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ORCIDBibTeX records: Sampo Pyysalo
@article{DBLP:journals/corr/abs-2403-14009,
author = {Ona de Gibert and
Graeme Nail and
Nikolay Arefyev and
Marta Ba{\~{n}}{\'{o}}n and
Jelmer van der Linde and
Shaoxiong Ji and
Jaume Zaragoza{-}Bernabeu and
Mikko Aulamo and
Gema Ram{\'{\i}}rez{-}S{\'{a}}nchez and
Andrey Kutuzov and
Sampo Pyysalo and
Stephan Oepen and
J{\"{o}}rg Tiedemann},
title = {A New Massive Multilingual Dataset for High-Performance Language Technologies},
journal = {CoRR},
volume = {abs/2403.14009},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2403.14009},
doi = {10.48550/ARXIV.2403.14009},
eprinttype = {arXiv},
eprint = {2403.14009},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2403-14009.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MirandaEscaladaMLEGPVK23,
author = {Antonio Miranda{-}Escalada and
Farrokh Mehryary and
Jouni Luoma and
Darryl Estrada{-}Zavala and
Luis Gasc{\'{o}} and
Sampo Pyysalo and
Alfonso Valencia and
Martin Krallinger},
title = {Overview of DrugProt task at BioCreative {VII:} data and methods for
large-scale text mining and knowledge graph generation of heterogenous
chemical-protein relations},
journal = {Database J. Biol. Databases Curation},
volume = {2023},
year = {2023},
url = {https://doi.org/10.1093/database/baad080},
doi = {10.1093/DATABASE/BAAD080},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/MirandaEscaladaMLEGPVK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/lre/LaippalaROKSBEP23,
author = {Veronika Laippala and
Samuel R{\"{o}}nnqvist and
Miika Oinonen and
Aki{-}Juhani Kyr{\"{o}}l{\"{a}}inen and
Anna Salmela and
Douglas Biber and
Jesse Egbert and
Sampo Pyysalo},
title = {Register identification from the unrestricted open Web using the Corpus
of Online Registers of English},
journal = {Lang. Resour. Evaluation},
volume = {57},
number = {3},
pages = {1045--1079},
year = {2023},
url = {https://doi.org/10.1007/s10579-022-09624-1},
doi = {10.1007/S10579-022-09624-1},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/lre/LaippalaROKSBEP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SzklarczykKKNMHGFDPBJM23,
author = {Damian Szklarczyk and
Rebecca Kirsch and
Mikaela Koutrouli and
Katerina C. Nastou and
Farrokh Mehryary and
Radja Hachilif and
Annika L. Gable and
Tao Fang and
Nadezhda T. Doncheva and
Sampo Pyysalo and
Peer Bork and
Lars Juhl Jensen and
Christian von Mering},
title = {The {STRING} database in 2023: protein-protein association networks
and functional enrichment analyses for any sequenced genome of interest},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {638--646},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1000},
doi = {10.1093/NAR/GKAC1000},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SzklarczykKKNMHGFDPBJM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/BassignanaGPGP23,
author = {Elisa Bassignana and
Filip Ginter and
Sampo Pyysalo and
Rob van der Goot and
Barbara Plank},
editor = {Anna Rogers and
Jordan L. Boyd{-}Graber and
Naoaki Okazaki},
title = {Silver Syntax Pre-training for Cross-Domain Relation Extraction},
booktitle = {Findings of the Association for Computational Linguistics: {ACL} 2023,
Toronto, Canada, July 9-14, 2023},
pages = {6984--6993},
publisher = {Association for Computational Linguistics},
year = {2023},
url = {https://doi.org/10.18653/v1/2023.findings-acl.436},
doi = {10.18653/V1/2023.FINDINGS-ACL.436},
timestamp = {Thu, 10 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl/BassignanaGPGP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/LuukkonenKLEKKG23,
author = {Risto Luukkonen and
Ville Komulainen and
Jouni Luoma and
Anni Eskelinen and
Jenna Kanerva and
Hanna{-}Mari Kupari and
Filip Ginter and
Veronika Laippala and
Niklas Muennighoff and
Aleksandra Piktus and
Thomas Wang and
Nouamane Tazi and
Teven Le Scao and
Thomas Wolf and
Osma Suominen and
Samuli Sairanen and
Mikko Merioksa and
Jyrki Heinonen and
Aija Vahtola and
Samuel Antao and
Sampo Pyysalo},
editor = {Houda Bouamor and
Juan Pino and
Kalika Bali},
title = {FinGPT: Large Generative Models for a Small Language},
booktitle = {Proceedings of the 2023 Conference on Empirical Methods in Natural
Language Processing, {EMNLP} 2023, Singapore, December 6-10, 2023},
pages = {2710--2726},
publisher = {Association for Computational Linguistics},
year = {2023},
url = {https://doi.org/10.18653/v1/2023.emnlp-main.164},
doi = {10.18653/V1/2023.EMNLP-MAIN.164},
timestamp = {Fri, 12 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/emnlp/LuukkonenKLEKKG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/MuennighoffRBST23,
author = {Niklas Muennighoff and
Alexander M. Rush and
Boaz Barak and
Teven Le Scao and
Nouamane Tazi and
Aleksandra Piktus and
Sampo Pyysalo and
Thomas Wolf and
Colin A. Raffel},
editor = {Alice Oh and
Tristan Naumann and
Amir Globerson and
Kate Saenko and
Moritz Hardt and
Sergey Levine},
title = {Scaling Data-Constrained Language Models},
booktitle = {Advances in Neural Information Processing Systems 36: Annual Conference
on Neural Information Processing Systems 2023, NeurIPS 2023, New Orleans,
LA, USA, December 10 - 16, 2023},
year = {2023},
url = {http://papers.nips.cc/paper\_files/paper/2023/hash/9d89448b63ce1e2e8dc7af72c984c196-Abstract-Conference.html},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/MuennighoffRBST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/BassignanaGPGP23,
author = {Elisa Bassignana and
Filip Ginter and
Sampo Pyysalo and
Rob van der Goot and
Barbara Plank},
editor = {Tanel Alum{\"{a}}e and
Mark Fishel},
title = {Multi-CrossRE {A} Multi-Lingual Multi-Domain Dataset for Relation
Extraction},
booktitle = {Proceedings of the 24th Nordic Conference on Computational Linguistics,
NoDaLiDa 2023, T{\'{o}}rshavn, Faroe Islands, May 22-24, 2023},
pages = {80--85},
publisher = {University of Tartu Library},
year = {2023},
url = {https://aclanthology.org/2023.nodalida-1.9},
timestamp = {Mon, 22 May 2023 16:42:56 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/BassignanaGPGP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/EskelinenSGPL23,
author = {Anni Eskelinen and
Laura Silvala and
Filip Ginter and
Sampo Pyysalo and
Veronika Laippala},
editor = {Tanel Alum{\"{a}}e and
Mark Fishel},
title = {Toxicity Detection in Finnish Using Machine Translation},
booktitle = {Proceedings of the 24th Nordic Conference on Computational Linguistics,
NoDaLiDa 2023, T{\'{o}}rshavn, Faroe Islands, May 22-24, 2023},
pages = {685--697},
publisher = {University of Tartu Library},
year = {2023},
url = {https://aclanthology.org/2023.nodalida-1.68},
timestamp = {Mon, 22 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/EskelinenSGPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-10985,
author = {Elisa Bassignana and
Filip Ginter and
Sampo Pyysalo and
Rob van der Goot and
Barbara Plank},
title = {Multi-CrossRE {A} Multi-Lingual Multi-Domain Dataset for Relation
Extraction},
journal = {CoRR},
volume = {abs/2305.10985},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.10985},
doi = {10.48550/ARXIV.2305.10985},
eprinttype = {arXiv},
eprint = {2305.10985},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-10985.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-11016,
author = {Elisa Bassignana and
Filip Ginter and
Sampo Pyysalo and
Rob van der Goot and
Barbara Plank},
title = {Silver Syntax Pre-training for Cross-Domain Relation Extraction},
journal = {CoRR},
volume = {abs/2305.11016},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.11016},
doi = {10.48550/ARXIV.2305.11016},
eprinttype = {arXiv},
eprint = {2305.11016},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-11016.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-16264,
author = {Niklas Muennighoff and
Alexander M. Rush and
Boaz Barak and
Teven Le Scao and
Aleksandra Piktus and
Nouamane Tazi and
Sampo Pyysalo and
Thomas Wolf and
Colin Raffel},
title = {Scaling Data-Constrained Language Models},
journal = {CoRR},
volume = {abs/2305.16264},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.16264},
doi = {10.48550/ARXIV.2305.16264},
eprinttype = {arXiv},
eprint = {2305.16264},
timestamp = {Wed, 07 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-16264.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-05640,
author = {Risto Luukkonen and
Ville Komulainen and
Jouni Luoma and
Anni Eskelinen and
Jenna Kanerva and
Hanna{-}Mari Kupari and
Filip Ginter and
Veronika Laippala and
Niklas Muennighoff and
Aleksandra Piktus and
Thomas Wang and
Nouamane Tazi and
Teven Le Scao and
Thomas Wolf and
Osma Suominen and
Samuli Sairanen and
Mikko Merioksa and
Jyrki Heinonen and
Aija Vahtola and
Samuel Antao and
Sampo Pyysalo},
title = {FinGPT: Large Generative Models for a Small Language},
journal = {CoRR},
volume = {abs/2311.05640},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.05640},
doi = {10.48550/ARXIV.2311.05640},
eprinttype = {arXiv},
eprint = {2311.05640},
timestamp = {Tue, 14 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-05640.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/LaippalaSRACDGK22,
author = {Veronika Laippala and
Anna Salmela and
Samuel R{\"{o}}nnqvist and
Alham Fikri Aji and
Li{-}Hsin Chang and
Asma Dhifallah and
Larissa Goulart and
Henna Kortelainen and
Marc P{\`{a}}mies and
Deise Prina Dutra and
Valtteri Skantsi and
Lintang Sutawika and
Sampo Pyysalo},
title = {Towards better structured and less noisy Web data: Oscar with Register
annotations},
booktitle = {Proceedings of the Eighth Workshop on Noisy User-generated Text, W-NUT@COLING
2022, Gyeongju, Republic of Korea, October 12 - 17, 2022},
pages = {215--221},
publisher = {Association for Computational Linguistics},
year = {2022},
url = {https://aclanthology.org/2022.wnut-1.23},
timestamp = {Thu, 20 Oct 2022 17:06:19 +0200},
biburl = {https://dblp.org/rec/conf/coling/LaippalaSRACDGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SzklarczykGNLKP21,
author = {Damian Szklarczyk and
Annika L. Gable and
Katerina C. Nastou and
David Lyon and
Rebecca Kirsch and
Sampo Pyysalo and
Nadezhda T. Doncheva and
Marc Legeay and
Tao Fang and
Peer Bork and
Lars Juhl Jensen and
Christian von Mering},
title = {The {STRING} database in 2021: customizable protein-protein networks,
and functional characterization of user-uploaded gene/measurement
