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Machine Learning in Computational Biology (MLCB) 2009

A NIPS 2009 workshop (Dec. 11) and mini-symposium (Dec. 10).



Talk Videos


For registration, lodging and transport, see the NIPS webpage

Workshop Description

The field of computational biology has seen dramatic growth over the past few years, both in terms of new available data, new scientific questions, and new challenges for learning and inference. In particular, biological data are often relationally structured and highly diverse, well-suited to approaches that combine multiple weak evidence from heterogeneous sources. These data may include sequenced genomes of a variety of organisms, gene expression data from multiple technologies, protein expression data, protein sequence and 3D structural data, protein interactions, gene ontology and pathway databases, genetic variation data (such as SNPs), and an enormous amount of textual data in the biological and medical literature. New types of scientific and clinical problems require the development of novel supervised and unsupervised learning methods that can use these growing resources. Furthermore, next generation sequencing technologies are yielding terabyte scale data sets that require novel algorithmic solutions.

The goal of this workshop is to present emerging problems and machine learning techniques in computational biology. We invited several speakers from the biology/bioinformatics community who will present current research problems in bioinformatics, and we will invite contributed talks on novel learning approaches in computational biology. We encourage contributions describing either progress on new bioinformatics problems or work on established problems using methods that are substantially different from standard approaches. Kernel methods, graphical models, feature selection, and other techniques applied to relevant bioinformatics problems would all be appropriate for the workshop.

Keynote Speakers

  • Daphne Koller, Stanford AI Lab, Stanford University (USA)
  • Roded Sharan, School of Computer Science, Tel-Aviv University (Israel)
  • Elizabeth Halloran, Fred Hutchinson Cancer Research Center (USA)
  • Eric Xing, School of Computer Science, Carnegie Mellon University (USA)

Program Committee

  • Florence d'Alche-Buc, Université d'Evry-Val d'Essonne, Genopole (France)
  • Mathieu Blanchette, McGill University (Canada)
  • Eleazar Eskin, UC Los Angeles (USA)
  • Nir Friedman, The Hebrew University of Jerusalem (Israel)
  • David Heckerman, Microsoft Research (USA)
  • Michael I. Jordan, UC Berkeley (USA)
  • Christina Leslie, Memorial Sloan-Kettering Cancer Research Center (USA)
  • Michal Linial, The Hebrew University of Jerusalem (Israel)
  • Quaid Morris, University of Toronto (Canada)
  • Klaus-Robert Müller, Technical University Berlin (Germany)
  • Dana Pe'er, Columbia University (USA)
  • Uwe Ohler, Duke University (USA)
  • Gunnar Rätsch, Friedrich Miescher Laboratory of the Max Planck Society (Germany)
  • Alexander Schliep, Rutgers University (USA)
  • Koji Tsuda, National Institute of Advanced Industrial Science and Technology (Japan)
  • Eric Xing, Carnegie Mellon University (USA)
  • ... and all the organizers (see below)

Additional Reviewers

  • Asa Ben-Hur, Colorado State University (USA)
  • Fabio de Bona, Friedrich Miescher Laboratory (Germany)
  • Philipp Drewe, Friedrich Miescher Laboratory (Germany)
  • Jason Ernst, Massachusetts Institute of Technology (USA)
  • Laurent Jacob, Mines Paris (France)
  • Oliver Kohlbacher, University Tübingen (Germany)
  • Julia Lasserre, Max Planck Institute for Molecular Genetics (Germany)
  • Tien-ho (Henry) Lin, Carnegie Mellon University (USA)
  • Yong Lu, Harvard Medical School (USA)
  • Cheng Soon Ong, ETH Zürich (Switzerland)
  • Etienne Roquain, University of Paris (France)
  • Sebastian J. Schultheiss, Friedrich Miescher Laboratory (Germany)
  • Sören Sonnenburg, Technical University Berlin (Germany)
  • Yoshihiro Yamanishi, Mines ParisTech and Curie Institute (France)
  • Xi Chen, Carnegie Mellon University (USA)
  • Alexandros Iliadis, Columbia University (USA)
  • Franck Rapaport, Memorial Sloan-Kettering Cancer Research Center (USA)
  • Xiaoyu Chen, University of Washington (USA)


  • Gal Chechik, Google Research, Google Inc. (Mountain View, USA)
  • Tomer Hertz, Fred Hutchinson Cancer Research Center (USA)
  • William Stafford Noble, Department of Genome Sciences, University of Washington (Seattle, USA)
  • Yanjun Qi, Machine Learning Department, NEC Labs America (Princeton, USA)
  • Jean-Philippe Vert, Centre for Computational Biology, Mines ParisTech (Fontainebleau, France)
  • Alexander Zien, LIFE Biosystems (Heidelberg, Germany)

Call for Submissions

The submission web site is closed now, Deadline was Sep 27th, 2009.
See the full call for submissions.

MLCB 2008

The MLCB 2008 took place at whistler, Dec 11-12 2008.
See video recordings of the talks, and the program of the workshop and mini symposium.

These pages are kindly hosted by the Friedrich Miescher Laboratory of the Max Planck Society.
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