Sampo Pyysalo - RankMe

155 papers A* 2A 1B 9Misc 1Journal 74Unranked 64

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	An Expanded Massive Multilingual Dataset for High-Performance Language Technologies (HPLT). ACL (1) Laurie Burchell, Ona De Gibert Bonet, Nikolay Arefyev, Mikko Aulamo, Marta Bañón, Pinzhen Chen, Mariia Fedorova, Liane Guillou, Barry Haddow, Jan Hajic, Jindrich Helcl, Erik Henriksson, Mateusz Klimaszewski, Ville Komulainen, Andrey Kutuzov, Joona Kytöniemi, Veronika Laippala, Petter Mæhlum, Bhavitvya Malik, Farrokh Mehryary, Vladislav Mikhailov, Nikita Moghe, Amanda Myntti, Dayyán O'Brien, Stephan Oepen, Proyag Pal, Jousia Piha, Sampo Pyysalo, Gema Ramírez-Sánchez, David Samuel, Pavel Stepachev, Jörg Tiedemann, Dusan Varis, Tereza Vojtechová, Jaume Zaragoza-Bernabeu
2025	J	`jnl`	An Expanded Massive Multilingual Dataset for High-Performance Language Technologies. CoRR Laurie Burchell, Ona de Gibert, Nikolay Arefyev, Mikko Aulamo, Marta Bañón, Pinzhen Chen, Mariia Fedorova, Liane Guillou, Barry Haddow, Jan Hajic, Jindrich Helcl, Erik Henriksson, Mateusz Klimaszewski, Ville Komulainen, Andrey Kutuzov, Joona Kytöniemi, Veronika Laippala, Petter Mæhlum, Bhavitvya Malik, Farrokh Mehryary, Vladislav Mikhailov, Nikita Moghe, Amanda Myntti, Dayyán O'Brien, Stephan Oepen, Proyag Pal, Jousia Piha, Sampo Pyysalo, Gema Ramírez-Sánchez, David Samuel, Pavel Stepachev, Jörg Tiedemann, Dusan Varis, Tereza Vojtechová, Jaume Zaragoza-Bernabeu
2025	—	`conf`	Aurora-M: Open Source Continual Pre-training for Multilingual Language and Code. COLING (Industry) 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 Barbosa Junior, Aleksandr Drozd, Jordan Clive, Kshitij Gupta, Liangyu Chen, Qi Sun, Ken Tsui, Nour Moustafa-Fahmy, Nicolo Monti, Tai Dang, Ziyang Luo, Tien-Tung Bui, Roberto Navigli, Virendra Mehta, Matthew Blumberg, Victor May, Hiep Nguyen, Sampo Pyysalo
2025	J	`jnl`	FIN-bench-v2: A Unified and Robust Benchmark Suite for Evaluating Finnish Large Language Models. CoRR Joona Kytöniemi, Jousia Piha, Akseli Reunamo, Fedor Vitiugin, Farrokh Mehryary, Sampo Pyysalo
2025	—	`conf`	Got Compute, but No Data: Lessons From Post-training a Finnish LLM. NoDaLiDa/Baltic-HLT Elaine Zosa, Ville Komulainen, Sampo Pyysalo
2025	J	`jnl`	Got Compute, but No Data: Lessons From Post-training a Finnish LLM. CoRR Elaine Zosa, Ville Komulainen, Sampo Pyysalo
2025	J	`jnl`	HPLT 3.0: Very Large-Scale Multilingual Resources for LLM and MT. Mono- and Bi-lingual Data, Multilingual Evaluation, and Pre-Trained Models. CoRR Stephan Oepen, Nikolay Arefev, Mikko Aulamo, Marta Bañón, Maja Buljan, Laurie Burchell, Lucas Georges Gabriel Charpentier, Pinzhen Chen, Mariya Fedorova, Ona de Gibert, Barry Haddow, Jan Hajic, Jindrich Helcl, Andrey Kutuzov, Veronika Laippala, Zihao Li, Risto Luukkonen, Bhavitvya Malik, Vladislav Mikhailov, Amanda Myntti, Dayyán O'Brien, Lucie Poláková, Sampo Pyysalo, Gema Ramírez-Sánchez, Janine Siewert, Pavel Stepachev, Jörg Tiedemann, Teemu Vahtola, Dusan Varis, Fedor Vitiugin, Tea Vojtechová, Jaume Zaragoza-Bernabeu
2025	J	`jnl`	LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations. Database J. Biol. Databases Curation Esmaeil Nourani, Evangelia-Mantelena Makri, Xiqing Mao, Sampo Pyysalo, Søren Brunak, Katerina C. Nastou, Lars Juhl Jensen
2025	—	`conf`	Poro 34B and the Blessing of Multilinguality. NoDaLiDa/Baltic-HLT Risto Luukkonen, Jonathan Burdge, Elaine Zosa, Aarne Talman, Ville Komulainen, Väinö Hatanpää, Peter Sarlin, Sampo Pyysalo
2025	J	`jnl`	Pretraining Finnish ModernBERTs. CoRR Akseli Reunamo, Laura-Maria Peltonen, Hans Moen, Sampo Pyysalo
2025	J	`jnl`	Register Always Matters: Analysis of LLM Pretraining Data Through the Lens of Language Variation. CoRR Amanda Myntti, Erik Henriksson, Veronika Laippala, Sampo Pyysalo
2025	J	`jnl`	Scaling Data-Constrained Language Models. J. Mach. Learn. Res. Niklas Muennighoff, Alexander M. Rush, Boaz Barak, Teven Le Scao, Aleksandra Piktus, Nouamane Tazi, Sampo Pyysalo, Thomas Wolf, Colin Raffel
2024	—	`conf`	A New Massive Multilingual Dataset for High-Performance Language Technologies. LREC/COLING 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