sets},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D605--D612},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1074},
doi = {10.1093/NAR/GKAA1074},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SzklarczykGNLKP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eacl/RepoSRHOSBEPL21,
author = {Liina Repo and
Valtteri Skantsi and
Samuel R{\"{o}}nnqvist and
Saara Hellstr{\"{o}}m and
Miika Oinonen and
Anna Salmela and
Douglas Biber and
Jesse Egbert and
Sampo Pyysalo and
Veronika Laippala},
editor = {Ionut{-}Teodor Sorodoc and
Madhumita Sushil and
Ece Takmaz and
Eneko Agirre},
title = {Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual
Classification of Registers},
booktitle = {Proceedings of the 16th Conference of the European Chapter of the
Association for Computational Linguistics: Student Research Workshop,
{EACL} 2021, Online, April 19-23, 2021},
pages = {183--191},
publisher = {Association for Computational Linguistics},
year = {2021},
url = {https://doi.org/10.18653/v1/2021.eacl-srw.24},
doi = {10.18653/V1/2021.EACL-SRW.24},
timestamp = {Thu, 20 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eacl/RepoSRHOSBEPL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/edm/ChangRKSPG21,
author = {Li{-}Hsin Chang and
Iiro Rastas and
Jenna Kanerva and
Valtteri Skantsi and
Sampo Pyysalo and
Filip Ginter},
editor = {Sharon I{-}Han Hsiao and
Shaghayegh (Sherry) Sahebi and
Fran{\c{c}}ois Bouchet and
Jill{-}J{\^{e}}nn Vie},
title = {Deep learning for sentence clustering in essay grading support},
booktitle = {Proceedings of the 14th International Conference on Educational Data
Mining, {EDM} 2021, virtual, June 29 - July 2, 2021},
publisher = {International Educational Data Mining Society},
year = {2021},
timestamp = {Wed, 09 Mar 2022 16:46:41 +0100},
biburl = {https://dblp.org/rec/conf/edm/ChangRKSPG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/PyysaloKVG21,
author = {Sampo Pyysalo and
Jenna Kanerva and
Antti Virtanen and
Filip Ginter},
editor = {Simon Dobnik and
Lilja {\O}vrelid},
title = {WikiBERT Models: Deep Transfer Learning for Many Languages},
booktitle = {Proceedings of the 23rd Nordic Conference on Computational Linguistics,
NoDaLiDa 2021, Reykjavik, Iceland (Online), May 31 - June 2, 2021},
pages = {1--10},
publisher = {Link{\"{o}}ping University Electronic Press, Sweden},
year = {2021},
url = {https://aclanthology.org/2021.nodalida-main.1/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/PyysaloKVG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/LuomaCGP21,
author = {Jouni Luoma and
Li{-}Hsin Chang and
Filip Ginter and
Sampo Pyysalo},
editor = {Simon Dobnik and
Lilja {\O}vrelid},
title = {Fine-grained Named Entity Annotation for Finnish},
booktitle = {Proceedings of the 23rd Nordic Conference on Computational Linguistics,
NoDaLiDa 2021, Reykjavik, Iceland (Online), May 31 - June 2, 2021},
pages = {135--144},
publisher = {Link{\"{o}}ping University Electronic Press, Sweden},
year = {2021},
url = {https://aclanthology.org/2021.nodalida-main.14/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/LuomaCGP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2102-07396,
author = {Liina Repo and
Valtteri Skantsi and
Samuel R{\"{o}}nnqvist and
Saara Hellstr{\"{o}}m and
Miika Oinonen and
Anna Salmela and
Douglas Biber and
Jesse Egbert and
Sampo Pyysalo and
Veronika Laippala},
title = {Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual
Classification of Registers},
journal = {CoRR},
volume = {abs/2102.07396},
year = {2021},
url = {https://arxiv.org/abs/2102.07396},
eprinttype = {arXiv},
eprint = {2102.07396},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2102-07396.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2104-11556,
author = {Li{-}Hsin Chang and
Iiro Rastas and
Sampo Pyysalo and
Filip Ginter},
title = {Deep learning for sentence clustering in essay grading support},
journal = {CoRR},
volume = {abs/2104.11556},
year = {2021},
url = {https://arxiv.org/abs/2104.11556},
eprinttype = {arXiv},
eprint = {2104.11556},
timestamp = {Tue, 27 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2104-11556.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2105-02477,
author = {Li{-}Hsin Chang and
Sampo Pyysalo and
Jenna Kanerva and
Filip Ginter},
title = {Quantitative Evaluation of Alternative Translations in a Corpus of
Highly Dissimilar Finnish Paraphrases},
journal = {CoRR},
volume = {abs/2105.02477},
year = {2021},
url = {https://arxiv.org/abs/2105.02477},
eprinttype = {arXiv},
eprint = {2105.02477},
timestamp = {Wed, 12 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2105-02477.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-13653,
author = {Samuel R{\"{o}}nnqvist and
Amanda Myntti and
Aki{-}Juhani Kyr{\"{o}}l{\"{a}}inen and
Sampo Pyysalo and
Veronika Laippala and
Filip Ginter},
title = {Explaining Classes through Word Attribution},
journal = {CoRR},
volume = {abs/2108.13653},
year = {2021},
url = {https://arxiv.org/abs/2108.13653},
eprinttype = {arXiv},
eprint = {2108.13653},
timestamp = {Fri, 03 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-13653.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KanervaGP20,
author = {Jenna Kanerva and
Filip Ginter and
Sampo Pyysalo},
title = {Dependency parsing of biomedical text with {BERT}},
journal = {{BMC} Bioinform.},
volume = {21-S},
number = {23},
pages = {580},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03905-8},
doi = {10.1186/S12859-020-03905-8},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KanervaGP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aclwac/LaippalaRHLRSSP20,
author = {Veronika Laippala and
Samuel R{\"{o}}nnqvist and
Saara Hellstr{\"{o}}m and
Juhani Luotolahti and
Liina Repo and
Anna Salmela and
Valtteri Skantsi and
Sampo Pyysalo},
editor = {Adrien Barbaresi and
Felix Bildhauer and
Roland Sch{\"{a}}fer and
Egon Stemle},
title = {From Web Crawl to Clean Register-Annotated Corpora},
booktitle = {Proceedings of the 12th Web as Corpus Workshop, WAC@LREC 2020, Marseille,
France, May 2020},
pages = {14--22},
publisher = {European Language Resources Association},
year = {2020},
url = {https://aclanthology.org/2020.wac-1.3/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/aclwac/LaippalaRHLRSSP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/LuomaP20,
author = {Jouni Luoma and
Sampo Pyysalo},
editor = {Donia Scott and
N{\'{u}}ria Bel and
Chengqing Zong},
title = {Exploring Cross-sentence Contexts for Named Entity Recognition with
{BERT}},
booktitle = {Proceedings of the 28th International Conference on Computational
Linguistics, {COLING} 2020, Barcelona, Spain (Online), December 8-13,
2020},
pages = {904--914},
publisher = {International Committee on Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.coling-main.78},
doi = {10.18653/V1/2020.COLING-MAIN.78},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/coling/LuomaP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/DumitrescuAP20,
author = {Stefan Daniel Dumitrescu and
Andrei{-}Marius Avram and
Sampo Pyysalo},
editor = {Trevor Cohn and
Yulan He and
Yang Liu},
title = {The birth of Romanian {BERT}},
booktitle = {Findings of the Association for Computational Linguistics: {EMNLP}
2020, Online Event, 16-20 November 2020},
series = {Findings of {ACL}},
volume = {{EMNLP} 2020},
pages = {4324--4328},
publisher = {Association for Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.findings-emnlp.387},
doi = {10.18653/V1/2020.FINDINGS-EMNLP.387},
timestamp = {Wed, 23 Mar 2022 10:11:55 +0100},
biburl = {https://dblp.org/rec/conf/emnlp/DumitrescuAP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwpt/KanervaGP20,
author = {Jenna Kanerva and
Filip Ginter and
Sampo Pyysalo},
editor = {Gosse Bouma and
Yuji Matsumoto and
Stephan Oepen and
Kenji Sagae and
Djam{\'{e}} Seddah and
Weiwei Sun and
Anders S{\o}gaard and
Reut Tsarfaty and
Dan Zeman},
title = {Turku Enhanced Parser Pipeline: From Raw Text to Enhanced Graphs in
the {IWPT} 2020 Shared Task},
booktitle = {Proceedings of the 16th International Conference on Parsing Technologies
and the {IWPT} 2020 Shared Task on Parsing into Enhanced Universal
Dependencies, {IWPT} 2020, Online, July 9, 2020},
pages = {162--173},
publisher = {Association for Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.iwpt-1.17},
doi = {10.18653/V1/2020.IWPT-1.17},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iwpt/KanervaGP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lrec/NivreMGHMPSTZ20,
author = {Joakim Nivre and
Marie{-}Catherine de Marneffe and
Filip Ginter and
Jan Hajic and
Christopher D. Manning and
Sampo Pyysalo and
Sebastian Schuster and
Francis M. Tyers and
Daniel Zeman},
editor = {Nicoletta Calzolari and
Fr{\'{e}}d{\'{e}}ric B{\'{e}}chet and
Philippe Blache and
Khalid Choukri and
Christopher Cieri and
Thierry Declerck and
Sara Goggi and
Hitoshi Isahara and
Bente Maegaard and
Joseph Mariani and
H{\'{e}}l{\`{e}}ne Mazo and
Asunci{\'{o}}n Moreno and
Jan Odijk and
Stelios Piperidis},
title = {Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection},
booktitle = {Proceedings of The 12th Language Resources and Evaluation Conference,
{LREC} 2020, Marseille, France, May 11-16, 2020},
pages = {4034--4043},
publisher = {European Language Resources Association},
year = {2020},
url = {https://aclanthology.org/2020.lrec-1.497/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/lrec/NivreMGHMPSTZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lrec/LuomaOPLP20,
author = {Jouni Luoma and
Miika Oinonen and
Maria Pyyk{\"{o}}nen and
Veronika Laippala and
Sampo Pyysalo},
editor = {Nicoletta Calzolari and
Fr{\'{e}}d{\'{e}}ric B{\'{e}}chet and
Philippe Blache and
Khalid Choukri and
Christopher Cieri and
Thierry Declerck and
Sara Goggi and
Hitoshi Isahara and
Bente Maegaard and
Joseph Mariani and
H{\'{e}}l{\`{e}}ne Mazo and
Asunci{\'{o}}n Moreno and
Jan Odijk and
Stelios Piperidis},
title = {A Broad-coverage Corpus for Finnish Named Entity Recognition},
booktitle = {Proceedings of The 12th Language Resources and Evaluation Conference,
{LREC} 2020, Marseille, France, May 11-16, 2020},
pages = {4615--4624},
publisher = {European Language Resources Association},
year = {2020},
url = {https://aclanthology.org/2020.lrec-1.567/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/lrec/LuomaOPLP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-10643,
