Simon Kocbek

  By
Simon Kocbek
Assistant Professor , Researcher
Naziv:Assistant Professor
Prostor:G2-M.31

Main research topics

  • Machine Learning.
  • Data and text mining.
  • Natural Language Processing.
  • Bioinformatics.
  • Health informatics.
  • Semantic Web.
  • IT Security.

Selected publications

Journal papers:
  • Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek et al., “BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services”, F1000Research, 2019.
  • Simon Kocbek, Primoz Kocbek, Andraz Stozer, et al., “Drug prescription records based prediction of polypharmacy in older population”, PeerJ, doi.org/10.7717/peerj.5765, 2018.
  • Frank P. Lin, Tudor Groza, Simon Kocbek, Erick Antezana, Richard J. Epstein, “The Cancer Care Treatment Outcome Ontology (CCTOO): a novel computable ontology for profiling treatment outcomes in patients with solid tumors”, JCO Clinical Cancer Informatics, 2, 1-14, 2018.
  • Simon Kocbek, Jin-Dong Kim, “Exploring biomedical ontology mappings with graph Theory Methods”, PeerJ, 5:e2990 https://doi.org/10.7717/peerj.2990, 2017.
  • Simon Kocbek, Lawrence Cavedon, et al., “Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources”, Journal of Biomedical Informatics, Vol 64, pp. 158–167, 2016.
  • Toshiaki Katayama, Wilkinson D Mark, Aoki-Kinoshita Kiyoko F., ... , 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, pp. 1-13, 2014.
  • 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 Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun’chi Tsujii, “AGRA: Analysis of Gene Ranking Algorithms”, Bioinformatics, 27(8), 1185-1186, 2011.
  • Simon Kocbek, Matjaz B. Juric, "Influence of security mechanisms on web services interoperability". Electrotechnical review (Slovenian version), Vol. 74, No. 3, pp. 113-118, 2007.
Conference papers:
  • Simon Kocbek, Bogdan Gabrys, “Automated Machine Learning Techniques in Prognostics of Railway Track Defects”, 19th IEEE International Conference on Data Mining, ICDM, LMID, 2019, Beijing, China.
  • Simon Kocbek, Primoz Kocbek, Tina Zupanic, et al., “Using machine learning and drug prescription records to predict mortality and polypharmacy in older type 2 diabetes mellitus patients”, 26th International Conference on Neural Information Processing of the Asia-Pacific Neural Network Society, ICONIP, 2019, Sydney, Australia.
  • Simon Kocbek, Tudor Groza, “Extracting disease-phenotype relations from text with diseasephenotype concept recognisers and association rule mining”, In IEEE International Symposium on Computer-Based Medical Systems, June 2017, Greece.
  • Frank Lin, Tudor Groza, Simon Kocbek, Erick Entanzana, Richard J Epstein, “The Cancer Care Treatment Outcomes Ontology (CCTO): A computable ontology for profiling treatment outcomes of patients with solid tumors.”, ASCO Annual Meeting, June 2017, Chicago, IL.
  • Simon Kocbek, Toyofumi Fujiwara, Jin-Dong Kim, Tudor Groza, “Evaluating a dictionary of human phenotype terms focusing on rare diseases”, In CompuTerm 2016, 5th International Workshop on Computational Terminology, December 2016, Osaka, Japan.
  • Simon Kocbek, Tudor Groza, “Building a dictionary of lexical variants for phenotype descriptors”, In BioNLP 2016, Workshop on Biomedical Natural Language Processing, The Association for Computational Linguistics, August 2016, Berlin, Germany.
  • Simon Kocbek, Lawrence Cavedon, et al., “Evaluating classification power of linked admission data sources with text mining”, Proceedings of the HISA Big Data 2015 conference, October 2015, Sydney, Australia.
  • Simon Kocbek, Karin Verspoor, Wray Buntine, “Exploring Temporal Patterns in Emergency Department Triage Notes with Topic Models”, Proceedings of the twelfth Annual Workshop of the Australasia Language Technology Association (ALTA 2014), November 26-28, 2014. Melbourne, Australia.