2024	J	`jnl`	A New Massive Multilingual Dataset for High-Performance Language Technologies. CoRR 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
2024	J	`jnl`	A Survey of Large Language Models for European Languages. CoRR Wazir Ali, Sampo Pyysalo
2024	J	`jnl`	Aurora-M: The First Open Source Multilingual Language Model Red-teamed according to the U.S. Executive Order. CoRR 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 Barbosa 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
2024	—	`conf`	Building Question-Answer Data Using Web Register Identification. LREC/COLING Anni Eskelinen, Amanda Myntti, Erik Henriksson, Sampo Pyysalo, Veronika Laippala
2024	J	`jnl`	Improving dictionary-based named entity recognition with deep learning. Bioinform. Katerina C. Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen
2024	J	`jnl`	Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition. Bioinform. Esmaeil Nourani, Mikaela Koutrouli, Yijia Xie, Danai Vagiaki, Sampo Pyysalo, Katerina C. Nastou, Søren Brunak, Lars Juhl Jensen
2024	J	`jnl`	Poro 34B and the Blessing of Multilinguality. CoRR Risto Luukkonen, Jonathan Burdge, Elaine Zosa, Aarne Talman, Ville Komulainen, Väinö Hatanpää, Peter Sarlin, Sampo Pyysalo
2024	J	`jnl`	RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. Database J. Biol. Databases Curation Katerina C. Nastou, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo, Lars Juhl Jensen
2024	J	`jnl`	STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature. Bioinform. Farrokh Mehryary, Katerina C. Nastou, Tomoko Ohta, Lars Juhl Jensen, Sampo Pyysalo
2023	A*	`conf`	FinGPT: Large Generative Models for a Small Language. EMNLP 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
2023	J	`jnl`	FinGPT: Large Generative Models for a Small Language. CoRR 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
2023	—	`conf`	Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction. NoDaLiDa Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
2023	J	`jnl`	Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction. CoRR Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
2023	J	`jnl`	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 Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger
2023	J	`jnl`	Register identification from the unrestricted open Web using the Corpus of Online Registers of English. Lang. Resour. Evaluation Veronika Laippala, Samuel Rönnqvist, Miika Oinonen, Aki-Juhani Kyröläinen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo
2023	J	`jnl`	S1000: a better taxonomic name corpus for biomedical information extraction. Bioinform. Jouni Luoma, Katerina C. Nastou, Tomoko Ohta, Harttu Toivonen, Evangelos Pafilis, Lars Juhl Jensen, Sampo Pyysalo
2023	A*	`conf`	Scaling Data-Constrained Language Models. NeurIPS Niklas Muennighoff, Alexander M. Rush, Boaz Barak, Teven Le Scao, Nouamane Tazi, Aleksandra Piktus, Sampo Pyysalo, Thomas Wolf, Colin A. Raffel
2023	J	`jnl`	Scaling Data-Constrained Language Models. CoRR Niklas Muennighoff, Alexander M. Rush, Boaz Barak, Teven Le Scao, Aleksandra Piktus, Nouamane Tazi, Sampo Pyysalo, Thomas Wolf, Colin Raffel
2023	—	`conf`	Silver Syntax Pre-training for Cross-Domain Relation Extraction. ACL (Findings) Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
2023	J	`jnl`	Silver Syntax Pre-training for Cross-Domain Relation Extraction. CoRR Elisa Bassignana, Filip Ginter, Sampo Pyysalo, Rob van der Goot, Barbara Plank
2023	J	`jnl`	The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 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
2023	—	`conf`	Toxicity Detection in Finnish Using Machine Translation. NoDaLiDa Anni Eskelinen, Laura Silvala, Filip Ginter, Sampo Pyysalo, Veronika Laippala
2022	—	`conf`	Towards better structured and less noisy Web data: Oscar with Register annotations. W-NUT@COLING 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
2021	—	`conf`	Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual Classification of Registers. EACL (Student Research Workshop) Liina Repo, Valtteri Skantsi, Samuel Rönnqvist, Saara Hellström, Miika Oinonen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo, Veronika Laippala