author = {Joakim Nivre and
Marie{-}Catherine de Marneffe and
Filip Ginter and
Jan Hajic and
Christopher D. Manning and
Sampo Pyysalo and
Sebastian Schuster and
Francis M. Tyers and
Daniel Zeman},
title = {Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection},
journal = {CoRR},
volume = {abs/2004.10643},
year = {2020},
url = {https://arxiv.org/abs/2004.10643},
eprinttype = {arXiv},
eprint = {2004.10643},
timestamp = {Tue, 28 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-10643.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-01538,
author = {Sampo Pyysalo and
Jenna Kanerva and
Antti Virtanen and
Filip Ginter},
title = {WikiBERT models: deep transfer learning for many languages},
journal = {CoRR},
volume = {abs/2006.01538},
year = {2020},
url = {https://arxiv.org/abs/2006.01538},
eprinttype = {arXiv},
eprint = {2006.01538},
timestamp = {Mon, 08 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-01538.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-01563,
author = {Jouni Luoma and
Sampo Pyysalo},
title = {Exploring Cross-sentence Contexts for Named Entity Recognition with
{BERT}},
journal = {CoRR},
volume = {abs/2006.01563},
year = {2020},
url = {https://arxiv.org/abs/2006.01563},
eprinttype = {arXiv},
eprint = {2006.01563},
timestamp = {Mon, 08 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-01563.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-08712,
author = {Stefan Daniel Dumitrescu and
Andrei{-}Marius Avram and
Sampo Pyysalo},
title = {The birth of Romanian {BERT}},
journal = {CoRR},
volume = {abs/2009.08712},
year = {2020},
url = {https://arxiv.org/abs/2009.08712},
eprinttype = {arXiv},
eprint = {2009.08712},
timestamp = {Wed, 23 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-08712.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-11639,
author = {Li{-}Hsin Chang and
Sampo Pyysalo and
Jenna Kanerva and
Filip Ginter},
title = {Towards Fully Bilingual Deep Language Modeling},
journal = {CoRR},
volume = {abs/2010.11639},
year = {2020},
url = {https://arxiv.org/abs/2010.11639},
eprinttype = {arXiv},
eprint = {2010.11639},
timestamp = {Tue, 27 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2010-11639.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PyysaloBAHSYGHS19,
author = {Sampo Pyysalo and
Simon Baker and
Imran Ali and
Stefan Haselwimmer and
Tejas Shah and
Andrew Young and
Yufan Guo and
Johan H{\"{o}}gberg and
Ulla Stenius and
Masashi Narita and
Anna Korhonen},
title = {{LION} {LBD:} a literature-based discovery system for cancer biology},
journal = {Bioinform.},
volume = {35},
number = {9},
pages = {1553--1561},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty845},
doi = {10.1093/BIOINFORMATICS/BTY845},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PyysaloBAHSYGHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ChiuMPWSKP19,
author = {Billy Chiu and
Olga Majewska and
Sampo Pyysalo and
Laura Wey and
Ulla Stenius and
Anna Korhonen and
Martha Palmer},
title = {A neural classification method for supporting the creation of BioVerbNet},
journal = {J. Biomed. Semant.},
volume = {10},
number = {1},
pages = {2:1--2:12},
year = {2019},
url = {https://doi.org/10.1186/s13326-018-0193-x},
doi = {10.1186/S13326-018-0193-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ChiuMPWSKP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/HakalaP19,
author = {Kai Hakala and
Sampo Pyysalo},
editor = {Jin{-}Dong Kim and
Claire N{\'{e}}dellec and
Robert Bossy and
Louise Del{\'{e}}ger},
title = {Biomedical Named Entity Recognition with Multilingual {BERT}},
booktitle = {Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, BioNLP-OST@EMNLP-IJNCLP
2019, Hong Kong, China, November 4, 2019},
pages = {56--61},
publisher = {Association for Computational Linguistics},
year = {2019},
url = {https://doi.org/10.18653/v1/D19-5709},
doi = {10.18653/V1/D19-5709},
timestamp = {Thu, 05 Aug 2021 17:36:17 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/HakalaP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/BaumgartnerBPCH19,
author = {William A. Baumgartner Jr. and
Michael Bada and
Sampo Pyysalo and
Manuel R. Ciosici and
Negacy D. Hailu and
Harrison Pielke{-}Lombardo and
Michael Regan and
Lawrence Hunter},
editor = {Jin{-}Dong Kim and
Claire N{\'{e}}dellec and
Robert Bossy and
Louise Del{\'{e}}ger},
title = {{CRAFT} Shared Tasks 2019 Overview - Integrated Structure, Semantics,
and Coreference},
booktitle = {Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, BioNLP-OST@EMNLP-IJNCLP
2019, Hong Kong, China, November 4, 2019},
pages = {174--184},
publisher = {Association for Computational Linguistics},
year = {2019},
url = {https://doi.org/10.18653/v1/D19-5725},
doi = {10.18653/V1/D19-5725},
timestamp = {Thu, 25 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/BaumgartnerBPCH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/NgoKGP19,
author = {Thang Minh Ngo and
Jenna Kanerva and
Filip Ginter and
Sampo Pyysalo},
editor = {Jin{-}Dong Kim and
Claire N{\'{e}}dellec and
Robert Bossy and
Louise Del{\'{e}}ger},
title = {Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the
{CRAFT} Structural Annotation Task},
booktitle = {Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, BioNLP-OST@EMNLP-IJNCLP
2019, Hong Kong, China, November 4, 2019},
pages = {206--215},
publisher = {Association for Computational Linguistics},
year = {2019},
url = {https://doi.org/10.18653/v1/D19-5728},
doi = {10.18653/V1/D19-5728},
timestamp = {Mon, 16 Dec 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bionlp/NgoKGP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/LaippalaKEBP19,
author = {Veronika Laippala and
Roosa Kyll{\"{o}}nen and
Jesse Egbert and
Douglas Biber and
Sampo Pyysalo},
editor = {Mareike Hartmann and
Barbara Plank},
title = {Toward Multilingual Identification of Online Registers},
booktitle = {Proceedings of the 22nd Nordic Conference on Computational Linguistics,
NoDaLiDa 2019, Turku, Finland, September 30 - October 2, 2019},
pages = {292--297},
publisher = {Link{\"{o}}ping University Electronic Press},
year = {2019},
url = {https://aclanthology.org/W19-6130/},
timestamp = {Thu, 05 Aug 2021 17:36:17 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/LaippalaKEBP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1912-07076,
author = {Antti Virtanen and
Jenna Kanerva and
Rami Ilo and
Jouni Luoma and
Juhani Luotolahti and
Tapio Salakoski and
Filip Ginter and
Sampo Pyysalo},
title = {Multilingual is not enough: {BERT} for Finnish},
journal = {CoRR},
volume = {abs/1912.07076},
year = {2019},
url = {http://arxiv.org/abs/1912.07076},
eprinttype = {arXiv},
eprint = {1912.07076},
timestamp = {Fri, 03 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1912-07076.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChiuPVK18,
author = {Billy Chiu and
Sampo Pyysalo and
Ivan Vulic and
Anna Korhonen},
title = {Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word
similarity in biomedicine},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {33:1--33:13},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2039-z},
doi = {10.1186/S12859-018-2039-Z},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChiuPVK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CrichtonGPK18,
author = {Gamal K. O. Crichton and
Yufan Guo and
Sampo Pyysalo and
Anna Korhonen},
title = {Neural networks for link prediction in realistic biomedical graphs:
a multi-dimensional evaluation of graph embedding-based approaches},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {176:1--176:11},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2163-9},
doi = {10.1186/S12859-018-2163-9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CrichtonGPK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BakerASPGHSK17,
author = {Simon Baker and
Imran Ali and
Ilona Silins and
Sampo Pyysalo and
Yufan Guo and
Johan H{\"{o}}gberg and
Ulla Stenius and
Anna Korhonen},
title = {Cancer Hallmarks Analytics Tool {(CHAT):} a text mining approach to
organize and evaluate scientific literature on cancer},
journal = {Bioinform.},
volume = {33},
number = {24},
pages = {3973--3981},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx454},
doi = {10.1093/BIOINFORMATICS/BTX454},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BakerASPGHSK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CrichtonPCK17,
author = {Gamal K. O. Crichton and
Sampo Pyysalo and
Billy Chiu and
Anna Korhonen},
title = {A neural network multi-task learning approach to biomedical named
entity recognition},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {368:1--368:14},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1776-8},
doi = {10.1186/S12859-017-1776-8},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CrichtonPCK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/conll/ZemanPSHNGLPPPT17,
author = {Daniel Zeman and
Martin Popel and
Milan Straka and
Jan Hajic and
Joakim Nivre and
Filip Ginter and
Juhani Luotolahti and
Sampo Pyysalo and
Slav Petrov and
Martin Potthast and
Francis M. Tyers and
Elena Badmaeva and
Memduh Gokirmak and
Anna Nedoluzhko and
Silvie Cinkov{\'{a}} and
Jan Hajic Jr. and
Jaroslava Hlav{\'{a}}cov{\'{a}} and
V{\'{a}}clava Kettnerov{\'{a}} and
Zdenka Uresov{\'{a}} and
Jenna Kanerva and
Stina Ojala and
Anna Missil{\"{a}} and
Christopher D. Manning and
Sebastian Schuster and
Siva Reddy and
Dima Taji and
Nizar Habash and
Herman Leung and
Marie{-}Catherine de Marneffe and
Manuela Sanguinetti and
Maria Simi and
Hiroshi Kanayama and
Valeria de Paiva and
Kira Droganova and
H{\'{e}}ctor Mart{\'{\i}}nez Alonso and
{\c{C}}agri {\c{C}}{\"{o}}ltekin and
Umut Sulubacak and
Hans Uszkoreit and
Vivien Macketanz and
Aljoscha Burchardt and
Kim Harris and
Katrin Marheinecke and
Georg Rehm and
Tolga Kayadelen and
Mohammed Attia and
Ali El{-}Kahky and
Zhuoran Yu and
Emily Pitler and
Saran Lertpradit and
Michael Mandl and
Jesse Kirchner and
Hector Fernandez Alcalde and
Jana Strnadov{\'{a}} and
Esha Banerjee and
Ruli Manurung and
Antonio Stella and
Atsuko Shimada and
Sookyoung Kwak and
Gustavo Mendon{\c{c}}a and
Tatiana Lando and
Rattima Nitisaroj and
Josie Li},
editor = {Jan Hajic and
Dan Zeman},
title = {CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal
Dependencies},
