Sampo Pyysalo
 


sampo.pyysalo@utu.fi




ORCID identifierhttps://orcid.org/0000-0002-6279-5000

Publications (Google Scholar)




Areas of expertise
natural language processing; machine learning; scientific text mining

Biography

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.



Research

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.



Teaching

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.



Publications
  
Go to first page
  
Go to previous page
  
3 of 3
  
Go to next page
  
Go to last page

  • 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 Refereed article in a conference publication )


  • 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 Refereed article in a conference publication )


  •   (2019)  
    • Linköping Electronic Conference Proceedings
    Proceedings of the 22nd Nordic Conference on Computational Linguistics Veronika Laippala, Roosa Kyllönen, Jesse Egbert, Douglas Biber, Sampo Pyysalo
    (
    A4 Refereed article in a conference publication )


  • 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 Refereed article in a conference publication )


  •   (2016)  
    • Bioinformatics
     Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
    (
    A1 Refereed original research article in a scientific journal)


  •   (2016)  Proceedings of the 4th BioNLP Shared Task Workshop Farrokh Mehryary, Jari Bjorne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
    (
    A4 Refereed article in a conference publication )


  •   (2015)  
    • BMC Bioinformatics
     Pyysalo S, Ohta T, Rak R, Rowley A, Chun HW, Jung SJ, Choi SP, Tsujii J, Ananiadou S
    (
    A1 Refereed original research article in a scientific journal)


  • SETS: Scalable and Efficient Tree Search in Dependency GraphsSharing annotations better: RESTful Open Annotation  (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 Refereed article in a conference publication )


  •   (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 Refereed article in a conference publication )


  • 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 Refereed article in a conference publication )


  • Towards Universal Web ParsebanksUniversal Dependencies for Finnish  (2015)  Proceedings of the International Conference on Dependency Linguistics (Depling'15) Juhani Luotolahti, Jenna Kanerva, Veronika Laippala, Sampo Pyysalo , Filip Ginter
    (
    A4 Refereed article in a conference publication )


  •   (2015)  Proceedings of the 20th Nordic Conference of Computational Linguistics (NODALIDA 2015) Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter
    (
    A4 Refereed article in a conference publication )


  • Distributional Semantic Resources for Biomedical Text ProcessingMatrix representations, linear transformations, and kernels for disambiguation in natural language  (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 Refereed article in a conference publication )


  • Large-scale event extraction from literature with multi-level gene normalization  (2013)  
    • PLoS ONE
     Van Landeghem Sofie, Björne Jari, Wei Chih-Hsuan, Hakala Kai, Pyysalo Sampo, Ananiadou Sophia, Kao Hung-Yu, Lu Zhiyong, Salakoski Tapio, Van de Peer Yves, Ginter Filip
    (
    A1 Refereed original research article in a scientific journal)


  •   (2009)  
    • Machine Learning
     Pahikkala T, Pyysalo S, Boberg J, Jarvinen J, Salakoski T
    (
    A1 Refereed original research article in a scientific journal)


  • 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 Refereed article in a conference publication )


  • Comparative analysis of five protein-protein interaction corpora  (2008)  
    • BMC Bioinformatics
     Pyysalo S, Airola A, Heimonen J, Bjorne J, Ginter F, Salakoski T
    (
    A1 Refereed original research article in a scientific journal)


  • 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 Refereed article in a conference publication )


  • Regularized Least-Squares for parse ranking  (2005)  
    • Lecture Notes in Computer Science
    Proceedings of the 6th International Symposium on Intelligent Data Analysis Tsivtsivadze E, Pahikkala T, Pyysalo S, Boberg J, Myllari A, Salakoski T
    (
    A4 Refereed article in a conference publication )



Last updated on 2023-18-12 at 07:51