My name is Sampo Pyysalo, and I am a research associate at the Language Technology Lab (LTL) at the University of Cambridge. My research is on natural language processing with a focus on biomedical text mining, in particular machine learning for information extraction.
I'm recently working mostly on event extraction from biomedical scientific publications, both organizing the BioNLP Shared Task series of events and participating in efforts applying information extraction methods to automatically analyze the entire available literature. I've also been contributing to the Universal Dependencies (UD) effort, including the UD Finnish dependency treebank.
For my publications, please see my google scholar page.
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, and Sophia Ananiadou. (2015). Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. BMC Bioinformatics, 16(Suppl 10), S2. [Open access]
Sampo Pyysalo, Jenna Kanerva, Anna Missilä, Veronika Laippala, Filip Ginter (2015). Universal Dependencies for Finnish. Proc. NODALIDA'15.
Sampo Pyysalo and Sophia Ananiadou (2014). Anatomical entity mention recognition at literature scale. Bioinformatics, 30(6), 868-875. [Open access]
Sofie Van Landeghem, Jari Björne, Chih-Hsuan Wei, Kai Hakala, Sampo Pyysalo, Sophia Ananiadou, Hung-Yu Kao, Zhiyong Lu, Tapio Salakoski, Yves Van de Peer, and Filip Ginter (2013). Large-scale event extraction from literature with multi-level gene normalization. PLoS One, 8(4), e55814. [Open access]
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Jun'ichi Tsujii, and Sophia Ananiadou (2012). Event extraction across multiple levels of biological organization. Bioinformatics, 28(18), i575-i581. [Open access]
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii, and Sophia Ananiadou (2012). Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC bioinformatics, 13(Suppl 11), S2. [Open access]
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun'ichi Tsujii.
Extracting bio-molecular events from literature - the BioNLP'09 shared task.
Computational Intelligence, 27(4):513-540, 2011.
Sophia Ananiadou, Sampo Pyysalo, Jun'ichi Tsujii, and Douglas B. Kell.
Event extraction for systems biology by text mining the literature.
Trends in Biotechnology, 28(7):381-390, 2010.
Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, and Tapio Salakoski.
Complex event extraction at pubmed scale.
Bioinformatics, 26(12):i382-i390, June 2010. [Open access]
Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, and Tapio Salakoski.
BioInfer: A corpus for information extraction in the biomedical domain.
BMC Bioinformatics, 8(50), 2007. [Open access]