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ORCIDSampo Pyysalo
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- affiliation: University of Cambridge, Department of Theoretical and Applied Linguistics, UK
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2020 – today
- 2024
[j42]Katerina C. Nastou
, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo, Lars Juhl Jensen:
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. Database J. Biol. Databases Curation 2024 (2024)- [c73]Ona de Gibert, Graeme Nail, Nikolay Arefyev, Marta Bañón, Jelmer van der Linde, Shaoxiong Ji, Jaume Zaragoza-Bernabeu, Mikko Aulamo, Gema Ramírez-Sánchez, Andrey Kutuzov, Sampo Pyysalo, Stephan Oepen, Jörg Tiedemann:
A New Massive Multilingual Dataset for High-Performance Language Technologies. LREC/COLING 2024: 1116-1128 - [c72]Anni Eskelinen, Amanda Myntti, Erik Henriksson, Sampo Pyysalo, Veronika Laippala:
Building Question-Answer Data Using Web Register Identification. LREC/COLING 2024: 2595-2611 - [i20]Ona de Gibert, Graeme Nail, Nikolay Arefyev, Marta Bañón, Jelmer van der Linde, Shaoxiong Ji, Jaume Zaragoza-Bernabeu, Mikko Aulamo, Gema Ramírez-Sánchez, Andrey Kutuzov, Sampo Pyysalo, Stephan Oepen, Jörg Tiedemann:
A New Massive Multilingual Dataset for High-Performance Language Technologies. CoRR abs/2403.14009 (2024) - [i19]Taishi Nakamura, Mayank Mishra, Simone Tedeschi, Yekun Chai, Jason T. Stillerman, Felix Friedrich, Prateek Yadav, Tanmay Laud, Minh Chien Vu, Terry Yue Zhuo, Diganta Misra, Ben Bogin, Xuan-Son Vu, Marzena Karpinska, Arnav Varma Dantuluri, Wojciech Kusa, Tommaso Furlanello, Rio Yokota, Niklas Muennighoff, Suhas Pai, Tosin P. Adewumi, Veronika Laippala, Xiaozhe Yao, Adalberto Junior, Alpay Ariyak, Aleksandr Drozd, Jordan Clive, Kshitij Gupta, Liangyu Chen, Qi Sun, Ken Tsui, Noah Persaud, Nour Moustafa-Fahmy, Tianlong Chen, Mohit Bansal, Nicolo Monti, Tai Dang, Ziyang Luo, Tien-Tung Bui, Roberto Navigli, Virendra Mehta, Matthew Blumberg, Victor May, Huu Nguyen, Sampo Pyysalo:
Aurora-M: The First Open Source Multilingual Language Model Red-teamed according to the U.S. Executive Order. CoRR abs/2404.00399 (2024) - [i18]Risto Luukkonen, Jonathan Burdge, Elaine Zosa, Aarne Talman, Ville Komulainen, Väinö Hatanpää, Peter Sarlin, Sampo Pyysalo:
Poro 34B and the Blessing of Multilinguality. CoRR abs/2404.01856 (2024) - [i17]Wazir Ali, Sampo Pyysalo:
A Survey of Large Language Models for European Languages. CoRR abs/2408.15040 (2024) - 2023
- [j41]Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger:
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. Database J. Biol. Databases Curation 2023 (2023) - [j40]Veronika Laippala, Samuel Rönnqvist, Miika Oinonen, Aki-Juhani Kyröläinen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo:
Register identification from the unrestricted open Web using the Corpus of Online Registers of English. Lang. Resour. Evaluation 57(3): 1045-1079 (2023) - [j39]Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina C. Nastou, Farrokh Mehryary, Radja Hachilif, Annika L. Gable, Tao Fang, Nadezhda T. Doncheva, Sampo Pyysalo, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51(D1): 638-646 (2023) - [c71]Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank:
Silver Syntax Pre-training for Cross-Domain Relation Extraction. ACL (Findings) 2023: 6984-6993 - [c70]Risto Luukkonen, Ville Komulainen, Jouni Luoma, Anni Eskelinen, Jenna Kanerva, Hanna-Mari Kupari, Filip Ginter, Veronika Laippala, Niklas Muennighoff, Aleksandra Piktus, Thomas Wang, Nouamane Tazi, Teven Le Scao, Thomas Wolf, Osma Suominen, Samuli Sairanen, Mikko Merioksa, Jyrki Heinonen, Aija Vahtola, Samuel Antao, Sampo Pyysalo:
FinGPT: Large Generative Models for a Small Language. EMNLP 2023: 2710-2726 - [c69]Niklas Muennighoff, Alexander M. Rush, Boaz Barak, Teven Le Scao, Nouamane Tazi, Aleksandra Piktus, Sampo Pyysalo, Thomas Wolf, Colin A. Raffel:
Scaling Data-Constrained Language Models. NeurIPS 2023 - [c68]Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank:
Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction. NoDaLiDa 2023: 80-85 - [c67]Anni Eskelinen, Laura Silvala, Filip Ginter, Sampo Pyysalo, Veronika Laippala:
Toxicity Detection in Finnish Using Machine Translation. NoDaLiDa 2023: 685-697 - [i16]Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank:
Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction. CoRR abs/2305.10985 (2023) - [i15]Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank:
Silver Syntax Pre-training for Cross-Domain Relation Extraction. CoRR abs/2305.11016 (2023) - [i14]Niklas Muennighoff, Alexander M. Rush, Boaz Barak, Teven Le Scao, Aleksandra Piktus, Nouamane Tazi, Sampo Pyysalo, Thomas Wolf, Colin Raffel:
Scaling Data-Constrained Language Models. CoRR abs/2305.16264 (2023) - [i13]Risto Luukkonen, Ville Komulainen, Jouni Luoma, Anni Eskelinen, Jenna Kanerva, Hanna-Mari Kupari, Filip Ginter, Veronika Laippala, Niklas Muennighoff, Aleksandra Piktus, Thomas Wang, Nouamane Tazi, Teven Le Scao, Thomas Wolf, Osma Suominen, Samuli Sairanen, Mikko Merioksa, Jyrki Heinonen, Aija Vahtola, Samuel Antao, Sampo Pyysalo:
FinGPT: Large Generative Models for a Small Language. CoRR abs/2311.05640 (2023) - 2022
- [c66]Veronika Laippala, Anna Salmela, Samuel Rönnqvist, Alham Fikri Aji, Li-Hsin Chang, Asma Dhifallah, Larissa Goulart, Henna Kortelainen, Marc Pàmies, Deise Prina Dutra, Valtteri Skantsi, Lintang Sutawika, Sampo Pyysalo:
Towards better structured and less noisy Web data: Oscar with Register annotations. W-NUT@COLING 2022: 215-221 - 2021
- [j38]Damian Szklarczyk, Annika L. Gable, Katerina C. Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T. Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49(Database-Issue): D605-D612 (2021) - [c65]Liina Repo, Valtteri Skantsi, Samuel Rönnqvist, Saara Hellström, Miika Oinonen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo, Veronika Laippala:
Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual Classification of Registers. EACL (Student Research Workshop) 2021: 183-191 - [c64]Li-Hsin Chang, Iiro Rastas, Jenna Kanerva, Valtteri Skantsi, Sampo Pyysalo, Filip Ginter:
Deep learning for sentence clustering in essay grading support. EDM 2021 - [c63]Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter:
WikiBERT Models: Deep Transfer Learning for Many Languages. NoDaLiDa 2021: 1-10 - [c62]Jouni Luoma, Li-Hsin Chang, Filip Ginter, Sampo Pyysalo:
Fine-grained Named Entity Annotation for Finnish. NoDaLiDa 2021: 135-144 - [i12]Liina Repo, Valtteri Skantsi, Samuel Rönnqvist, Saara Hellström, Miika Oinonen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo, Veronika Laippala:
Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual Classification of Registers. CoRR abs/2102.07396 (2021) - [i11]Li-Hsin Chang, Iiro Rastas, Sampo Pyysalo, Filip Ginter:
Deep learning for sentence clustering in essay grading support. CoRR abs/2104.11556 (2021) - [i10]Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter:
Quantitative Evaluation of Alternative Translations in a Corpus of Highly Dissimilar Finnish Paraphrases. CoRR abs/2105.02477 (2021) - [i9]Samuel Rönnqvist, Amanda Myntti, Aki-Juhani Kyröläinen, Sampo Pyysalo, Veronika Laippala, Filip Ginter:
Explaining Classes through Word Attribution. CoRR abs/2108.13653 (2021) - 2020
- [j37]Jenna Kanerva, Filip Ginter, Sampo Pyysalo:
Dependency parsing of biomedical text with BERT. BMC Bioinform. 21-S(23): 580 (2020) - [c61]Veronika Laippala, Samuel Rönnqvist, Saara Hellström, Juhani Luotolahti, Liina Repo, Anna Salmela, Valtteri Skantsi, Sampo Pyysalo:
From Web Crawl to Clean Register-Annotated Corpora. WAC@LREC 2020: 14-22 - [c60]Jouni Luoma, Sampo Pyysalo:
Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. COLING 2020: 904-914 - [c59]Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo:
The birth of Romanian BERT. EMNLP (Findings) 2020: 4324-4328 - [c58]Jenna Kanerva, Filip Ginter, Sampo Pyysalo:
Turku Enhanced Parser Pipeline: From Raw Text to Enhanced Graphs in the IWPT 2020 Shared Task. IWPT 2020 2020: 162-173 - [c57]Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Jan Hajic, Christopher D. Manning, Sampo Pyysalo, Sebastian Schuster, Francis M. Tyers, Daniel Zeman:
Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection. LREC 2020: 4034-4043 - [c56]Jouni Luoma, Miika Oinonen, Maria Pyykönen, Veronika Laippala, Sampo Pyysalo:
A Broad-coverage Corpus for Finnish Named Entity Recognition. LREC 2020: 4615-4624 - [i8]Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Jan Hajic, Christopher D. Manning, Sampo Pyysalo, Sebastian Schuster, Francis M. Tyers, Daniel Zeman:
Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection. CoRR abs/2004.10643 (2020) - [i7]Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter:
WikiBERT models: deep transfer learning for many languages. CoRR abs/2006.01538 (2020) - [i6]Jouni Luoma, Sampo Pyysalo:
Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. CoRR abs/2006.01563 (2020) - [i5]Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo:
The birth of Romanian BERT. CoRR abs/2009.08712 (2020) - [i4]Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter:
Towards Fully Bilingual Deep Language Modeling. CoRR abs/2010.11639 (2020)
2010 – 2019
- 2019
- [j36]Sampo Pyysalo, Simon Baker, Imran Ali, Stefan Haselwimmer, Tejas Shah, Andrew Young, Yufan Guo, Johan Högberg, Ulla Stenius, Masashi Narita, Anna Korhonen:
LION LBD: a literature-based discovery system for cancer biology. Bioinform. 35(9): 1553-1561 (2019) - [j35]Billy Chiu, Olga Majewska, Sampo Pyysalo, Laura Wey, Ulla Stenius, Anna Korhonen, Martha Palmer:
A neural classification method for supporting the creation of BioVerbNet. J. Biomed. Semant. 10(1): 2:1-2:12 (2019) - [c55]Kai Hakala, Sampo Pyysalo:
Biomedical Named Entity Recognition with Multilingual BERT. BioNLP-OST@EMNLP-IJNCLP 2019: 56-61 - [c54]William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter:
CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference. BioNLP-OST@EMNLP-IJNCLP 2019: 174-184 - [c53]Thang Minh Ngo, Jenna Kanerva, Filip Ginter, Sampo Pyysalo:
Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task. BioNLP-OST@EMNLP-IJNCLP 2019: 206-215 - [c52]Veronika Laippala, Roosa Kyllönen, Jesse Egbert, Douglas Biber, Sampo Pyysalo:
Toward Multilingual Identification of Online Registers. NODALIDA 2019: 292-297 - [i3]Antti Virtanen, Jenna Kanerva, Rami Ilo, Jouni Luoma, Juhani Luotolahti, Tapio Salakoski, Filip Ginter, Sampo Pyysalo:
Multilingual is not enough: BERT for Finnish. CoRR abs/1912.07076 (2019) - 2018
- [j34]Billy Chiu, Sampo Pyysalo, Ivan Vulic, Anna Korhonen:
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. BMC Bioinform. 19(1): 33:1-33:13 (2018) - [j33]Gamal K. O. Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen:
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. BMC Bioinform. 19(1): 176:1-176:11 (2018) - 2017
- [j32]Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo, Johan Högberg, Ulla Stenius, Anna Korhonen:
Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinform. 33(24): 3973-3981 (2017) - [j31]Gamal K. O. Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen:
A neural network multi-task learning approach to biomedical named entity recognition. BMC Bioinform. 18(1): 368:1-368:14 (2017) - [c51]Daniel Zeman, Martin Popel, Milan Straka, Jan Hajic, Joakim Nivre, Filip Ginter, Juhani Luotolahti, Sampo Pyysalo, Slav Petrov, Martin Potthast, Francis M. Tyers, Elena Badmaeva, Memduh Gokirmak, Anna Nedoluzhko, Silvie Cinková, Jan Hajic Jr., Jaroslava Hlavácová, Václava Kettnerová, Zdenka Uresová, Jenna Kanerva, Stina Ojala, Anna Missilä, Christopher D. Manning, Sebastian Schuster, Siva Reddy, Dima Taji, Nizar Habash, Herman Leung, Marie-Catherine de Marneffe, Manuela Sanguinetti, Maria Simi, Hiroshi Kanayama, Valeria de Paiva, Kira Droganova, Héctor Martínez Alonso, Çagri Çöltekin, Umut Sulubacak, Hans Uszkoreit, Vivien Macketanz, Aljoscha Burchardt, Kim Harris, Katrin Marheinecke, Georg Rehm, Tolga Kayadelen, Mohammed Attia, Ali El-Kahky, Zhuoran Yu, Emily Pitler, Saran Lertpradit, Michael Mandl, Jesse Kirchner, Hector Fernandez Alcalde, Jana Strnadová, Esha Banerjee, Ruli Manurung, Antonio Stella, Atsuko Shimada, Sookyoung Kwak, Gustavo Mendonça, Tatiana Lando, Rattima Nitisaroj, Josie Li:
CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies. CoNLL Shared Task (2) 2017: 1-19 - [c50]Jenna Kanerva, Sampo Pyysalo, Filip Ginter:
Fully Delexicalized Contexts for Syntax-Based Word Embeddings. DepLing 2017: 83-91 - 2016
- [j30]Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo:
Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinform. 32(2): 276-282 (2016) - [c49]Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter:
Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016. BioNLP (Shared Task) 2016: 73-81 - [c48]Billy Chiu, Gamal K. O. Crichton, Anna Korhonen, Sampo Pyysalo:
How to Train good Word Embeddings for Biomedical NLP. BioNLP@ACL 2016: 166-174 - [c47]Simon Baker, Anna Korhonen, Sampo Pyysalo:
Cancer Hallmark Text Classification Using Convolutional Neural Networks. BioTxtM@COLING 2016 2016: 1-9 - [c46]Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo:
Attending to Characters in Neural Sequence Labeling Models. COLING 2016: 309-318 - [c45]Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Yoav Goldberg, Jan Hajic, Christopher D. Manning, Ryan T. McDonald, Slav Petrov, Sampo Pyysalo, Natalia Silveira, Reut Tsarfaty, Daniel Zeman:
Universal Dependencies v1: A Multilingual Treebank Collection. LREC 2016 - [c44]Yuka Tateisi, Tomoko Ohta, Sampo Pyysalo, Yusuke Miyao, Akiko Aizawa:
Typed Entity and Relation Annotation on Computer Science Papers. LREC 2016 - [c43]Billy Chiu, Anna Korhonen, Sampo Pyysalo:
Intrinsic Evaluation of Word Vectors Fails to Predict Extrinsic Performance. RepEval@ACL 2016: 1-6 - [i2]Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo:
Attending to Characters in Neural Sequence Labeling Models. CoRR abs/1611.04361 (2016) - 2015
- [j29]Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou:
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. BMC Bioinform. 16(S10): S2 (2015) - [c42]Sampo Pyysalo, Jorge Campos, Juan Miguel Cejuela, Filip Ginter, Kai Hakala, Chen Li, Pontus Stenetorp, Lars Juhl Jensen:
Sharing annotations better: RESTful Open Annotation. ACL (System Demonstrations) 2015: 91-96 - [c41]Juhani Luotolahti, Jenna Kanerva, Veronika Laippala, Sampo Pyysalo, Filip Ginter:
Towards Universal Web Parsebanks. DepLing 2015: 211-220 - [c40]Juhani Luotolahti, Jenna Kanerva, Sampo Pyysalo, Filip Ginter:
SETS: Scalable and Efficient Tree Search in Dependency Graphs. HLT-NAACL 2015: 51-55 - [c39]Veronika Laippala, Jenna Kanerva, Anna Missilä, Sampo Pyysalo, Tapio Salakoski, Filip Ginter:
Towards the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality. NODALIDA 2015: 107-116 - [c38]Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter:
Universal Dependencies for Finnish. NODALIDA 2015: 163-172 - 2014
- [j28]Sampo Pyysalo, Sophia Ananiadou:
Anatomical entity mention recognition at literature scale. Bioinform. 30(6): 868-875 (2014) - [j27]Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou, Jun'ichi Tsujii:
Generalising semantic category disambiguation with large lexical resources for fun and profit. J. Biomed. Semant. 5: 26 (2014) - 2013
- [j26]Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou:
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinform. 29(13): 44-52 (2013) - [j25]Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou:
BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinform. 14: 2 (2013) - [j24]Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou:
Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinform. 14: 175 (2013) - [c37]Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum:
Overview of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) 2013: 1-7 - [c36]Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou:
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) 2013: 58-66 - [c35]Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou, Jun'ichi Tsujii:
Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) 2013: 67-75 - [e4]Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum:
Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, August 9, 2013. Association for Computational Linguistics 2013, ISBN 978-1-937284-55-8 [contents] - 2012
- [j23]Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou:
Event extraction across multiple levels of biological organization. Bioinform. 28(18): 575-581 (2012) - [j22]Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou:
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinform. 13(S-11): S2 (2012) - [c34]Pontus Stenetorp, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii:
Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far. ExProM@ACL 2012: 47-56 - [c33]Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski:
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL 2012: 82-90 - [c32]Sampo Pyysalo, Pontus Stenetorp, Tomoko Ohta, Jin-Dong Kim, Sophia Ananiadou:
New Resources and Perspectives for Biomedical Event Extraction. BioNLP@HLT-NAACL 2012: 100-108 - [c31]Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii:
brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL 2012: 102-107 - 2011
- [j21]Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo, Nigel Collier, Udo Hahn:
Towards mature use of semantic resources for biomedical analyses. J. Biomed. Semant. 2(S-5): I1 (2011) - [j20]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. 2(S-5): S1 (2011) - [j19]Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii:
Event extraction for DNA methylation. J. Biomed. Semant. 2(S-5): S2 (2011) - [j18]Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
An analysis of gene/protein associations at PubMed scale. J. Biomed. Semant. 2(S-5): S5 (2011) - [j17]Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12: 481 (2011) - [j16]Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii:
Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. Comput. Intell. 27(4): 513-540 (2011) - [c30]Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan L. T. Nguyen, Jun'ichi Tsujii:
Overview of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) 2011: 1-6 - [c29]Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii:
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) 2011: 16-25 - [c28]Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou:
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) 2011: 26-35 - [c27]Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) 2011: 83-88 - [c26]Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii:
From Pathways to Biomolecular Events: Opportunities and Challenges. BioNLP@ACL 2011: 105-113 - [c25]Pontus Stenetorp, Goran Topic, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii:
BioNLP Shared Task 2011: Supporting Resources. BioNLP@ACL (Shared Task) 2011: 112-120 - [c24]Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Jun'ichi Tsujii:
Towards Exhaustive Event Extraction for Protein Modifications. BioNLP@ACL 2011: 114-123 - [c23]Pontus Stenetorp, Sampo Pyysalo, Jun'ichi Tsujii:
SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation. BioNLP@ACL 2011: 136-145 - [e3]Jun'ichi Tsujii, Jin-Dong Kim, Sampo Pyysalo:
Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon, USA, June 24, 2011. Association for Computational Linguistics 2011, ISBN 9781937284091 [contents] - [e2]Nigel Collier, Udo Hahn, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo:
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, Cambridge, United Kingdom, October, 2010. CEUR Workshop Proceedings 714, CEUR-WS.org 2011 [contents] - 2010
- [j15]Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski:
Complex event extraction at PubMed scale. Bioinform. 26(12): 382-390 (2010) - [j14]Filip Ginter, Jari Björne, Sampo Pyysalo:
Event extraction on PubMed scale. BMC Bioinform. 11(S-5): O2 (2010) - [j13]Sampo Pyysalo:
Entities, relations, events: representing biomolecular semantics. BMC Bioinform. 11(S-5): O6 (2010) - [j12]Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii:
Medie and Info-pubmed: 2010 update. BMC Bioinform. 11(S-5): P7 (2010) - [j11]Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
Improving the Inter-Corpora Compatibility for protein Annotations. J. Bioinform. Comput. Biol. 8(5): 901-916 (2010) - [j10]Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii:
A Re-Evaluation of Biomedical Named Entity-Term Relations. J. Bioinform. Comput. Biol. 8(5): 917-928 (2010) - [c22]Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jin-Dong Kim, Jun'ichi Tsujii:
Event Extraction for Post-Translational Modifications. BioNLP@ACL 2010: 19-27 - [c21]Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski:
Scaling up Biomedical Event Extraction to the Entire PubMed. BioNLP@ACL 2010: 28-36 - [c20]Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii:
A Comparative Study of Syntactic Parsers for Event Extraction. BioNLP@ACL 2010: 37-45 - [c19]Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Daniel E. Sullivan, Chunhong Mao, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou:
Towards Event Extraction from Full Texts on Infectious Diseases. BioNLP@ACL 2010: 132-140 - [c18]Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer:
Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL 2010: 144-152 - [c17]Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii:
Evaluating Dependency Representations for Event Extraction. COLING 2010: 779-787 - [c16]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine 2010 - [c15]Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii:
Event extraction for DNA methylation. Semantic Mining in Biomedicine 2010 - [c14]Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
An Analysis of gene/protein associations at PubMed scale. Semantic Mining in Biomedicine 2010
2000 – 2009
- 2009
- [j9]Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii:
Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinform. 10: 403 (2009) - [j8]Filip Ginter, Hanna Suominen, Sampo Pyysalo, Tapio Salakoski:
Combining hidden Markov models and latent semantic analysis for topic segmentation and labeling: Method and clinical application. Int. J. Medical Informatics 78(12): 1-6 (2009) - [j7]Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski:
Towards automated processing of clinical Finnish: Sublanguage analysis and a rule-based parser. Int. J. Medical Informatics 78(12): 7-12 (2009) - [j6]Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
Matrix representations, linear transformations, and kernels for disambiguation in natural language. Mach. Learn. 74(2): 133-158 (2009) - [c13]Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii:
Overview of BioNLP'09 Shared Task on Event Extraction. BioNLP@HLT-NAACL (Shared Task) 2009: 1-9 - [c12]Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii:
Static Relations: a Piece in the Biomedical Information Extraction Puzzle. BioNLP@HLT-NAACL 2009: 1-9 - [c11]Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang, Jun'ichi Tsujii:
Incorporating GENETAG-style annotation to GENIA corpus. BioNLP@HLT-NAACL 2009: 106-107 - [c10]Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski:
Learning to Extract Biological Event and Relation Graphs. NODALIDA 2009: 18-25 - 2008
- [j5]Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski:
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinform. 9(S-11) (2008) - [j4]Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski:
Comparative analysis of five protein-protein interaction corpora. BMC Bioinform. 9(S-3) (2008) - [c9]Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski:
A Graph Kernel for Protein-Protein Interaction Extraction. BioNLP 2008: 1-9 - 2007
- [j3]Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinform. 8 (2007) - [c8]Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen, Tapio Salakoski:
On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA. BioNLP@ACL 2007: 25-32 - 2006
- [j2]Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko:
Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinform. 7(S-3) (2006) - [j1]Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. Int. J. Medical Informatics 75(6): 430-442 (2006) - [c7]Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski:
Regular Approximation of Link Grammar. FinTAL 2006: 564-575 - [c6]Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko:
Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. SMBM 2006 - [e1]Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala:
Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings. Lecture Notes in Computer Science 4139, Springer 2006, ISBN 3-540-37334-9 [contents] - [i1]Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko:
Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. CoRR abs/cs/0606119 (2006) - 2005
- [c5]Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. FLAIRS 2005: 442-448 - [c4]Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski:
Regularized Least-Squares for Parse Ranking. IDA 2005: 464-474 - 2004
- [c3]Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Jeppe Koivula:
Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. NLPBA/BioNLP 2004 - [c2]Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. Rough Sets and Current Trends in Computing 2004: 780-785 - [c1]Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
Ontology-Based Feature Transformations: A Data-Driven Approach. EsTAL 2004: 280-291
Coauthor Index
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