Department of Computer Science
Bahen Centre
40 St. George St
Toronto, ON M5S 2E4
Bahen Centre, Room 4159

Research Interests

Machine Learning
  • Directed and undirected graphical models
  • Neural networks & Deep Learning
  • Feature Learning
  • Natural language processing
  • Probabilistic visualization
  • Bayesian Statistics
  • Large-scale inference
Computational Biology
  • Alternative Splicing
  • Flow Cytometry


since Sept. 2011
PhD in Computer Science program, University of Toronto
MSc in Statistics (with distinction), Humboldt-Universität zu Berlin, Germany
Sept. 2009 — May 2010 & Sept. — Dec. 2010
Visiting graduate student at University of British Columbia, Vancouver
BSc in Economics, Humboldt-Universität zu Berlin


Department of Computer Science
Bahen Centre
40 St. George St
Toronto, ON M5S 2E4
Bahen Centre, Room 4159


Peer-reviewed papers

The splicing code reveals new insights into the genetic determinants of disease

Hui Y. Xiong, Babak Alipanahi, Leo J. Lee, Hannes Bretschneider, Daniele Merico, Ryan K.C. Yuen, Yimin Hua, Serge Gueroussov, Hamed S. Najafabadi, Timothy R. Hughes, Quaid Morris, Yoseph Barash, Adrian R. Krainer, Nebojsa Jojic, Stephen W. Scherer, Benjamin J. Blencowe, Brendan J. Frey

Science, 2015, vol 347 (6218)   html

Critical Assessment of Automated Flow-Cytometry Analysis Techniques

Nima Aghaeepour, Greg Finak, the FlowCAP Consortium, the Dream Consortium, Holger Hoos, Tim R. Mosmann, Raphael Gottardo, Ryan R. Brinkman, and Richard H. Scheuermann

Nature Methods, Feb 10, 2013   html pdf

Master thesis

Hierarchical False Discovery Rates: Large-scale Inference for Plate-based High-throughput Phenotyping Methods, Berlin, June 2011   pdf

Invited Talks

13 December, 2014
Analysis of cryptic splice sites with deep convolutional networks
Machine Learning in Computational Biology Workshop at NIPS 2014, Montreal pdf
14 June, 2013
Neural networks to predict the locations of ASS events and PSI values
Montreal-Toronto Computational Molecular and Systems Biology Retreat
16 February 2012
Visualizing Neural Networks with t-SNE
Machine Learning Seminar, University of Toronto
21 September 2010
FlowVB: Automatic determination of the number of mixture components in Flow Cytometry with Variational Bayes
FlowCAP Summit, National Institutes of Health, Bethesda, MD

Grants & Awards

MSc in Statistics with distinction
2008 — 2011
Studienstiftung des deutschen Volkes (German National Merit Foundation), Fellow


CSC 321: Neural Networks
Teaching Assistant, Winter 2014 and 2015
CSC 411 F: Machine Learning and Data Mining
Teaching Assistant, Fall 2011 and 2012


Sept — Dec 2013
Microsoft Research, Redmond, WA
March — April 2007
Oxera Economic Consulting, Oxford, UK

Research Assistantships

since Sept 2011
Professor Brendan Frey,
Department of Electrical and Computer Engineering, University of Toronto
Sept — Dec 2010
Professor Jennifer Bryan,
Department of Statistics, University of British Columbia
2007 — 2010
Professor Nikolaus Hautsch,
School of Business and Economics, Humboldt-Universität zu Berlin


Hebel, GPU-accelerated Deep Learning Library in Python.
Featured on Hacker News frontpage on 12/05/13, over 1,000 stars on Github.
cuddn-python-wrappers, Python wrappers for the NVIDIA cuDNN library.