs.CPM.2016.15, author = {Jiang, Haitao and Fan, Chenglin and Yang, Boting and Zhong, Farong and Zhu, Daming and Zhu, Binhai}, title = {{Genomic Scaffold Filling Revisited}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {15:1--15:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.15}, URN = {urn:nbn:de:0030-drops-60791}, doi = {10.4230/LIPIcs.CPM.2016.15}, annote = {Keywords: Computational biology, Approximation algorithms, FPT algorithms, NP- completeness} }
Ron Shamir, Meirav Zehavi, and Ron Zeira. A Linear-Time Algorithm for the Copy Number Transformation Problem. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 16:1-16:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{shamir_et_al:LIPIcs.CPM.2016.16, author = {Shamir, Ron and Zehavi, Meirav and Zeira, Ron}, title = {{A Linear-Time Algorithm for the Copy Number Transformation Problem}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {16:1--16:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.16}, URN = {urn:nbn:de:0030-drops-60789}, doi = {10.4230/LIPIcs.CPM.2016.16}, annote = {Keywords: Genome Rearrangement, Copy Number} }
Amir Carmel, Dekel Tsur, and Michal Ziv-Ukelson. On Almost Monge All Scores Matrices. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 17:1-17:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{carmel_et_al:LIPIcs.CPM.2016.17, author = {Carmel, Amir and Tsur, Dekel and Ziv-Ukelson, Michal}, title = {{On Almost Monge All Scores Matrices}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {17:1--17:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.17}, URN = {urn:nbn:de:0030-drops-60770}, doi = {10.4230/LIPIcs.CPM.2016.17}, annote = {Keywords: Sequence alignment, longest common subsequences, DIST matrices, Monge matrices, all path score computations.} }
Pawel Gawrychowski, Oleg Merkurev, Arseny Shur, and Przemyslaw Uznanski. Tight Tradeoffs for Real-Time Approximation of Longest Palindromes in Streams. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 18:1-18:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2016.18, author = {Gawrychowski, Pawel and Merkurev, Oleg and Shur, Arseny and Uznanski, Przemyslaw}, title = {{Tight Tradeoffs for Real-Time Approximation of Longest Palindromes in Streams}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {18:1--18:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.18}, URN = {urn:nbn:de:0030-drops-60765}, doi = {10.4230/LIPIcs.CPM.2016.18}, annote = {Keywords: streaming algorithms, space lower bounds, real-time algorithms, palin- dromes, Monte Carlo algorithms} }
Sara Geizhals and Dina Sokol. Finding Maximal 2-Dimensional Palindromes. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 19:1-19:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{geizhals_et_al:LIPIcs.CPM.2016.19, author = {Geizhals, Sara and Sokol, Dina}, title = {{Finding Maximal 2-Dimensional Palindromes}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {19:1--19:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.19}, URN = {urn:nbn:de:0030-drops-60752}, doi = {10.4230/LIPIcs.CPM.2016.19}, annote = {Keywords: palindrome, pattern matching, 2-Dimensional, centrosymmetric factor} }
Mika Amit, Philip Bille, Patrick Hagge Cording, Inge Li Gørtz, and Hjalte Wedel Vildhøj. Boxed Permutation Pattern Matching. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 20:1-20:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{amit_et_al:LIPIcs.CPM.2016.20, author = {Amit, Mika and Bille, Philip and Hagge Cording, Patrick and Li G{\o}rtz, Inge and Wedel Vildh{\o}j, Hjalte}, title = {{Boxed Permutation Pattern Matching}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {20:1--20:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.20}, URN = {urn:nbn:de:0030-drops-60744}, doi = {10.4230/LIPIcs.CPM.2016.20}, annote = {Keywords: Permutation, Subsequence, Pattern Matching, Order Preserving, Boxed Mesh Pattern} }
Tatiana Starikovskaya. Longest Common Substring with Approximately k Mismatches. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 21:1-21:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{starikovskaya:LIPIcs.CPM.2016.21, author = {Starikovskaya, Tatiana}, title = {{Longest Common Substring with Approximately k Mismatches}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {21:1--21:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.21}, URN = {urn:nbn:de:0030-drops-60720}, doi = {10.4230/LIPIcs.CPM.2016.21}, annote = {Keywords: Randomised algorithms, string similarity measures, longest common substring, sketching, locality-sensitive hashing} }
Takuya Takagi, Shunsuke Inenaga, and Hiroki Arimura. Fully-online Construction of Suffix Trees for Multiple Texts. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 22:1-22:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{takagi_et_al:LIPIcs.CPM.2016.22, author = {Takagi, Takuya and Inenaga, Shunsuke and Arimura, Hiroki}, title = {{Fully-online Construction of Suffix Trees for Multiple Texts}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {22:1--22:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.22}, URN = {urn:nbn:de:0030-drops-60719}, doi = {10.4230/LIPIcs.CPM.2016.22}, annote = {Keywords: suffix trees, DAWGs, multiple texts, online algorithms} }
