CV - Karsten Borgwardt

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ETH Zurich

Dep. Biosysteme

Prof. Dr. Karsten M. Borgwardt

BSB G 4

Mattenstrasse 26

4058 Basel

Switzerland

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Biography

Picture of Prof. Dr. Karsten Borgwardt  
Karsten M. Borgwardt

I was born in Kaiserslautern, Germany in December 1980. From 1999 to 2004, I studied Computer Science at the Ludwig-Maximilians-Universität in Munich. In 2003, I completed a Master Course in Biology at the University of Oxford. My Bioinformatics project on gene finding during this time was supervised by Dr Irmtraud Meyer (now professor at UBC Vancouver). I was a scholar of the Stiftung Maximilianeum, the German Academic Merit Foundation, and the Bavarian Scholarship for the Gifted during these years. I wrote my master thesis in Computer Science at the NICTA Statistical Machine Learning Group in Canberra, supervised by Prof. Alex Smola (now Professor at Carnegie Mellon University) and Prof. SVN (Vishy) Vishwanathan (now Professor at Purdue University). From January 2005 to August 2007, I was a research and teaching assistant in Prof. Hans-Peter Kriegel's Database and Data Mining Group at the Ludwig-Maximilians-University in Munich. In May 2007, I completed my PhD thesis on ''Graph Kernels''. My thesis later on won the Heinz-Schwärtzel-Dissertation Award (best PhD thesis award) by the three computer science departments in Munich (LMU, TU, UniBw). From September 2007 to August 2008 I was a postdoctoral research associate in the Machine Learning Group at the University of Cambridge, UK, headed by Prof. Zoubin Ghahramani.

In September 2008, I moved to Tübingen to head the newly established joint research group for Machine Learning & Computational Biology of the Max-Planck-Institute for Biological Cybernetics (Prof. Bernhard Schölkopf) and the Max-Planck-Institute for Developmental Biology (Prof. Detlef Weigel) as a W2 Research Group Leader. In 2010, my position and group were tenured. In 2011, my group joined the newly established Max Planck Institute for Intelligent Systems. In September 2011, I joined the Universität Tübingen as Professor of Data Mining in the Life Sciences in the Computer Science Department. In 2012, I spent my first sabbatical at Prof. Mark Daly's lab at Massachusetts General Hospital and the Broad Institute. Since January 2013, I am the Scientific Coordinator of the European Marie Curie Initial Training Network on "Machine Learning for Personalized Medicine" (mlpm.eu) with 12 partner labs in 8 countries, and 3.75 million EUR funding by the European Union. In November 2013, I received the Krupp Award for Young Professors, including a prize money of 1 million EUR.

I moved to ETH Zürich as Associate Professor of Data Mining and joined its Biosystems Department in June 2014. In November 2014, I received a Starting Grant from the ERC backup scheme of the Swiss National Science Fonds. Business Journal Capital listed me as one of the "Top 40 under 40" in Science from Germany in 2014, 2015 and 2016.

In March 2017, I was promoted to the rank of Full Professor at ETH Zürich.

 

Awards

Year Award
2014 & 2015 & 2016 One of the "Top 40 under 40" in Science in Germany, according to Business Journal Capital
2014 Starting Grant from the ERC backup scheme of the Swiss National Science Foundation (1.4 million CHF plus overheads)
2013 Krupp Award for Young Professors (annual award of 1 million EUR for one professor in Germany of age less than 38)
2013-16 Scientific Coordinator of Marie Curie Network on "Machine Learning for Personalized Medicine" (3.75 million EUR funding, 12 partner labs in 8 countries)
2009 NIPS Outstanding Student Paper Award (as supervisor and co-author of Nino Shervashidze)
2007 Heinz Schwärtzel Dissertation Award for Foundations of Computer Science
2007 Scholar of the German Academic Merit Foundation (Studienstiftung des deutschen Volkes) as PhD student
2002 Scholar of the German Academic Merit Foundation (Studienstiftung des deutschen Volkes) as undergraduate student
1999 Scholar of the Bavarian Foundation for the Gifted (BayBFG)
1999 Scholar of the Stiftung Maximilianeum, Munich for Highly Gifted Students

