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Bioinformatics & Systems Biology Experts

Simon Kocbek

Research Officer
Clinical Genomics
Garvan Institute of Medical Research
Australia

Biography

Dr Simon Kocbek is a computer scientist with several years of research and software engineering experience. Prior to joining Garvan, Simon held various research positions and was a recipient of internationally competitive fellowships. Simon’s main research interest is in how data can be understood and used by computers to improve quality of life. He has spent most of his time applying and improving supervised machine learning algorithms to datasets in areas of health, medicine and biological research. He has a great interest in text mining and technologies like semantic web and ontologies. He has been a program committee member for prestigious Natural Language Processing (NLP) conferences such as ACL 2017 and EMNLP 2017. Recently, Simon has been focusing on automatically classifying patients based on hospital admission data and applying topic modelling techniques to clinical text. Currently, he works on NLP problems within phenotype analytics stack. Any prospective students interested in these areas are welcome to get in touch.

Research Interest

Data Mining and Text Mining, Natural Language Processing, Bioinformatics and Healthcare, Big Data, Semantic Web and Ontologies, Computer Security

Publications

  • Gregor Stiglic, Simon Kocbek, Igor Pernek, Peter Kokol, "Comprehensive Decision Tree Models in Bioinformatics", PLoS ONE, 7(3), 2012.

  • Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-dong Kim, Igor Pernek, Yoshimasa Tsuru-oka, Peter Kokol, Sophia Ananiadou, Jun’chi Tsujii, “AGRA: Analysis of Gene Ranking Algorithms”, Bioinformatics, 27(8), 1185-1186, 2011.

  • Toshiaki Katayama Email author, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, et al., "BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains." Journal of Biomedical Semantics 5, no. 1, 1-13, 2014.

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