Sampo Pyysalo
sampo.pyysalo@utu.fi ORCID-tunniste: https://orcid.org/0000-0002-6279-5000 |
natural language processing; machine learning; scientific text mining
I am a researcher in the TurkuNLP group (https://turkunlp.org/) and Research Fellow at the Department of Computing, University of Turku. My work focuses on machine learning for natural language processing, with particular application domains including scientific text mining, Finnish language technology, and large language models.
After defending my PhD thesis in computer science at the University of Turku, I held researcher positions at the University of Tokyo, University of Manchester and University of Cambridge before returning to the University of Turku in 2019.
The primary focus of my research is on natural language processing using machine learning approaches, with recent emphasis on deep learning methods and large language models. I have been working on scientific text mining as an application area for nearly 20 years, with specific focus on the English biomedical literature, and have in recent years also addressed a variety of tasks in the processing of Finnish text as well as multi- and cross-lingual applications. My work covers the full range of natural language processing development from initial task design to the development of practical applications and organizing community challenges, including also running manual annotation efforts and developing annotation tools and machine learning methods for various natural language processing tasks.
My current teaching focuses on the natural language processing study module shared between the departments of Languages and Computing, with courses ranging from introductory to a course on deep learning for natural language processing.
- CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics,and Coreference (2019) Proceedings of the 5th Workshop on BioNLP Open Shared Tasks William A Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task (2019) Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Thang Minh Ngo, Jenna Kanerva, Filip Ginter, Sampo Pyysalo
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Toward Multilingual Identification of Online Registers (2019)
- Linköping Electronic Conference Proceedings
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies (2017) Proceedings of the CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies Zeman D, Popel M, Straka M, Hajič J, Nivre J, Ginter F, Luotolahti J, Pyysalo S, Petrov S, Potthast M, Tyers F, Badmaeva E, Gökırmak M, Nedoluzhko A, Cinková S, Hajič jr. J, Hlaváčová J, Kettnerová V, Urešová Z, Kanerva J, Ojala S, Missilä A, Manning C, Schuster S, Reddy S, Taji D, Habash N, Leung H, Marneffe M, Sanguinetti M, Simi M, Kanayama H, Paiva V, Droganova K, Martínez Alonso H, Uszkoreit H, Macketanz V, Burchardt A, Harris K, Marheinecke K, Rehm G, Kayadelen T, Attia M, Elkahky A, Yu Z, Pitler E, Lertpradit S, Mandl M, Kirchner J, Fernandez Alcalde H, Strnadova J, Banerjee E, Manurung R, Stella A, Shimada A, Kwak S, Mendonçca G, Lando T, Nitisaroj R, Li J
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Cell line name recognition in support of the identification of synthetic lethality in cancer from text – Cell line name recognition (2016)
- Bioinformatics
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä ) - Deep Learning With Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016 (2016) Proceedings of the 4th BioNLP Shared Task Workshop Farrokh Mehryary, Jari Bjorne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013 (2015)
- BMC Bioinformatics
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä ) - SETS: Scalable and Efficient Tree Search in Dependency Graphs (2015) Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations Juhani Luotolahti, Jenna Kanerva, Sampo Pyysalo, Filip Ginter
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Sharing annotations better: RESTful Open Annotation (2015) Proceedings of ACL-IJCNLP 2015 System Demonstrations Pyysalo Sampo, Campos Jorge, Cejuela Juan Miguel, Ginter Filip, Hakala Kai, Li Chen, Stenetorp Pontus, Jensen Lars Juhl
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Towards the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality (2015) 20th Nordic Conference of Computational Linguistics (Nodalida 2015) Laippala Veronika, Kanerva Jenna, Pyysalo Sampo, Missilä Anna, Salakoski Tapio, Ginter Filip
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Towards Universal Web Parsebanks (2015) Proceedings of the International Conference on Dependency Linguistics (Depling'15) Juhani Luotolahti, Jenna Kanerva, Veronika Laippala, Sampo Pyysalo , Filip Ginter
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Universal Dependencies for Finnish (2015) Proceedings of the 20th Nordic Conference of Computational Linguistics (NODALIDA 2015) Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Distributional Semantic Resources for Biomedical Text Processing (2013) Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM '13) Pyysalo Sampo, Ginter Filip, Moen Hans, Salakoski Tapio, Ananiadou Sophia
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Large-scale event extraction from literature with multi-level gene normalization (2013)
- PLoS ONE
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä ) - Matrix representations, linear transformations, and kernels for disambiguation in natural language (2009)
- Machine Learning
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä ) - A Graph Kernel for Protein-Protein Interaction Extraction (2008) Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008) Airola A, Pyysalo S, Björne J, Pahikkala T, Ginter F, Salakoski T
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Comparative analysis of five protein-protein interaction corpora (2008)
- BMC Bioinformatics
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä ) - Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description (2008) Proceedings of the ICML/UAI workshop on Machine Learning in health care applications Suominen H, Ginter F, Pyysalo S, Airola A, Pahikkala T, Salanterä S, Salakoski T
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa) - Regularized Least-Squares for parse ranking (2005)
- Lecture Notes in Computer Science
(A4 Vertaisarvioitu artikkeli konferenssijulkaisussa)