  • Simon Kocbek, Jin-Dong Kim, Jean-Luc Perret, Patricia L. Whetzel, “Visualizing ontology mappings to help ontology engineers identify relevant ontologies for their reuse”, Proceedings of the 4th International Conference on Biomedical Ontology (ICBO 2013), July 8-9, 2013, Montreal, Canada.
  • Simon Kocbek, Jean-Luc Perret, Jin-Dong Kim, “Applying Visualization Techniques to Biomedical Ontology Mappings”, 6th IEEE Pacific Visualization (PacificVis 2013), February 26- March 1, 2013, Sydney, Australia.
  • Simon Kocbek, Jean-Luc Perret, Jin-Dong Kim, “Visual presentation of mappings between biomedical ontologies”, Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013), November 28-30, 2012, Paris, France.
  • Gregor Stiglic, Simon Kocbek, Igor Pernek, Peter Kokol, “Tuning Decision Tree Models by Imposing Visual Constraints”. Machine Learning and Data Mining (MLDM 2011), August 30 - September 3, 2011, New York.
  • Simon Kocbek, Gregor Stiglic, Igor Pernek, Peter Kokol, "Stability of different feature selection methods for selecting protein sequence descriptors in protein solubility classification problem". In: DILLON, Tharam (ed.). Proceedings of the 23rd IEEE International Symposium on Computer- Based Medical Systems (CBMS 2010), October 12-15, 2010, Perth, Australia. Piscataway: IEEE, cop. 2010, [50-55].
  • Gregor Stiglic, Simon Kocbek, Peter Kokol, "Comprehensibility of classifiers for future microarray analysis datasets", Pattern Recognition in Bioinformatics (PRIB 2009), September 7- 9, 2009, Sheffield UK, supplementary proceedings, [1-11].
  • Gregor Stiglic, Simon Kocbek, Peter Kokol, "Unsupervised variance based preprocessing of microarray data", 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS), Albuquerque, New Mexico, USA, August 3-4, 2009, (Proceedings - IEEE Symposium on Computer-Based Medical Systems), [1-4].
  • Simon Kocbek, Gregor Stiglic, Peter Kokol, "Novel Classification Scheme for Temporal Genomic and Proteomic Problems", Pattern Recognition In Bioinformatics (PRIB 2008), October 15-17, 2008, Melbourne, Australia, Supplementary proceedings.
  • Ee Hui Lim, David Suter, Simon Kocbek, “Unsupervised plane data clustering based on modified Dirichlet Process Mixture Model method”, Proceedings of the Eighth IASTED International Conference on Visualization, Imaging, and Image Processing, September 1-3, 2008, Palma de Mallorca, Spain, [148-155].
  • Mateja Verlic, Gregor Stiglic, Simon Kocbek, Peter Kokol, "Sentiment in science - a case study of CBMS contributions in years 2003 to 2007", In: Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems, June 17-19, 2008, Jyväskylä, Finland, [138143].
  • Simon Kocbek, Primož Kosec, Peter Kokol, Mitja Lenic, Matjaž Debevc. "Discovering new knowledge with advanced data mining tool", ICALT 2007: Seventh International Conference on Advanced Learning Technologies, July 18-20, 2007, Niigata, Japan, Los Alamitos: IEEE Computer Society, cop. 2007, [408-410].

Study and research abroad

  • Senior researcher, University of Technology Sydney, Australia. Jul 2018 – Dec 2019
  • Senior researcher, Garvan Institute, Sydney, Australia. Mar 2016 – May 2018
  • Researcher, National ICT Australia, Melbourne, Australia. Nov 2013 – Mar 2014
  • Project researcher, Database Center for Life Science, Tokyo, Japan. Jul 2012 – Oct 2013
  • Visiting researcher, Monash University, Melbourne, Australia. Oct 2008 – Sep 2009
  • Visiting researcher, Yonsei University, Seoul, South Korea. Oct 2008 – Sep 2009

Certificates

  • Machine Learning, Coursera, Stanford University, ID NPKXZ44QWXPL, Jul 2017.

Awards

  • Invited researcher, ROIS, Japan. Dec 2016 in Mar 2017
  • Endeavour Research Award, Australia. Oct 2009 – Apr 2010
  • Visiting Researcher Grant, NIIED, South Korea. Oct 2008 – Sep 2009
  • Travel Award, Pattern Recognition in Bioinformatics, Australia. 2008
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