Academic Degrees

Logo LMU Munich  
2007

Ph.D. in Computer Science  

Data Mining & Database Unit, Chairholder: Prof. Hans-Peter Kriegel, Ludwig-Maximilians-Universität München

Logo LMU Munich  
2004

Diplom (M.Sc. equivalent) in Computer Science  

Department of Mathematics, Computer Science & Statistics, Ludwig-Maximilians-Universität München

Logo of University of Oxford  
2003

M.Sc. in Biology  

Department of Zoology, University of Oxford

Employment & Education History

Since 2017

Full Professor of Data Mining

Department Biosystems Science and Engineering (D-BSSE), ETH Zürich

Since 2014

Associate Professor of Data Mining

Department Biosystems Science and Engineering (D-BSSE), ETH Zürich

Logo University of Tübingen

2011-2014

Professor (~Associate Professor) of Data Mining in the Life Sciences

Department of Computer Science, Eberhard Karls Universität Tübingen

2008-2014

2008-2014

W2 Research Group Leader (~Assistant Professor, tenured since 2010)

Machine Learning and Comptational Biology Research Group, Max Planck Institutes Tübingen, Directors D. Weigel and B. Schölkopf

2007-2008

2007-2008

Postdoctoral Research Associate

Machine Learning Group,  Chairholder: Prof. Zoubin Ghahramani, University of Cambridge

2005-2007

PhD Student & Research Assistant

Data Mining & Database Unit, Chairholder: Prof. Hans-Peter Kriegel, Ludwig-Maximilians-Universität München

2004

2004

Academic Visitor (for writing master thesis in Computer Science)

Machine Learning Group,  Prof. Alex Smola, Prof. SVN Vishwanathan, NICTA Canberra, Australia

2002-2003

Student of Biology (M.Sc. in 2003)

Department of Zoology, University of Oxford

1999-2004

Student of Computer Science (Diplom in 2004)

Department of Mathematics, Computer Science & Statistics, Ludwig-Maximilians-Universität München (on leave for studying in Oxford during academic year 2002/03)

Research Grants

Year Funding/Experience
2015 Partner node in Horizon2020 research network on MRI classification (520.000 CHF, 5 years, contract signed)
2014 Starting Grant for Significant Pattern Mining (ERC backup scheme oft he Swiss National Science Foundation, 1.42 million CHF, 5 years)
2013 Alfried Krupp Award for Young Professors (1 million EUR, 5 years)
2013 Scientific Coordinator of a Marie Curie Initial Training Network for "Machine Learning for Personalized Medicine" (in total: 14 PhD students at 12 labs in 8 countries, network budget: 3.75 million EUR, own budget: 0.75 million EUR, 4 years)
2012 Co-founder & scientific mentor of the Tübingen-based bioinformatics service company Computomics (computomics.com)
2010 Research grant from DFG for Kernels on Large, Labeled Graphs (German Research Council, 3 years approx. 240.000 EUR)

Services to the Scientific Community

Scientific Coordinator

 

Editorial Board Member

  • Journal of Machine Learning Research (Action Editor, since 2013)
  • IEEE Transactions on Pattern Analysis and Machine Intelligence (Associate Editor, since 2012)
  • Springer’s Machine Learning Journal (Editorial Board Member, elected in 2011)

 

Programme Chair

  • Machine Learning for Personalized Medicine Summer School 2013 (65 participants)
  • Machine Learning for Systems Biology 2012 (Workshop with 150 participants)
  • Machine Learning Summer School 2011, Purdue (co-organizer, 200 participants)
  • NIPS Workshop: Personalized Medicine Workshop 2011 (Workshop with 50 participants)
  • Mining and Learning on Graphs 2009 (Workshop with 100 participants)
  • NIPS Workshop: Transfer Learning on Structured Data 2009 (50 participants)
  • NIPS Workshop: Structured Input Structured Output 2008 (Workshop with 50 participants)

 

Area Chair

  • ICML 2013, NIPS 2013, NIPS 2014, AISTATS 2015, KDD 2016

Plus reviewer for numerous leading journals and conferences in Bioinformatics, Machine Learning, Data Mining, Applied Mathematics and Genetics

Publications

Please see here for a complete list of publications.

 
 
Page URL: https://www.bsse.ethz.ch/mlcb/karsten/profile-karsten.html
23.03.2017
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