Publications

Refereed Publications

  • I. Goodfellow, D. Warde-Farley, M. Mirza, A. Courville & Y. Bengio. “Maxout Networks”. Proceedings of the 30th International Conference on Machine Learning (ICML 2013) [PDF]
  • G. Mesnil, Y. Dauphin, X. Glorot, S. Rifai, Y. Bengio, I. Goodfellow, E. Lavoie, X. Muller, G. Desjardins, D. Warde-Farley, P. Vincent, A. Courville, & J. Bergstra. “Unsupervised and Transfer Learning Challenge: A Deep Learning Approach”. JMLR Workshop and Conference Proceedings 7 (2011), Workshop on Unsupervised and Transfer Learning (accepted).
  • J. Bergstra, O. Breuleux, F. Bastien, P. Lamblin, R. Pascanu, G. Desjardins, J. Turian, D. Warde-Farley & Y. Bengio. “Theano: A CPU and GPU Math Compiler in Python”. Proceedings of the 9th Annual Python In Science Conference (SciPy 2010). [PDF]
  • D. Warde-Farley*, S. Donaldson*, O. Comes*, K. Zuberi*, R. Badrawi, P. Chao, M. Franz, C. Grouios, F. Kazi, C. Tannus Lopes, A. Maitland, S. Mostafavi, J. Montojo, Q. Shao, G. Wright, G. Bader and Q. Morris. “The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function”. Nucleic Acids Research 2010 Jul 1;38 Suppl:W214-20. [Full Text (HTML)] [Screen PDF] [Print PDF]
  • I.W. Taylor, R. Linding, D. Warde-Farley, Y. Liu, C. Pesquita, D. Faria, S. Bull, T. Pawson, Q. Morris, and J.L. Wrana. “Dynamic modularity in protein interaction networks predicts breast cancer outcome”. Nature Biotechnology 2009, 27, 199–204. [Abstract]
  • S. Mostafavi, D. Ray, D. Warde-Farley, C. Grouios, and Q.D. Morris. “GeneMANIA: a real-time Multiple Association Network Integration Algorithm for predicting gene function”. Genome Biology 2008, 9(Suppl 1):S4. [PDF]
  • L. Pena-Castillo, M. Tasan, C.L. Myers, H. Lee, T. Joshi, C. Zhang, Y. Guan, M. Leone, A. Pagnani, W.K. Kim, C. Krumpelman, W. Tian, G. Obozinski, Y. Qi, S. Mostafavi, G.N. Lin, G. Berriz, F. Gibbons, G. Lanckriet, J. Qiu, C. Grant, Z. Barutcuoglu, D.P. Hill , D. Warde-Farley, C. Grouios, D. Ray, J.A. Blake, M. Deng, M.I. Jordan, W.S. Noble, Q. Morris, J. Klein-Seetharaman, Z. Bar-Joseph, T. Chen, F. Sun, O.G. Troyanskaya, E.M. Marcotte, D. Xu, T.R. Hughes, and F.P. Roth. “A critical assessment of M. musculus gene function prediction using integrated genomic evidence”. Genome Biology 2008, 9(Suppl 1):S2 [PDF]

* = joint first-authorship

Poster Presentations

  • D. Warde-Farley, Y. Chong, J. Koh, J. Moffat, and Q. Morris. "A mixture model approach to high-throughput cell cycle analysis in budding yeast". Presented at Intelligent Systems in Molecular Biology (ISMB) 2010, Boston, USA.