ICS 280 Material

Slides/presentations

• 10/18/04: Kernel methods and application to graphs, molecular structures, chemistry (pdf)
• 10/04/04: Kernel methods and application to sequences (pdf)
• 09/27/04: Tutorial on kernel methods for classification (pdf)
• 09/27/04: Introduction slides, organization of the class (pdf,ppt)

Links

• http://www.learning-with-kernels.org/
• http://www.kernel-machines.org/
• http://www.support-vector.net/
• A Java applet that allows you to play with SVMs, click here
• The Kernel Journal Club, organized by Gang Liang and Max Welling
• Professor Baldi's webpage
• A powerful search engine for scientific papers: Citeseer

References (to be completed soon)

• Tutorial, introduction
  • C. J. C. Burges. A Tutorial on Support Vector Machines for Pattern Recognition. Knowledge Discovery and Data Mining, 2(2), 1998. (ps.gz and ps files can be viewed with GSView)
  • K.-R. Müller, S. Mika, G. Rätsch, K. Tsuda, and B. Schölkopf. An introduction to kernel-based learning algorithms. IEEE Neural Networks, 12(2):181-201, May 2001.
  • A. J. Smola and B. Schölkopf. A Tutorial on Support Vector Regression. NeuroCOLT Technical Report NC-TR-98-030, Royal Holloway College, University of London, UK, 1998.
  • A presentation given by N. Cristianini at ICML'01.
  • B. Schölkopf, A. Smola, K.-R. Müller. Nonlinear Component Analysis as a Kernel Eigenvalue Problem. Neural Computation, 10:1299-1319, 1998.
  • P.H. Chen, C.-J. Lin, and B. Schölkopf. A tutorial on nu-support vector machines. 2003.
  
  
• Kernel Methods and Bioinformatics
  • Lanckriet et al. A statistical framework for data fusion
  • R. Kuang, E. Ie, K. Wang, K. Wang, M. Siddiqi, Y. Freund, C. Leslie. Profile-based string kernels for remote homology detection and motif extraction. Computational Systems Biology Conference, 2004. In press
  • C. Leslie, E. Eskin, A. Cohen, J. Weston, and W. Noble. Mismatch String Kernels for Discriminative Protein Classification. Bioinformatics 20(4):467-76 (2004). (A draft version of this paper is available here)
  • C. Leslie, E. Eskin, J. Weston, and W. Noble. Mismatch String Kernels for SVM Protein Classification. Neural Information Processing Systems 2002 (NIPS 2002), Vancouver, December 9-14, 2002.
  • J.-P. Vert, M. Kanehisa. Graph-Driven Features Extraction From Microarray Data using diffusion kernels and kernel CCA. Neural Information Processing Systems 2002 (NIPS 2002), Vancouver, December 9-14, 2002.
  • J.-P. Vert. A Tree Kernel to Analyze Phylogenetic Profiles. Bioinformatics (proceedings of ISMB'02) (2002).

Non exhaustive list of papers to be presented by students

• C. J. C. Burges. A Tutorial on Support Vector Machines for Pattern Recognition. Knowledge Discovery and Data Mining, 2(2), 1998.
• B. Schölkopf, A. Smola, K.-R. Müller. Nonlinear Component Analysis as a Kernel Eigenvalue Problem. Neural Computation, 10:1299-1319, 1998.
• J.-P. Vert. A Tree Kernel to Analyze Phylogenetic Profiles. Bioinformatics (proceedings of ISMB'02) (2002).
• All the papers cited on N. Cristianini's Support Vector Machines in Computational Biology page
• All the papers from kernel-machines.org publications page