booktitle = {Proceedings of the CoNLL 2017 Shared Task: Multilingual Parsing from
Raw Text to Universal Dependencies, Vancouver, Canada, August 3-4,
2017},
pages = {1--19},
publisher = {Association for Computational Linguistics},
year = {2017},
url = {https://doi.org/10.18653/v1/K17-3001},
doi = {10.18653/V1/K17-3001},
timestamp = {Thu, 25 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/conll/ZemanPSHNGLPPPT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/depling/KanervaPG17,
author = {Jenna Kanerva and
Sampo Pyysalo and
Filip Ginter},
editor = {Simonetta Montemagni and
Joakim Nivre},
title = {Fully Delexicalized Contexts for Syntax-Based Word Embeddings},
booktitle = {Proceedings of the Fourth International Conference on Dependency Linguistics,
Depling 2017, Pisa, Italy, September 18-20, 2017},
pages = {83--91},
publisher = {Link{\"{o}}ping University Electronic Press},
year = {2017},
url = {https://aclanthology.org/W17-6511/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/depling/KanervaPG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaewphanLOPGP16,
author = {Suwisa Kaewphan and
Sofie Van Landeghem and
Tomoko Ohta and
Yves Van de Peer and
Filip Ginter and
Sampo Pyysalo},
title = {Cell line name recognition in support of the identification of synthetic
lethality in cancer from text},
journal = {Bioinform.},
volume = {32},
number = {2},
pages = {276--282},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv570},
doi = {10.1093/BIOINFORMATICS/BTV570},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaewphanLOPGP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/MehryaryBPSG16,
author = {Farrokh Mehryary and
Jari Bj{\"{o}}rne and
Sampo Pyysalo and
Tapio Salakoski and
Filip Ginter},
editor = {Claire Nedellec and
Robert Bossy and
Jin{-}Dong Kim},
title = {Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP
Shared Task 2016},
booktitle = {Proceedings of the 4th BioNLP Shared Task Workshop, BioNLP 2016, Berlin,
Germany, August 13, 2016},
pages = {73--81},
publisher = {Association for Computational Linguistics},
year = {2016},
url = {https://doi.org/10.18653/v1/W16-3009},
doi = {10.18653/V1/W16-3009},
timestamp = {Fri, 06 Aug 2021 00:41:22 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/MehryaryBPSG16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/ChiuCKP16,
author = {Billy Chiu and
Gamal K. O. Crichton and
Anna Korhonen and
Sampo Pyysalo},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Jun'ichi Tsujii},
title = {How to Train good Word Embeddings for Biomedical {NLP}},
booktitle = {Proceedings of the 15th Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2016, Berlin, Germany, August 12, 2016},
pages = {166--174},
publisher = {Association for Computational Linguistics},
year = {2016},
url = {https://doi.org/10.18653/v1/W16-2922},
doi = {10.18653/V1/W16-2922},
timestamp = {Fri, 06 Aug 2021 00:41:22 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/ChiuCKP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/BakerKP16,
author = {Simon Baker and
Anna Korhonen and
Sampo Pyysalo},
editor = {Sophia Ananiadou and
Riza Batista{-}Navarro and
Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Paul Thompson},
title = {Cancer Hallmark Text Classification Using Convolutional Neural Networks},
booktitle = {Proceedings of the Fifth Workshop on Building and Evaluating Resources
for Biomedical Text Mining, BioTxtM@COLING 2016, Osaka, Japan, December
12, 2016},
pages = {1--9},
publisher = {The {COLING} 2016 Organizing Committee},
year = {2016},
url = {https://aclanthology.org/W16-5101/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/coling/BakerKP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/ReiCP16,
author = {Marek Rei and
Gamal K. O. Crichton and
Sampo Pyysalo},
editor = {Nicoletta Calzolari and
Yuji Matsumoto and
Rashmi Prasad},
title = {Attending to Characters in Neural Sequence Labeling Models},
booktitle = {{COLING} 2016, 26th International Conference on Computational Linguistics,
Proceedings of the Conference: Technical Papers, December 11-16, 2016,
Osaka, Japan},
pages = {309--318},
publisher = {{ACL}},
year = {2016},
url = {https://aclanthology.org/C16-1030/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/coling/ReiCP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lrec/NivreMGGHMMPPST16,
author = {Joakim Nivre and
Marie{-}Catherine de Marneffe and
Filip Ginter and
Yoav Goldberg and
Jan Hajic and
Christopher D. Manning and
Ryan T. McDonald and
Slav Petrov and
Sampo Pyysalo and
Natalia Silveira and
Reut Tsarfaty and
Daniel Zeman},
editor = {Nicoletta Calzolari and
Khalid Choukri and
Thierry Declerck and
Sara Goggi and
Marko Grobelnik and
Bente Maegaard and
Joseph Mariani and
H{\'{e}}l{\`{e}}ne Mazo and
Asunci{\'{o}}n Moreno and
Jan Odijk and
Stelios Piperidis},
title = {Universal Dependencies v1: {A} Multilingual Treebank Collection},
booktitle = {Proceedings of the Tenth International Conference on Language Resources
and Evaluation {LREC} 2016, Portoro{\v{z}}, Slovenia, May 23-28, 2016},
publisher = {European Language Resources Association {(ELRA)}},
year = {2016},
url = {http://www.lrec-conf.org/proceedings/lrec2016/summaries/348.html},
timestamp = {Mon, 19 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/lrec/NivreMGGHMMPPST16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lrec/TateisiOPMA16,
author = {Yuka Tateisi and
Tomoko Ohta and
Sampo Pyysalo and
Yusuke Miyao and
Akiko Aizawa},
editor = {Nicoletta Calzolari and
Khalid Choukri and
Thierry Declerck and
Sara Goggi and
Marko Grobelnik and
Bente Maegaard and
Joseph Mariani and
H{\'{e}}l{\`{e}}ne Mazo and
Asunci{\'{o}}n Moreno and
Jan Odijk and
Stelios Piperidis},
title = {Typed Entity and Relation Annotation on Computer Science Papers},
booktitle = {Proceedings of the Tenth International Conference on Language Resources
and Evaluation {LREC} 2016, Portoro{\v{z}}, Slovenia, May 23-28, 2016},
publisher = {European Language Resources Association {(ELRA)}},
year = {2016},
url = {http://www.lrec-conf.org/proceedings/lrec2016/summaries/784.html},
timestamp = {Mon, 19 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/lrec/TateisiOPMA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/repeval/ChiuKP16,
author = {Billy Chiu and
Anna Korhonen and
Sampo Pyysalo},
title = {Intrinsic Evaluation of Word Vectors Fails to Predict Extrinsic Performance},
booktitle = {Proceedings of the 1st Workshop on Evaluating Vector-Space Representations
for NLP, RepEval@ACL 2016, Berlin, Germany, August 2016},
pages = {1--6},
publisher = {Association for Computational Linguistics},
year = {2016},
url = {https://doi.org/10.18653/v1/W16-2501},
doi = {10.18653/V1/W16-2501},
timestamp = {Fri, 06 Aug 2021 00:41:19 +0200},
biburl = {https://dblp.org/rec/conf/repeval/ChiuKP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ReiCP16,
author = {Marek Rei and
Gamal K. O. Crichton and
Sampo Pyysalo},
title = {Attending to Characters in Neural Sequence Labeling Models},
journal = {CoRR},
volume = {abs/1611.04361},
year = {2016},
url = {http://arxiv.org/abs/1611.04361},
eprinttype = {arXiv},
eprint = {1611.04361},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ReiCP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PyysaloORRCJCTA15,
author = {Sampo Pyysalo and
Tomoko Ohta and
Rafal Rak and
Andrew Rowley and
Hong{-}Woo Chun and
Sung{-}Jae Jung and
Sung{-}Pil Choi and
Jun'ichi Tsujii and
Sophia Ananiadou},
title = {Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP
Shared Task 2013},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S10}},
pages = {S2},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-s10-s2},
doi = {10.1186/1471-2105-16-S10-S2},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PyysaloORRCJCTA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/PyysaloCCGHLSJ15,
author = {Sampo Pyysalo and
Jorge Campos and
Juan Miguel Cejuela and
Filip Ginter and
Kai Hakala and
Chen Li and
Pontus Stenetorp and
Lars Juhl Jensen},
title = {Sharing annotations better: RESTful Open Annotation},
booktitle = {Proceedings of the 53rd Annual Meeting of the Association for Computational
Linguistics and the 7th International Joint Conference on Natural
Language Processing of the Asian Federation of Natural Language Processing,
{ACL} 2015, July 26-31, 2015, Beijing, China, System Demonstrations},
pages = {91--96},
publisher = {The Association for Computer Linguistics},
year = {2015},
url = {https://doi.org/10.3115/v1/p15-4016},
doi = {10.3115/V1/P15-4016},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl/PyysaloCCGHLSJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/depling/LuotolahtiKLPG15,
author = {Juhani Luotolahti and
Jenna Kanerva and
Veronika Laippala and
Sampo Pyysalo and
Filip Ginter},
editor = {Eva Hajicov{\'{a}} and
Joakim Nivre},
title = {Towards Universal Web Parsebanks},
booktitle = {Proceedings of the Third International Conference on Dependency Linguistics,
DepLing 2015, August 24-26 2015, Uppsala University, Uppsala, Sweden},
pages = {211--220},
publisher = {Uppsala University, Department of Linguistics and Philology},
year = {2015},
url = {https://aclanthology.org/W15-2124/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/depling/LuotolahtiKLPG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/naacl/LuotolahtiKPG15,
author = {Juhani Luotolahti and
Jenna Kanerva and
Sampo Pyysalo and
Filip Ginter},
editor = {Rada Mihalcea and
Joyce Yue Chai and
Anoop Sarkar},
title = {{SETS:} Scalable and Efficient Tree Search in Dependency Graphs},
booktitle = {{NAACL} {HLT} 2015, The 2015 Conference of the North American Chapter
of the Association for Computational Linguistics: Human Language Technologies,
Denver, Colorado, USA, May 31 - June 5, 2015},
pages = {51--55},
publisher = {The Association for Computational Linguistics},
year = {2015},
url = {https://doi.org/10.3115/v1/n15-3011},
doi = {10.3115/V1/N15-3011},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/naacl/LuotolahtiKPG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/LaippalaKMPSG15,
author = {Veronika Laippala and
Jenna Kanerva and
Anna Missil{\"{a}} and
Sampo Pyysalo and
Tapio Salakoski and
Filip Ginter},
editor = {Be{\'{a}}ta Megyesi},
title = {Towards the Classification of the Finnish Internet Parsebank: Detecting
Translations and Informality},