2021	J	`jnl`	Beyond the English Web: Zero-Shot Cross-Lingual and Lightweight Monolingual Classification of Registers. CoRR Liina Repo, Valtteri Skantsi, Samuel Rönnqvist, Saara Hellström, Miika Oinonen, Anna Salmela, Douglas Biber, Jesse Egbert, Sampo Pyysalo, Veronika Laippala
2021	B	`conf`	Deep learning for sentence clustering in essay grading support. EDM Li-Hsin Chang, Iiro Rastas, Jenna Kanerva, Valtteri Skantsi, Sampo Pyysalo, Filip Ginter
2021	J	`jnl`	Deep learning for sentence clustering in essay grading support. CoRR Li-Hsin Chang, Iiro Rastas, Sampo Pyysalo, Filip Ginter
2021	J	`jnl`	Explaining Classes through Word Attribution. CoRR Samuel Rönnqvist, Amanda Myntti, Aki-Juhani Kyröläinen, Sampo Pyysalo, Veronika Laippala, Filip Ginter
2021	—	`conf`	Fine-grained Named Entity Annotation for Finnish. NoDaLiDa Jouni Luoma, Li-Hsin Chang, Filip Ginter, Sampo Pyysalo
2021	J	`jnl`	Quantitative Evaluation of Alternative Translations in a Corpus of Highly Dissimilar Finnish Paraphrases. CoRR Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter
2021	J	`jnl`	The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 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
2021	—	`conf`	WikiBERT Models: Deep Transfer Learning for Many Languages. NoDaLiDa Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter
2020	B	`conf`	A Broad-coverage Corpus for Finnish Named Entity Recognition. LREC Jouni Luoma, Miika Oinonen, Maria Pyykönen, Veronika Laippala, Sampo Pyysalo
2020	J	`jnl`	Dependency parsing of biomedical text with BERT. BMC Bioinform. Jenna Kanerva, Filip Ginter, Sampo Pyysalo
2020	B	`conf`	Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. COLING Jouni Luoma, Sampo Pyysalo
2020	J	`jnl`	Exploring Cross-sentence Contexts for Named Entity Recognition with BERT. CoRR Jouni Luoma, Sampo Pyysalo
2020	—	`conf`	From Web Crawl to Clean Register-Annotated Corpora. WAC@LREC Veronika Laippala, Samuel Rönnqvist, Saara Hellström, Juhani Luotolahti, Liina Repo, Anna Salmela, Valtteri Skantsi, Sampo Pyysalo
2020	—	`conf`	The birth of Romanian BERT. EMNLP (Findings) Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo
2020	J	`jnl`	The birth of Romanian BERT. CoRR Stefan Daniel Dumitrescu, Andrei-Marius Avram, Sampo Pyysalo
2020	J	`jnl`	Towards Fully Bilingual Deep Language Modeling. CoRR Li-Hsin Chang, Sampo Pyysalo, Jenna Kanerva, Filip Ginter
2020	—	`conf`	Turku Enhanced Parser Pipeline: From Raw Text to Enhanced Graphs in the IWPT 2020 Shared Task. IWPT 2020 Jenna Kanerva, Filip Ginter, Sampo Pyysalo
2020	B	`conf`	Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection. LREC Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Jan Hajic, Christopher D. Manning, Sampo Pyysalo, Sebastian Schuster, Francis M. Tyers, Daniel Zeman
2020	J	`jnl`	Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection. CoRR Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Jan Hajic, Christopher D. Manning, Sampo Pyysalo, Sebastian Schuster, Francis M. Tyers, Daniel Zeman
2020	J	`jnl`	WikiBERT models: deep transfer learning for many languages. CoRR Sampo Pyysalo, Jenna Kanerva, Antti Virtanen, Filip Ginter
2019	J	`jnl`	A neural classification method for supporting the creation of BioVerbNet. J. Biomed. Semant. Billy Chiu, Olga Majewska, Sampo Pyysalo, Laura Wey, Ulla Stenius, Anna Korhonen, Martha Palmer
2019	—	`conf`	Biomedical Named Entity Recognition with Multilingual BERT. BioNLP-OST@EMNLP-IJNCLP Kai Hakala, Sampo Pyysalo
2019	—	`conf`	CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference. BioNLP-OST@EMNLP-IJNCLP William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter
2019	J	`jnl`	LION LBD: a literature-based discovery system for cancer biology. Bioinform. Sampo Pyysalo, Simon Baker, Imran Ali, Stefan Haselwimmer, Tejas Shah, Andrew Young, Yufan Guo, Johan Högberg, Ulla Stenius, Masashi Narita, Anna Korhonen
2019	J	`jnl`	Multilingual is not enough: BERT for Finnish. CoRR Antti Virtanen, Jenna Kanerva, Rami Ilo, Jouni Luoma, Juhani Luotolahti, Tapio Salakoski, Filip Ginter, Sampo Pyysalo
2019	—	`conf`	Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task. BioNLP-OST@EMNLP-IJNCLP Thang Minh Ngo, Jenna Kanerva, Filip Ginter, Sampo Pyysalo