Uwe Baier. Linear-time Suffix Sorting - A New Approach for Suffix Array Construction. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 23:1-23:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{baier:LIPIcs.CPM.2016.23, author = {Baier, Uwe}, title = {{Linear-time Suffix Sorting - A New Approach for Suffix Array Construction}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {23:1--23:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.23}, URN = {urn:nbn:de:0030-drops-60698}, doi = {10.4230/LIPIcs.CPM.2016.23}, annote = {Keywords: Suffix array, sorting algorithm, linear time} }
Tsvi Kopelowitz and Robert Krauthgamer. Color-Distance Oracles and Snippets. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 24:1-24:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{kopelowitz_et_al:LIPIcs.CPM.2016.24, author = {Kopelowitz, Tsvi and Krauthgamer, Robert}, title = {{Color-Distance Oracles and Snippets}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {24:1--24:10}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.24}, URN = {urn:nbn:de:0030-drops-60684}, doi = {10.4230/LIPIcs.CPM.2016.24}, annote = {Keywords: Snippets, Text Indexing, Distance Oracles, Near Neighbor Search} }
Pawel Gawrychowski, Gad M. Landau, Shay Mozes, and Oren Weimann. The Nearest Colored Node in a Tree. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 25:1-25:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2016.25, author = {Gawrychowski, Pawel and Landau, Gad M. and Mozes, Shay and Weimann, Oren}, title = {{The Nearest Colored Node in a Tree}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {25:1--25:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.25}, URN = {urn:nbn:de:0030-drops-60674}, doi = {10.4230/LIPIcs.CPM.2016.25}, annote = {Keywords: Marked ancestor, Vertex-label distance oracles, Nearest colored descend- ant, Top-trees} }
Johannes Fischer, Dominik Köppl, and Florian Kurpicz. On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 26:1-26:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{fischer_et_al:LIPIcs.CPM.2016.26, author = {Fischer, Johannes and K\"{o}ppl, Dominik and Kurpicz, Florian}, title = {{On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {26:1--26:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.26}, URN = {urn:nbn:de:0030-drops-60669}, doi = {10.4230/LIPIcs.CPM.2016.26}, annote = {Keywords: parallel algorithms, pattern matching, approximate string matching} }
Yoshiaki Matsuoka, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda, and Florin Manea. Factorizing a String into Squares in Linear Time. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 27:1-27:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{matsuoka_et_al:LIPIcs.CPM.2016.27, author = {Matsuoka, Yoshiaki and Inenaga, Shunsuke and Bannai, Hideo and Takeda, Masayuki and Manea, Florin}, title = {{Factorizing a String into Squares in Linear Time}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {27:1--27:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.27}, URN = {urn:nbn:de:0030-drops-60645}, doi = {10.4230/LIPIcs.CPM.2016.27}, annote = {Keywords: Squares, Runs, Factorization of Strings} }
Tomasz Kociumaka. Minimal Suffix and Rotation of a Substring in Optimal Time. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 28:1-28:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{kociumaka:LIPIcs.CPM.2016.28, author = {Kociumaka, Tomasz}, title = {{Minimal Suffix and Rotation of a Substring in Optimal Time}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {28:1--28:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.28}, URN = {urn:nbn:de:0030-drops-60626}, doi = {10.4230/LIPIcs.CPM.2016.28}, annote = {Keywords: minimal suffix, minimal rotation, Lyndon factorization, substring canon- ization, substring queries} }
Jérémy Barbay. Optimal Prefix Free Codes with Partial Sorting. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 29:1-29:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{barbay:LIPIcs.CPM.2016.29, author = {Barbay, J\'{e}r\'{e}my}, title = {{Optimal Prefix Free Codes with Partial Sorting}}, booktitle = {27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)}, pages = {29:1--29:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-012-5}, ISSN = {1868-8969}, year = {2016}, volume = {54}, editor = {Grossi, Roberto and Lewenstein, Moshe}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.29}, URN = {urn:nbn:de:0030-drops-60635}, doi = {10.4230/LIPIcs.CPM.2016.29}, annote = {Keywords: Deferred Data Structure, Huffman, Median, Optimal Prefix Free Codes, van Leeuwen.} }
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