booktitle = {Proceedings of the 20th Nordic Conference of Computational Linguistics,
{NODALIDA} 2015, Institute of the Lithuanian Language, Vilnius, Lithuania,
May 11-13, 2015},
series = {Link{\"{o}}ping Electronic Conference Proceedings},
volume = {109},
pages = {107--116},
publisher = {Link{\"{o}}ping University Electronic Press / Association for
Computational Linguistics},
year = {2015},
url = {http://www.ep.liu.se/ecp/article.asp?issue=109\&\#38;article=015\&\#38;volume=},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/LaippalaKMPSG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/PyysaloKMLG15,
author = {Sampo Pyysalo and
Jenna Kanerva and
Anna Missil{\"{a}} and
Veronika Laippala and
Filip Ginter},
editor = {Be{\'{a}}ta Megyesi},
title = {Universal Dependencies for Finnish},
booktitle = {Proceedings of the 20th Nordic Conference of Computational Linguistics,
{NODALIDA} 2015, Institute of the Lithuanian Language, Vilnius, Lithuania,
May 11-13, 2015},
series = {Link{\"{o}}ping Electronic Conference Proceedings},
volume = {109},
pages = {163--172},
publisher = {Link{\"{o}}ping University Electronic Press / Association for
Computational Linguistics},
year = {2015},
url = {http://www.ep.liu.se/ecp/article.asp?issue=109\&\#38;article=021\&\#38;volume=},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/PyysaloKMLG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PyysaloA14,
author = {Sampo Pyysalo and
Sophia Ananiadou},
title = {Anatomical entity mention recognition at literature scale},
journal = {Bioinform.},
volume = {30},
number = {6},
pages = {868--875},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt580},
doi = {10.1093/BIOINFORMATICS/BTT580},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PyysaloA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/StenetorpPAT14,
author = {Pontus Stenetorp and
Sampo Pyysalo and
Sophia Ananiadou and
Jun'ichi Tsujii},
title = {Generalising semantic category disambiguation with large lexical resources
for fun and profit},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {26},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-26},
doi = {10.1186/2041-1480-5-26},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/StenetorpPAT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MiwaORRKPA13,
author = {Makoto Miwa and
Tomoko Ohta and
Rafal Rak and
Andrew Rowley and
Douglas B. Kell and
Sampo Pyysalo and
Sophia Ananiadou},
title = {A method for integrating and ranking the evidence for biochemical
pathways by mining reactions from text},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {44--52},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt227},
doi = {10.1093/BIOINFORMATICS/BTT227},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MiwaORRKPA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MihailaOPA13,
author = {Claudiu Mihaila and
Tomoko Ohta and
Sampo Pyysalo and
Sophia Ananiadou},
title = {BioCause: Annotating and analysing causality in the biomedical domain},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {2},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-2},
doi = {10.1186/1471-2105-14-2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MihailaOPA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MiwaPOA13,
author = {Makoto Miwa and
Sampo Pyysalo and
Tomoko Ohta and
Sophia Ananiadou},
title = {Wide coverage biomedical event extraction using multiple partially
overlapping corpora},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {175},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-175},
doi = {10.1186/1471-2105-14-175},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MiwaPOA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/NedellecBKKOPZ13,
author = {Claire N{\'{e}}dellec and
Robert Bossy and
Jin{-}Dong Kim and
Jung{-}Jae Kim and
Tomoko Ohta and
Sampo Pyysalo and
Pierre Zweigenbaum},
editor = {Claire N{\'{e}}dellec and
Robert Bossy and
Jin{-}Dong Kim and
Jung{-}Jae Kim and
Tomoko Ohta and
Sampo Pyysalo and
Pierre Zweigenbaum},
title = {Overview of BioNLP Shared Task 2013},
booktitle = {Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria,
August 9, 2013},
pages = {1--7},
publisher = {Association for Computational Linguistics},
year = {2013},
url = {https://aclanthology.org/W13-2001/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/NedellecBKKOPZ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloOA13,
author = {Sampo Pyysalo and
Tomoko Ohta and
Sophia Ananiadou},
editor = {Claire N{\'{e}}dellec and
Robert Bossy and
Jin{-}Dong Kim and
Jung{-}Jae Kim and
Tomoko Ohta and
Sampo Pyysalo and
Pierre Zweigenbaum},
title = {Overview of the Cancer Genetics {(CG)} task of BioNLP Shared Task
2013},
booktitle = {Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria,
August 9, 2013},
pages = {58--66},
publisher = {Association for Computational Linguistics},
year = {2013},
url = {https://aclanthology.org/W13-2008/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloOA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/OhtaPRRCJCAT13,
author = {Tomoko Ohta and
Sampo Pyysalo and
Rafal Rak and
Andrew Rowley and
Hong{-}Woo Chun and
Sung{-}Jae Jung and
Sung{-}Pil Choi and
Sophia Ananiadou and
Jun'ichi Tsujii},
editor = {Claire N{\'{e}}dellec and
Robert Bossy and
Jin{-}Dong Kim and
Jung{-}Jae Kim and
Tomoko Ohta and
Sampo Pyysalo and
Pierre Zweigenbaum},
title = {Overview of the Pathway Curation {(PC)} task of BioNLP Shared Task
2013},
booktitle = {Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria,
August 9, 2013},
pages = {67--75},
publisher = {Association for Computational Linguistics},
year = {2013},
url = {https://aclanthology.org/W13-2009/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/OhtaPRRCJCAT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/bionlp/2013-s,
editor = {Claire N{\'{e}}dellec and
Robert Bossy and
Jin{-}Dong Kim and
Jung{-}Jae Kim and
Tomoko Ohta and
Sampo Pyysalo and
Pierre Zweigenbaum},
title = {Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria,
August 9, 2013},
publisher = {Association for Computational Linguistics},
year = {2013},
url = {https://aclanthology.org/W13-2000/},
isbn = {978-1-937284-55-8},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/2013-s.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PyysaloOMCTA12,
author = {Sampo Pyysalo and
Tomoko Ohta and
Makoto Miwa and
Han{-}Cheol Cho and
Junichi Tsujii and
Sophia Ananiadou},
title = {Event extraction across multiple levels of biological organization},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {575--581},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts407},
doi = {10.1093/BIOINFORMATICS/BTS407},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PyysaloOMCTA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PyysaloORSMWSTA12,
author = {Sampo Pyysalo and
Tomoko Ohta and
Rafal Rak and
Daniel E. Sullivan and
Chunhong Mao and
Chunxia Wang and
Bruno W. S. Sobral and
Jun'ichi Tsujii and
Sophia Ananiadou},
title = {Overview of the ID, {EPI} and {REL} tasks of BioNLP Shared Task 2011},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-11}},
pages = {S2},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S11-S2},
doi = {10.1186/1471-2105-13-S11-S2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PyysaloORSMWSTA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/StenetorpPOAT12,
author = {Pontus Stenetorp and
Sampo Pyysalo and
Tomoko Ohta and
Sophia Ananiadou and
Jun'ichi Tsujii},
editor = {Roser Morante and
Caroline Sporleder},
title = {Bridging the Gap Between Scope-based and Event-based Negation/Speculation
Annotations: {A} Bridge Not Too Far},
booktitle = {Proceedings of the Workshop on Extra-Propositional Aspects of Meaning
in Computational Linguistics, ExProM@ACL 2012, Jeju, Republic of Korea,
July 13, 2012},
pages = {47--56},
publisher = {Association for Computational Linguistics},
year = {2012},
url = {https://aclanthology.org/W12-3806/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl/StenetorpPOAT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/BjorneLPOGPAS12,
author = {Jari Bj{\"{o}}rne and
Sofie Van Landeghem and
Sampo Pyysalo and
Tomoko Ohta and
Filip Ginter and
Yves Van de Peer and
Sophia Ananiadou and
Tapio Salakoski},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Bonnie L. Webber and
Jun'ichi Tsujii and
John Pestian},
title = {PubMed-Scale Event Extraction for Post-Translational Modifications,
Epigenetics and Protein Structural Relations},
booktitle = {Proceedings of the 2012 Workshop on Biomedical Natural Language Processing,
BioNLP@HLT-NAACL Montr{\`{e}}al, Canada, June 8, 2012},
pages = {82--90},
publisher = {Association for Computational Linguistics},
year = {2012},
url = {https://aclanthology.org/W12-2410/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/BjorneLPOGPAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloSOKA12,
author = {Sampo Pyysalo and
Pontus Stenetorp and
Tomoko Ohta and
Jin{-}Dong Kim and
Sophia Ananiadou},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Bonnie L. Webber and
Jun'ichi Tsujii and
John Pestian},
title = {New Resources and Perspectives for Biomedical Event Extraction},
booktitle = {Proceedings of the 2012 Workshop on Biomedical Natural Language Processing,
BioNLP@HLT-NAACL Montr{\`{e}}al, Canada, June 8, 2012},
pages = {100--108},
publisher = {Association for Computational Linguistics},
year = {2012},
url = {https://aclanthology.org/W12-2412/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloSOKA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eacl/StenetorpPTOAT12,
author = {Pontus Stenetorp and
Sampo Pyysalo and
Goran Topic and
Tomoko Ohta and
Sophia Ananiadou and
Jun'ichi Tsujii},
editor = {Walter Daelemans and
Mirella Lapata and
Llu{\'{\i}}s M{\`{a}}rquez},
title = {brat: a Web-based Tool for NLP-Assisted Text Annotation},
booktitle = {{EACL} 2012, 13th Conference of the European Chapter of the Association
for Computational Linguistics, Avignon, France, April 23-27, 2012},
pages = {102--107},
publisher = {The Association for Computer Linguistics},
year = {2012},
url = {https://aclanthology.org/E12-2021/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/eacl/StenetorpPTOAT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/Rebholz-SchuhmannRPCH11,
author = {Dietrich Rebholz{-}Schuhmann and
Fabio Rinaldi and
Sampo Pyysalo and
Nigel Collier and
Udo Hahn},
title = {Towards mature use of semantic resources for biomedical analyses},
journal = {J. Biomed. Semant.},
volume = {2},
number = {{S-5}},
pages = {I1},
year = {2011},
url = {http://www.jbiomedsem.com/content/2/S5/I1},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/Rebholz-SchuhmannRPCH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/HoehndorfNPOOR11,
author = {Robert Hoehndorf and
Axel{-}Cyrille Ngonga Ngomo and
Sampo Pyysalo and
Tomoko Ohta and
Anika Oellrich and
Dietrich Rebholz{-}Schuhmann},
title = {Ontology design patterns to disambiguate relations between genes and
gene products in {GENIA}},
journal = {J. Biomed. Semant.},
volume = {2},
number = {{S-5}},
pages = {S1},
year = {2011},
url = {http://www.jbiomedsem.com/content/2/S5/S1},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/HoehndorfNPOOR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/OhtaPMT11,
author = {Tomoko Ohta and
Sampo Pyysalo and
Makoto Miwa and
Jun'ichi Tsujii},
title = {Event extraction for {DNA} methylation},
journal = {J. Biomed. Semant.},
volume = {2},
number = {{S-5}},
pages = {S2},
year = {2011},
url = {http://www.jbiomedsem.com/content/2/S5/S2},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/OhtaPMT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/PyysaloOT11,
author = {Sampo Pyysalo and
Tomoko Ohta and
Jun'ichi Tsujii},
title = {An analysis of gene/protein associations at PubMed scale},
journal = {J. Biomed. Semant.},
volume = {2},
number = {{S-5}},
pages = {S5},
year = {2011},
url = {http://www.jbiomedsem.com/content/2/S5/S5},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/PyysaloOT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KanoBGSBHCVRHKBLPPMANPORRSCKPOT11,
author = {Yoshinobu Kano and
Jari Bj{\"{o}}rne and
Filip Ginter and
Tapio Salakoski and
Ekaterina Buyko and
Udo Hahn and
K. Bretonnel Cohen and
Karin Verspoor and
Christophe Roeder and
Lawrence E. Hunter and
Halil Kilicoglu and
Sabine Bergler and
Sofie Van Landeghem and
Thomas Van Parys and
Yves Van de Peer and
Makoto Miwa and
Sophia Ananiadou and
Mariana L. Neves and
Alberto D. Pascual{-}Montano and
Arzucan {\"{O}}zg{\"{u}}r and
Dragomir R. Radev and
Sebastian Riedel and
Rune S{\ae}tre and
Hong{-}Woo Chun and
Jin{-}Dong Kim and
Sampo Pyysalo and
Tomoko Ohta and
Jun'ichi Tsujii},
title = {U-Compare bio-event meta-service: compatible BioNLP event extraction
services},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {481},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-481},
doi = {10.1186/1471-2105-12-481},
timestamp = {Thu, 17 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KanoBGSBHCVRHKBLPPMANPORRSCKPOT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ci/KimOPKT11,
author = {Jin{-}Dong Kim and
Tomoko Ohta and
Sampo Pyysalo and
Yoshinobu Kano and
Jun'ichi Tsujii},
title = {Extracting Bio-molecular Events from literature - the BioNLP'09 Shared
Task},
journal = {Comput. Intell.},
volume = {27},
number = {4},
pages = {513--540},
year = {2011},
url = {https://doi.org/10.1111/j.1467-8640.2011.00398.x},
doi = {10.1111/J.1467-8640.2011.00398.X},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ci/KimOPKT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/KimPOBNT11,
author = {Jin{-}Dong Kim and
Sampo Pyysalo and
Tomoko Ohta and
Robert Bossy and
Ngan L. T. Nguyen and
Jun'ichi Tsujii},
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {Overview of BioNLP Shared Task 2011},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
pages = {1--6},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-1801/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/KimPOBNT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/OhtaPT11a,
author = {Tomoko Ohta and
Sampo Pyysalo and
Jun'ichi Tsujii},
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {Overview of the Epigenetics and Post-translational Modifications {(EPI)}
task of BioNLP Shared Task 2011},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
pages = {16--25},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-1803/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/OhtaPT11a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloORSMWSTA11,
author = {Sampo Pyysalo and
Tomoko Ohta and
Rafal Rak and
Daniel E. Sullivan and
Chunhong Mao and
Chunxia Wang and
Bruno W. S. Sobral and
Jun'ichi Tsujii and
Sophia Ananiadou},
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {Overview of the Infectious Diseases {(ID)} task of BioNLP Shared Task
2011},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
pages = {26--35},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-1804/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloORSMWSTA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloOT11,
author = {Sampo Pyysalo and
Tomoko Ohta and
Jun'ichi Tsujii},
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {Overview of the Entity Relations {(REL)} supporting task of BioNLP
Shared Task 2011},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
pages = {83--88},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-1812/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloOT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/OhtaPT11,
author = {Tomoko Ohta and
Sampo Pyysalo and
Jun'ichi Tsujii},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {From Pathways to Biomolecular Events: Opportunities and Challenges},
booktitle = {Proceedings of the 2011 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011},
pages = {105--113},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-0214/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/OhtaPT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/StenetorpTPOKT11,
author = {Pontus Stenetorp and
Goran Topic and
Sampo Pyysalo and
Tomoko Ohta and
Jin{-}Dong Kim and
Jun'ichi Tsujii},
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {BioNLP Shared Task 2011: Supporting Resources},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
pages = {112--120},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-1816/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/StenetorpTPOKT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloOMT11,
author = {Sampo Pyysalo and
Tomoko Ohta and
Makoto Miwa and
Jun'ichi Tsujii},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Towards Exhaustive Event Extraction for Protein Modifications},
booktitle = {Proceedings of the 2011 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011},
pages = {114--123},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-0215/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloOMT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/StenetorpPT11,
author = {Pontus Stenetorp and
Sampo Pyysalo and
Jun'ichi Tsujii},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {SimSem: Fast Approximate String Matching in Relation to Semantic Category
Disambiguation},
booktitle = {Proceedings of the 2011 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011},
pages = {136--145},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-0218/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/StenetorpPT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/bionlp/2011-s,
editor = {Jun'ichi Tsujii and
Jin{-}Dong Kim and
Sampo Pyysalo},
title = {Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon,
USA, June 24, 2011},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/volumes/W11-18/},
isbn = {9781937284091},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/2011-s.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/smbm/2010,
editor = {Nigel Collier and
Udo Hahn and
Dietrich Rebholz{-}Schuhmann and
Fabio Rinaldi and
Sampo Pyysalo},
title = {Proceedings of the Fourth International Symposium for Semantic Mining
in Biomedicine, Cambridge, United Kingdom, October, 2010},
series = {{CEUR} Workshop Proceedings},
volume = {714},
publisher = {CEUR-WS.org},
year = {2011},
url = {https://ceur-ws.org/Vol-714},
urn = {urn:nbn:de:0074-714-1},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/smbm/2010.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BjorneGPTS10,
author = {Jari Bj{\"{o}}rne and
Filip Ginter and
Sampo Pyysalo and
Jun'ichi Tsujii and
Tapio Salakoski},
title = {Complex event extraction at PubMed scale},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {382--390},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq180},
doi = {10.1093/BIOINFORMATICS/BTQ180},
timestamp = {Tue, 01 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BjorneGPTS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GinterBP10,
author = {Filip Ginter and
Jari Bj{\"{o}}rne and
Sampo Pyysalo},
title = {Event extraction on PubMed scale},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-5}},
pages = {O2},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S5-O2},
doi = {10.1186/1471-2105-11-S5-O2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GinterBP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Pyysalo10,
author = {Sampo Pyysalo},
title = {Entities, relations, events: representing biomolecular semantics},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-5}},
pages = {O6},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S5-O6},
doi = {10.1186/1471-2105-11-S5-O6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Pyysalo10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OhtaMOMSPT10,
author = {Tomoko Ohta and
Takuya Matsuzaki and
Naoaki Okazaki and
Makoto Miwa and
Rune S{\ae}tre and
Sampo Pyysalo and
Jun'ichi Tsujii},
title = {Medie and Info-pubmed: 2010 update},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-5}},
pages = {P7},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S5-P7},
doi = {10.1186/1471-2105-11-S5-P7},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/OhtaMOMSPT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/WangKSPOT10,
author = {Yue Wang and
Jin{-}Dong Kim and
Rune S{\ae}tre and
Sampo Pyysalo and
Tomoko Ohta and
Jun'ichi Tsujii},
title = {Improving the Inter-Corpora Compatibility for protein Annotations},
journal = {J. Bioinform. Comput. Biol.},
volume = {8},
number = {5},
pages = {901--916},
year = {2010},
url = {https://doi.org/10.1142/S0219720010004999},
doi = {10.1142/S0219720010004999},
timestamp = {Tue, 02 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/WangKSPOT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/OhtaPKT10,
author = {Tomoko Ohta and
Sampo Pyysalo and
Jin{-}Dong Kim and
Jun'ichi Tsujii},
title = {A Re-Evaluation of Biomedical Named Entity-Term Relations},
journal = {J. Bioinform. Comput. Biol.},
volume = {8},
number = {5},
pages = {917--928},
year = {2010},
url = {https://doi.org/10.1142/S0219720010005014},
doi = {10.1142/S0219720010005014},
timestamp = {Mon, 26 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/OhtaPKT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/OhtaPMKT10,
author = {Tomoko Ohta and
Sampo Pyysalo and
Makoto Miwa and
Jin{-}Dong Kim and
Jun'ichi Tsujii},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Event Extraction for Post-Translational Modifications},
booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010},
pages = {19--27},
publisher = {Association for Computational Linguistics},
year = {2010},
url = {https://aclanthology.org/W10-1903/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/OhtaPMKT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/BjorneGPTS10,
author = {Jari Bj{\"{o}}rne and
Filip Ginter and
Sampo Pyysalo and
Jun'ichi Tsujii and
Tapio Salakoski},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Scaling up Biomedical Event Extraction to the Entire PubMed},
booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010},
pages = {28--36},
publisher = {Association for Computational Linguistics},
year = {2010},
url = {https://aclanthology.org/W10-1904/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/BjorneGPTS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/MiwaPHT10,
author = {Makoto Miwa and
Sampo Pyysalo and
Tadayoshi Hara and
Jun'ichi Tsujii},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {A Comparative Study of Syntactic Parsers for Event Extraction},
booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010},
pages = {37--45},
publisher = {Association for Computational Linguistics},
year = {2010},
url = {https://aclanthology.org/W10-1905/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/MiwaPHT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloOCSMSTA10,
author = {Sampo Pyysalo and
Tomoko Ohta and
Han{-}Cheol Cho and
Daniel E. Sullivan and
Chunhong Mao and
Bruno W. S. Sobral and
Jun'ichi Tsujii and
Sophia Ananiadou},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Towards Event Extraction from Full Texts on Infectious Diseases},
booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010},
pages = {132--140},
publisher = {Association for Computational Linguistics},
year = {2010},
url = {https://aclanthology.org/W10-1919/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloOCSMSTA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/LandeghemPOP10,
author = {Sofie Van Landeghem and
Sampo Pyysalo and
Tomoko Ohta and
Yves Van de Peer},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Integration of Static Relations to Enhance Event Extraction from Text},
booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010},
pages = {144--152},
publisher = {Association for Computational Linguistics},
year = {2010},
url = {https://aclanthology.org/W10-1921/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/LandeghemPOP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/MiwaPHT10,
author = {Makoto Miwa and
Sampo Pyysalo and
Tadayoshi Hara and
Jun'ichi Tsujii},
editor = {Chu{-}Ren Huang and
Dan Jurafsky},
title = {Evaluating Dependency Representations for Event Extraction},
booktitle = {{COLING} 2010, 23rd International Conference on Computational Linguistics,
Proceedings of the Conference, 23-27 August 2010, Beijing, China},
pages = {779--787},
publisher = {Tsinghua University Press},
year = {2010},
url = {https://aclanthology.org/C10-1088/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/coling/MiwaPHT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/smbm/HoehndorfNPOOR10,
author = {Robert Hoehndorf and
Axel{-}Cyrille Ngonga Ngomo and
Sampo Pyysalo and
Tomoko Ohta and
Anika Oellrich and
Dietrich Rebholz{-}Schuhmann},
editor = {Nigel Collier and
Udo Hahn and
Dietrich Rebholz{-}Schuhmann and
Fabio Rinaldi and
Sampo Pyysalo},
title = {Applying ontology design patterns to the implementation of relations
in {GENIA}},
booktitle = {Proceedings of the Fourth International Symposium for Semantic Mining
in Biomedicine, Cambridge, United Kingdom, October, 2010},
series = {{CEUR} Workshop Proceedings},
volume = {714},
publisher = {CEUR-WS.org},
year = {2010},
url = {https://ceur-ws.org/Vol-714/Paper04\_Hoehndorf.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:16 +0100},
biburl = {https://dblp.org/rec/conf/smbm/HoehndorfNPOOR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/smbm/OhtaPMT10,
author = {Tomoko Ohta and
Sampo Pyysalo and
Makoto Miwa and
Jun'ichi Tsujii},
editor = {Nigel Collier and
Udo Hahn and
Dietrich Rebholz{-}Schuhmann and
Fabio Rinaldi and
Sampo Pyysalo},
title = {Event extraction for {DNA} methylation},
booktitle = {Proceedings of the Fourth International Symposium for Semantic Mining
in Biomedicine, Cambridge, United Kingdom, October, 2010},
series = {{CEUR} Workshop Proceedings},
volume = {714},
publisher = {CEUR-WS.org},
year = {2010},
url = {https://ceur-ws.org/Vol-714/Paper06\_Ohta.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/smbm/OhtaPMT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/smbm/PyysaloOT10,
author = {Sampo Pyysalo and
Tomoko Ohta and
Jun'ichi Tsujii},
editor = {Nigel Collier and
Udo Hahn and
Dietrich Rebholz{-}Schuhmann and
Fabio Rinaldi and
Sampo Pyysalo},
title = {An Analysis of gene/protein associations at PubMed scale},
booktitle = {Proceedings of the Fourth International Symposium for Semantic Mining
in Biomedicine, Cambridge, United Kingdom, October, 2010},
series = {{CEUR} Workshop Proceedings},
volume = {714},
publisher = {CEUR-WS.org},
year = {2010},
url = {https://ceur-ws.org/Vol-714/Paper07\_Pyysalo.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/smbm/PyysaloOT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangKSPT09,
author = {Yue Wang and
Jin{-}Dong Kim and
Rune S{\ae}tre and
Sampo Pyysalo and
Jun'ichi Tsujii},
title = {Investigating heterogeneous protein annotations toward cross-corpora
utilization},
journal = {{BMC} Bioinform.},
volume = {10},
pages = {403},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-403},
doi = {10.1186/1471-2105-10-403},
timestamp = {Tue, 02 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangKSPT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmi/GinterSPS09,
author = {Filip Ginter and
Hanna Suominen and
Sampo Pyysalo and
Tapio Salakoski},
title = {Combining hidden Markov models and latent semantic analysis for topic
segmentation and labeling: Method and clinical application},
journal = {Int. J. Medical Informatics},
volume = {78},
number = {12},
pages = {1--6},
year = {2009},
url = {https://doi.org/10.1016/j.ijmedinf.2009.02.003},
doi = {10.1016/J.IJMEDINF.2009.02.003},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijmi/GinterSPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmi/LaippalaGPS09,
author = {Veronika Laippala and
Filip Ginter and
Sampo Pyysalo and
Tapio Salakoski},
title = {Towards automated processing of clinical Finnish: Sublanguage analysis
and a rule-based parser},
journal = {Int. J. Medical Informatics},
volume = {78},
number = {12},
pages = {7--12},
year = {2009},
url = {https://doi.org/10.1016/j.ijmedinf.2009.02.005},
doi = {10.1016/J.IJMEDINF.2009.02.005},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijmi/LaippalaGPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ml/PahikkalaPBJS09,
author = {Tapio Pahikkala and
Sampo Pyysalo and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
title = {Matrix representations, linear transformations, and kernels for disambiguation
in natural language},
journal = {Mach. Learn.},
volume = {74},
number = {2},
pages = {133--158},
year = {2009},
url = {https://doi.org/10.1007/s10994-008-5082-6},
doi = {10.1007/S10994-008-5082-6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ml/PahikkalaPBJS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/KimOPKT09,
author = {Jin{-}Dong Kim and
Tomoko Ohta and
Sampo Pyysalo and
Yoshinobu Kano and
Jun'ichi Tsujii},
title = {Overview of BioNLP'09 Shared Task on Event Extraction},
booktitle = {Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared
Task, BioNLP@HLT-NAACL 2009 - Shared Task, Boulder, Colorado, USA,
June 5, 2009},
pages = {1--9},
publisher = {Association for Computational Linguistics},
year = {2009},
url = {https://aclanthology.org/W09-1401/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/KimOPKT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloOKT09,
author = {Sampo Pyysalo and
Tomoko Ohta and
Jin{-}Dong Kim and
Jun'ichi Tsujii},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Static Relations: a Piece in the Biomedical Information Extraction
Puzzle},
booktitle = {Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, Boulder,
Colorado, USA, June 4-5, 2009},
pages = {1--9},
publisher = {Association for Computational Linguistics},
year = {2009},
url = {https://aclanthology.org/W09-1301/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloOKT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/OhtaKPWT09,
author = {Tomoko Ohta and
Jin{-}Dong Kim and
Sampo Pyysalo and
Yue Wang and
Jun'ichi Tsujii},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Incorporating GENETAG-style annotation to {GENIA} corpus},
booktitle = {Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, Boulder,
Colorado, USA, June 4-5, 2009},
pages = {106--107},
publisher = {Association for Computational Linguistics},
year = {2009},
url = {https://aclanthology.org/W09-1313/},
timestamp = {Tue, 02 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/OhtaKPWT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nodalida/BjorneGHPS09,
author = {Jari Bj{\"{o}}rne and
Filip Ginter and
Juho Heimonen and
Sampo Pyysalo and
Tapio Salakoski},
editor = {Kristiina Jokinen and
Eckhard Bick},
title = {Learning to Extract Biological Event and Relation Graphs},
booktitle = {Proceedings of the 17th Nordic Conference of Computational Linguistics,
{NODALIDA} 2009, Odense, Denmark, May 14-16, 2009},
pages = {18--25},
publisher = {Northern European Association for Language Technology {(NEALT)}},
year = {2009},
url = {https://aclanthology.org/W09-4605/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nodalida/BjorneGHPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AirolaPBPGS08,
author = {Antti Airola and
Sampo Pyysalo and
Jari Bj{\"{o}}rne and
Tapio Pahikkala and
Filip Ginter and
Tapio Salakoski},
title = {All-paths graph kernel for protein-protein interaction extraction
with evaluation of cross-corpus learning},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-11}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S11-S2},
doi = {10.1186/1471-2105-9-S11-S2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AirolaPBPGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PyysaloAHBGS08,
author = {Sampo Pyysalo and
Antti Airola and
Juho Heimonen and
Jari Bj{\"{o}}rne and
Filip Ginter and
Tapio Salakoski},
title = {Comparative analysis of five protein-protein interaction corpora},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-3}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S3-S6},
doi = {10.1186/1471-2105-9-S3-S6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PyysaloAHBGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/AirolaPBPGS08,
author = {Antti Airola and
Sampo Pyysalo and
Jari Bj{\"{o}}rne and
Tapio Pahikkala and
Filip Ginter and
Tapio Salakoski},
editor = {Dina Demner{-}Fushman and
Sophia Ananiadou and
Kevin Bretonnel Cohen and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {A Graph Kernel for Protein-Protein Interaction Extraction},
booktitle = {Proceedings of the Workshop on Current Trends in Biomedical Natural
Language Processing, BioNLP 2008, Columbus, Ohio, USA, June 19, 2008},
pages = {1--9},
publisher = {Association for Computational Linguistics},
year = {2008},
url = {https://aclanthology.org/W08-0601/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/AirolaPBPGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PyysaloGHBBJS07,
author = {Sampo Pyysalo and
Filip Ginter and
Juho Heimonen and
Jari Bj{\"{o}}rne and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
title = {BioInfer: a corpus for information extraction in the biomedical domain},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-50},
doi = {10.1186/1471-2105-8-50},
timestamp = {Mon, 26 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PyysaloGHBBJS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloGLHHS07,
author = {Sampo Pyysalo and
Filip Ginter and
Veronika Laippala and
Katri Haverinen and
Juho Heimonen and
Tapio Salakoski},
editor = {K. Bretonnel Cohen and
Dina Demner{-}Fushman and
Carol Friedman and
Lynette Hirschman and
John Pestian},
title = {On the unification of syntactic annotations under the Stanford dependency
scheme: {A} case study on BioInfer and {GENIA}},
booktitle = {Biological, translational, and clinical language processing, BioNLP@ACL
2007, Prague, Czech Republic, June 29, 2007},
pages = {25--32},
publisher = {Association for Computational Linguistics},
year = {2007},
url = {https://aclanthology.org/W07-1004/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloGLHHS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PyysaloSAN06,
author = {Sampo Pyysalo and
Tapio Salakoski and
Sophie Aubin and
Adeline Nazarenko},
title = {Lexical adaptation of link grammar to the biomedical sublanguage:
a comparative evaluation of three approaches},
journal = {{BMC} Bioinform.},
volume = {7},
number = {{S-3}},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-S3-S2},
doi = {10.1186/1471-2105-7-S3-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PyysaloSAN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmi/PyysaloGPBJS06,
author = {Sampo Pyysalo and
Filip Ginter and
Tapio Pahikkala and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
title = {Evaluation of two dependency parsers on biomedical corpus targeted
at protein-protein interactions},
journal = {Int. J. Medical Informatics},
volume = {75},
number = {6},
pages = {430--442},
year = {2006},
url = {https://doi.org/10.1016/j.ijmedinf.2005.06.009},
doi = {10.1016/J.IJMEDINF.2005.06.009},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijmi/PyysaloGPBJS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fintal/GinterPBS06,
author = {Filip Ginter and
Sampo Pyysalo and
Jorma Boberg and
Tapio Salakoski},
editor = {Tapio Salakoski and
Filip Ginter and
Sampo Pyysalo and
Tapio Pahikkala},
title = {Regular Approximation of Link Grammar},
booktitle = {Advances in Natural Language Processing, 5th International Conference
on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4139},
pages = {564--575},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11816508\_56},
doi = {10.1007/11816508\_56},
timestamp = {Sat, 30 Sep 2023 09:41:16 +0200},
biburl = {https://dblp.org/rec/conf/fintal/GinterPBS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/smbm/PyysaloSAN06,
author = {Sampo Pyysalo and
Tapio Salakoski and
Sophie Aubin and
Adeline Nazarenko},
editor = {Sophia Ananiadou and
Juliane Fluck},
title = {Lexical Adaptation of Link Grammar to the Biomedical Sublanguage:
a Comparative Evaluation of Three Approaches},
booktitle = {Proceedings of the Second International Symposium on Semantic Mining
in Biomedicine, Jena, Germany, April 9-12, 2006},
series = {{CEUR} Workshop Proceedings},
volume = {177},
publisher = {CEUR-WS.org},
year = {2006},
url = {https://ceur-ws.org/Vol-177/paper\_pyysalo\_title\_abstract.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:16 +0100},
biburl = {https://dblp.org/rec/conf/smbm/PyysaloSAN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/fintal/2006,
editor = {Tapio Salakoski and
Filip Ginter and
Sampo Pyysalo and
Tapio Pahikkala},
title = {Advances in Natural Language Processing, 5th International Conference
on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4139},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11816508},
doi = {10.1007/11816508},
isbn = {3-540-37334-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fintal/2006.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-cs-0606119,
author = {Sampo Pyysalo and
Tapio Salakoski and
Sophie Aubin and
Adeline Nazarenko},
title = {Lexical Adaptation of Link Grammar to the Biomedical Sublanguage:
a Comparative Evaluation of Three Approaches},
journal = {CoRR},
volume = {abs/cs/0606119},
year = {2006},
url = {http://arxiv.org/abs/cs/0606119},
eprinttype = {arXiv},
eprint = {cs/0606119},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-cs-0606119.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/flairs/PahikkalaPGBJS05,
author = {Tapio Pahikkala and
Sampo Pyysalo and
Filip Ginter and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
editor = {Ingrid Russell and
Zdravko Markov},
title = {Kernels Incorporating Word Positional Information in Natural Language
Disambiguation Tasks},
booktitle = {Proceedings of the Eighteenth International Florida Artificial Intelligence
Research Society Conference, Clearwater Beach, Florida, {USA}},
pages = {442--448},
publisher = {{AAAI} Press},
year = {2005},
url = {http://www.aaai.org/Library/FLAIRS/2005/flairs05-073.php},
timestamp = {Wed, 26 Oct 2022 08:35:28 +0200},
biburl = {https://dblp.org/rec/conf/flairs/PahikkalaPGBJS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ida/TsivtsivadzePPBMS05,
author = {Evgeni Tsivtsivadze and
Tapio Pahikkala and
Sampo Pyysalo and
Jorma Boberg and
Aleksandr Myll{\"{a}}ri and
Tapio Salakoski},
editor = {A. Fazel Famili and
Joost N. Kok and
Jos{\'{e}} Mar{\'{\i}}a Pe{\~{n}}a S{\'{a}}nchez and
Arno Siebes and
A. J. Feelders},
title = {Regularized Least-Squares for Parse Ranking},
booktitle = {Advances in Intelligent Data Analysis VI, 6th International Symposium
on Intelligent Data Analysis, {IDA} 2005, Madrid, Spain, September
8-10, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3646},
pages = {464--474},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11552253\_42},
doi = {10.1007/11552253\_42},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ida/TsivtsivadzePPBMS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloGPBJSK04,
author = {Sampo Pyysalo and
Filip Ginter and
Tapio Pahikkala and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski and
Jeppe Koivula},
editor = {Nigel Collier and
Patrick Ruch and
Adeline Nazarenko},
title = {Analysis of Link Grammar on Biomedical Dependency Corpus Targeted
at Protein-Protein Interactions},
booktitle = {Proceedings of the International Joint Workshop on Natural Language
Processing in Biomedicine and its Applications, NLPBA/BioNLP 2004,
Geneva, Switzerland, August 28-29, 2004},
year = {2004},
url = {https://aclanthology.org/W04-1203/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloGPBJSK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/rsctc/GinterPPBJS04,
author = {Filip Ginter and
Tapio Pahikkala and
Sampo Pyysalo and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
editor = {Shusaku Tsumoto and
Roman Slowinski and
Henryk Jan Komorowski and
Jerzy W. Grzymala{-}Busse},
title = {Extracting Protein-Protein Interaction Sentences by Applying Rough
Set Data Analysis},
booktitle = {Rough Sets and Current Trends in Computing, 4th International Conference,
{RSCTC} 2004, Uppsala, Sweden, June 1-5, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3066},
pages = {780--785},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-25929-9\_99},
doi = {10.1007/978-3-540-25929-9\_99},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/rsctc/GinterPPBJS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/tal/GinterPBJS04,
author = {Filip Ginter and
Sampo Pyysalo and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
editor = {Jos{\'{e}} Luis Vicedo Gonz{\'{a}}lez and
Patricio Mart{\'{\i}}nez{-}Barco and
Rafael Mu{\~{n}}oz and
Maximiliano Saiz{-}Noeda},
title = {Ontology-Based Feature Transformations: {A} Data-Driven Approach},
booktitle = {Advances in Natural Language Processing, 4th International Conference,
EsTAL 2004, Alicante, Spain, October 20-22, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3230},
pages = {280--291},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30228-5\_25},
doi = {10.1007/978-3-540-30228-5\_25},
timestamp = {Tue, 14 May 2019 10:00:49 +0200},
biburl = {https://dblp.org/rec/conf/tal/GinterPBJS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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