2019	—	`conf`	Toward Multilingual Identification of Online Registers. NODALIDA Veronika Laippala, Roosa Kyllönen, Jesse Egbert, Douglas Biber, Sampo Pyysalo
2018	J	`jnl`	Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. BMC Bioinform. Billy Chiu, Sampo Pyysalo, Ivan Vulic, Anna Korhonen
2018	J	`jnl`	Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. BMC Bioinform. Gamal K. O. Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen
2017	J	`jnl`	A neural network multi-task learning approach to biomedical named entity recognition. BMC Bioinform. Gamal K. O. Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen
2017	J	`jnl`	Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinform. Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo, Johan Högberg, Ulla Stenius, Anna Korhonen
2017	—	`conf`	CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies. CoNLL Shared Task (2) 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
2017	—	`conf`	Fully Delexicalized Contexts for Syntax-Based Word Embeddings. DepLing Jenna Kanerva, Sampo Pyysalo, Filip Ginter
2016	B	`conf`	Attending to Characters in Neural Sequence Labeling Models. COLING Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo
2016	J	`jnl`	Attending to Characters in Neural Sequence Labeling Models. CoRR Marek Rei, Gamal K. O. Crichton, Sampo Pyysalo
2016	—	`conf`	Cancer Hallmark Text Classification Using Convolutional Neural Networks. BioTxtM@COLING 2016 Simon Baker, Anna Korhonen, Sampo Pyysalo
2016	J	`jnl`	Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinform. Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
2016	—	`conf`	Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016. BioNLP (Shared Task) Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
2016	—	`conf`	How to Train good Word Embeddings for Biomedical NLP. BioNLP@ACL Billy Chiu, Gamal K. O. Crichton, Anna Korhonen, Sampo Pyysalo
2016	—	`conf`	Intrinsic Evaluation of Word Vectors Fails to Predict Extrinsic Performance. RepEval@ACL Billy Chiu, Anna Korhonen, Sampo Pyysalo
2016	B	`conf`	Typed Entity and Relation Annotation on Computer Science Papers. LREC Yuka Tateisi, Tomoko Ohta, Sampo Pyysalo, Yusuke Miyao, Akiko Aizawa
2016	B	`conf`	Universal Dependencies v1: A Multilingual Treebank Collection. LREC 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
2015	J	`jnl`	Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. BMC Bioinform. Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou
2015	—	`conf`	SETS: Scalable and Efficient Tree Search in Dependency Graphs. HLT-NAACL Juhani Luotolahti, Jenna Kanerva, Sampo Pyysalo, Filip Ginter
2015	—	`conf`	Sharing annotations better: RESTful Open Annotation. ACL (System Demonstrations) Sampo Pyysalo, Jorge Campos, Juan Miguel Cejuela, Filip Ginter, Kai Hakala, Chen Li, Pontus Stenetorp, Lars Juhl Jensen
2015	—	`conf`	Towards Universal Web Parsebanks. DepLing Juhani Luotolahti, Jenna Kanerva, Veronika Laippala, Sampo Pyysalo, Filip Ginter
2015	—	`conf`	Towards the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality. NODALIDA Veronika Laippala, Jenna Kanerva, Anna Missilä, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
2015	—	`conf`	Universal Dependencies for Finnish. NODALIDA Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter
2014	J	`jnl`	Anatomical entity mention recognition at literature scale. Bioinform. Sampo Pyysalo, Sophia Ananiadou
2014	J	`jnl`	Generalising semantic category disambiguation with large lexical resources for fun and profit. J. Biomed. Semant. Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou, Jun'ichi Tsujii
2013	J	`jnl`	A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinform. Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou
2013	J	`jnl`	BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinform. Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou
2013	—	`conf`	Overview of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum
2013	—	`conf`	Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
2013	—	`conf`	Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou, Jun'ichi Tsujii
2013	—	`ed.`	Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, August 9, 2013 BioNLP@ACL (Shared Task) Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum
2013	J	`jnl`	Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinform. Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
2012	—	`conf`	Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far. ExProM@ACL Pontus Stenetorp, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
2012	J	`jnl`	Event extraction across multiple levels of biological organization. Bioinform. Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou
2012	—	`conf`	New Resources and Perspectives for Biomedical Event Extraction. BioNLP@HLT-NAACL Sampo Pyysalo, Pontus Stenetorp, Tomoko Ohta, Jin-Dong Kim, Sophia Ananiadou
2012	J	`jnl`	Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinform. Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2012	—	`conf`	PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
2012	A	`conf`	brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
2011	J	`jnl`	An analysis of gene/protein associations at PubMed scale. J. Biomed. Semant. Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2011	—	`conf`	BioNLP Shared Task 2011: Supporting Resources. BioNLP@ACL (Shared Task) Pontus Stenetorp, Goran Topic, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
2011	J	`jnl`	Event extraction for DNA methylation. J. Biomed. Semant. Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
2011	J	`jnl`	Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. Comput. Intell. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
2011	—	`conf`	From Pathways to Biomolecular Events: Opportunities and Challenges. BioNLP@ACL Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
2011	J	`jnl`	Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2011	—	`conf`	Overview of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan L. T. Nguyen, Jun'ichi Tsujii
2011	—	`conf`	Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2011	—	`conf`	Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
2011	—	`conf`	Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2011	—	`ed.`	Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon, USA, June 24, 2011 BioNLP@ACL (Shared Task) Jun'ichi Tsujii, Jin-Dong Kim, Sampo Pyysalo
2011	—	`ed.`	Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, Cambridge, United Kingdom, October, 2010 Semantic Mining in Biomedicine Nigel Collier, Udo Hahn, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo
2011	—	`conf`	SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation. BioNLP@ACL Pontus Stenetorp, Sampo Pyysalo, Jun'ichi Tsujii
2011	—	`conf`	Towards Exhaustive Event Extraction for Protein Modifications. BioNLP@ACL Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Jun'ichi Tsujii
2011	J	`jnl`	Towards mature use of semantic resources for biomedical analyses. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo, Nigel Collier, Udo Hahn
2011	J	`jnl`	U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 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
2010	—	`conf`	A Comparative Study of Syntactic Parsers for Event Extraction. BioNLP@ACL Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii
2010	J	`jnl`	A Re-Evaluation of Biomedical Named Entity-Term Relations. J. Bioinform. Comput. Biol. Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii
2010	—	`conf`	An Analysis of gene/protein associations at PubMed scale. Semantic Mining in Biomedicine Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010	—	`conf`	Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Complex event extraction at PubMed scale. Bioinform. Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
2010	J	`jnl`	Entities, relations, events: representing biomolecular semantics. BMC Bioinform. Sampo Pyysalo
2010	B	`conf`	Evaluating Dependency Representations for Event Extraction. COLING Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii
2010	—	`conf`	Event Extraction for Post-Translational Modifications. BioNLP@ACL Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jin-Dong Kim, Jun'ichi Tsujii
2010	—	`conf`	Event extraction for DNA methylation. Semantic Mining in Biomedicine Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
2010	J	`jnl`	Event extraction on PubMed scale. BMC Bioinform. Filip Ginter, Jari Björne, Sampo Pyysalo
