Sampo Pyysalo

ORCID

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 61

Top Venues

Publications

Anni Eskelinen, Amanda Myntti, Erik Henriksson, Sampo Pyysalo, Veronika Laippala
Building Question-Answer Data Using Web Register Identification. LREC/COLING (2024)
Risto Luukkonen, Jonathan Burdge, Elaine Zosa, Aarne Talman, Ville Komulainen, Väinö Hatanpää, Peter Sarlin, Sampo Pyysalo
Poro 34B and the Blessing of Multilinguality. CoRR (2024)
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 (2024)
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)
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 (2024)
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) (2023)
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)
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)
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 (2023)
Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction. CoRR (2023)
Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
Silver Syntax Pre-training for Cross-Domain Relation Extraction. CoRR (2023)
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 (2023)
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)
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)
Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
Silver Syntax Pre-training for Cross-Domain Relation Extraction. ACL (Findings) (2023)
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) (2023)
Anni Eskelinen, Laura Silvala, Filip Ginter, Sampo Pyysalo, Veronika Laippala
Toxicity Detection in Finnish Using Machine Translation. NoDaLiDa (2023)
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)
Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter
Quantitative Evaluation of Alternative Translations in a Corpus of Highly Dissimilar Finnish Paraphrases. CoRR (2021)
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) (2021)
Li-Hsin Chang, Iiro Rastas, Sampo Pyysalo, Filip Ginter
Deep learning for sentence clustering in essay grading support. CoRR (2021)
Li-Hsin Chang, Iiro Rastas, Jenna Kanerva, Valtteri Skantsi, Sampo Pyysalo, Filip Ginter
Deep learning for sentence clustering in essay grading support. EDM (2021)
Samuel Rönnqvist, Amanda Myntti, Aki-Juhani Kyröläinen, Sampo Pyysalo, Veronika Laippala, Filip Ginter
Explaining Classes through Word Attribution. CoRR (2021)
Jouni Luoma, Li-Hsin Chang, Filip Ginter, Sampo Pyysalo
Fine-grained Named Entity Annotation for Finnish. NoDaLiDa (2021)
Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter
WikiBERT Models: Deep Transfer Learning for Many Languages. NoDaLiDa (2021)
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)
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 (2021)
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)
Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo
The birth of Romanian BERT. EMNLP (Findings) (2020)
Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter
WikiBERT models: deep transfer learning for many languages. CoRR (2020)
Jouni Luoma, Sampo Pyysalo
Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. CoRR (2020)
Jouni Luoma, Sampo Pyysalo
Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. COLING (2020)
Jouni Luoma, Miika Oinonen, Maria Pyykönen, Veronika Laippala, Sampo Pyysalo
A Broad-coverage Corpus for Finnish Named Entity Recognition. LREC (2020)
Jenna Kanerva, Filip Ginter, Sampo Pyysalo
Dependency parsing of biomedical text with BERT. BMC Bioinform. (23) (2020)
Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter
Towards Fully Bilingual Deep Language Modeling. CoRR (2020)
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)
Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo
The birth of Romanian BERT. CoRR (2020)
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)
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 (2020)
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)
Veronika Laippala, Roosa Kyllönen, Jesse Egbert, Douglas Biber, Sampo Pyysalo
Toward Multilingual Identification of Online Registers. NODALIDA (2019)
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)
Antti Virtanen, Jenna Kanerva, Rami Ilo, Jouni Luoma, Juhani Luotolahti, Tapio Salakoski, Filip Ginter, Sampo Pyysalo
Multilingual is not enough: BERT for Finnish. CoRR (2019)
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) (2019)
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) (2019)
Kai Hakala, Sampo Pyysalo
Biomedical Named Entity Recognition with Multilingual BERT. BioNLP-OST@EMNLP-IJNCLP (2019)
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) (2018)
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) (2018)
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)
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) (2017)
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) (2017)
Jenna Kanerva, Sampo Pyysalo, Filip Ginter
Fully Delexicalized Contexts for Syntax-Based Word Embeddings. DepLing (2017)
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)
Simon Baker, Anna Korhonen, Sampo Pyysalo
Cancer Hallmark Text Classification Using Convolutional Neural Networks. BioTxtM@COLING 2016 (2016)
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) (2016)
Billy Chiu, Anna Korhonen, Sampo Pyysalo
Intrinsic Evaluation of Word Vectors Fails to Predict Extrinsic Performance. RepEval@ACL (2016)
Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo
Attending to Characters in Neural Sequence Labeling Models. COLING (2016)
Billy Chiu, Gamal K. O. Crichton, Anna Korhonen, Sampo Pyysalo
How to Train good Word Embeddings for Biomedical NLP. BioNLP@ACL (2016)
Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo
Attending to Characters in Neural Sequence Labeling Models. CoRR (2016)
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)
Yuka Tateisi, Tomoko Ohta, Sampo Pyysalo, Yusuke Miyao, Akiko Aizawa
Typed Entity and Relation Annotation on Computer Science Papers. LREC (2016)
Juhani Luotolahti, Jenna Kanerva, Sampo Pyysalo, Filip Ginter
SETS: Scalable and Efficient Tree Search in Dependency Graphs. HLT-NAACL (2015)
Juhani Luotolahti, Jenna Kanerva, Veronika Laippala, Sampo Pyysalo, Filip Ginter
Towards Universal Web Parsebanks. DepLing (2015)
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) (2015)
Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter
Universal Dependencies for Finnish. NODALIDA (2015)
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)
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)
Sampo Pyysalo, Sophia Ananiadou
Anatomical entity mention recognition at literature scale. Bioinform. 30 (6) (2014)
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 (2014)
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)
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)
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) (2013)
Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinform. 14 (2013)
Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) (2013)
Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou
BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinform. 14 (2013)
Sampo Pyysalo, Pontus Stenetorp, Tomoko Ohta, Jin-Dong Kim, Sophia Ananiadou
New Resources and Perspectives for Biomedical Event Extraction. BioNLP@HLT-NAACL (2012)
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou
Event extraction across multiple levels of biological organization. Bioinform. 28 (18) (2012)
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)
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)
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)
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) (2012)
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)
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) (2011)
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) (2011)
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Jun'ichi Tsujii
Towards Exhaustive Event Extraction for Protein Modifications. BioNLP@ACL (2011)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
Event extraction for DNA methylation. J. Biomed. Semant. 2 (S-5) (2011)
Pontus Stenetorp, Sampo Pyysalo, Jun'ichi Tsujii
SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation. BioNLP@ACL (2011)
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)
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)
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)
Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
From Pathways to Biomolecular Events: Opportunities and Challenges. BioNLP@ACL (2011)
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
An analysis of gene/protein associations at PubMed scale. J. Biomed. Semant. 2 (S-5) (2011)
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 (2011)
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)
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) (2011)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jin-Dong Kim, Jun'ichi Tsujii
Event Extraction for Post-Translational Modifications. BioNLP@ACL (2010)
Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
Scaling up Biomedical Event Extraction to the Entire PubMed. BioNLP@ACL (2010)
Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii
A Comparative Study of Syntactic Parsers for Event Extraction. BioNLP@ACL (2010)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
Event extraction for DNA methylation. Semantic Mining in Biomedicine (2010)
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) (2010)

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Sampo Pyysalo