2010	J	`jnl`	Improving the Inter-Corpora Compatibility for protein Annotations. J. Bioinform. Comput. Biol. Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010	—	`conf`	Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer
2010	J	`jnl`	Medie and Info-pubmed: 2010 update. BMC Bioinform. Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii
2010	—	`conf`	Scaling up Biomedical Event Extraction to the Entire PubMed. BioNLP@ACL Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
2010	—	`conf`	Towards Event Extraction from Full Texts on Infectious Diseases. BioNLP@ACL Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Daniel E. Sullivan, Chunhong Mao, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2009	J	`jnl`	Combining hidden Markov models and latent semantic analysis for topic segmentation and labeling: Method and clinical application. Int. J. Medical Informatics Filip Ginter, Hanna Suominen, Sampo Pyysalo, Tapio Salakoski
2009	—	`conf`	Incorporating GENETAG-style annotation to GENIA corpus. BioNLP@HLT-NAACL Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang, Jun'ichi Tsujii
2009	J	`jnl`	Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinform. Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii
2009	—	`conf`	Learning to Extract Biological Event and Relation Graphs. NODALIDA Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski
2009	J	`jnl`	Matrix representations, linear transformations, and kernels for disambiguation in natural language. Mach. Learn. Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2009	—	`conf`	Overview of BioNLP'09 Shared Task on Event Extraction. BioNLP@HLT-NAACL (Shared Task) Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
2009	—	`conf`	Static Relations: a Piece in the Biomedical Information Extraction Puzzle. BioNLP@HLT-NAACL Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
2009	J	`jnl`	Towards automated processing of clinical Finnish: Sublanguage analysis and a rule-based parser. Int. J. Medical Informatics Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski
2008	—	`conf`	A Graph Kernel for Protein-Protein Interaction Extraction. BioNLP Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski
2008	J	`jnl`	All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinform. Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski
2008	J	`jnl`	Comparative analysis of five protein-protein interaction corpora. BMC Bioinform. Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski
2007	J	`jnl`	BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinform. Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2007	—	`conf`	On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA. BioNLP@ACL Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen, Tapio Salakoski
2006	—	`ed.`	Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings FinTAL Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala
2006	J	`jnl`	Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. Int. J. Medical Informatics Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2006	J	`jnl`	Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches CoRR Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	—	`conf`	Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. SMBM Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	J	`jnl`	Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinform. Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	—	`conf`	Regular Approximation of Link Grammar. FinTAL Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski
2005	Misc	`conf`	Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. FLAIRS Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2005	B	`conf`	Regularized Least-Squares for Parse Ranking. IDA Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski
2004	—	`conf`	Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. NLPBA/BioNLP Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Jeppe Koivula
2004	—	`conf`	Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. Rough Sets and Current Trends in Computing Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2004	—	`conf`	Ontology-Based Feature Transformations: A Data-Driven Approach. EsTAL Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski