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2 classes: ICS 280, BIT Forum

2 classes: ICS 280, BIT Forum Meeting only on Mondays from 5 to 6:20 in CS2 136 (BIT). (P. Baldi and L. Ralaivola) ICS 280: Baldi group meeting and projects. Perhaps Welling’s AI seminar (ICS 279) will merge. http://www.ics.uci.edu/~welling/teaching/ICS279/AIseminar.html. Material.

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2 classes: ICS 280, BIT Forum

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  1. 2 classes: ICS 280, BIT Forum • Meeting only on Mondays from 5 to 6:20 in CS2 136 (BIT). (P. Baldi and L. Ralaivola) • ICS 280: Baldi group meeting and projects. • Perhaps Welling’s AI seminar (ICS 279) will merge. • http://www.ics.uci.edu/~welling/teaching/ICS279/AIseminar.html

  2. Material • First few weeks: introduction to kernel methods, in particular kernel for sequences and molecular graphs, and their applications to bioinformatics problems (Ralaivola and Baldi) • Followed by: more or less self-organized presentations by students, postdoctoral fellows, and faculty of research results, research problems/projects, recent articles in the literature etc. • Please come up with suggestions by 10/4.

  3. Additional Kernel Resources • Kernel journal club: Friday at 11 in ICS 432, alternating with AI stat seminar (Welling). • http://www.ics.uci.edu/~welling/teatimetalks/KernelClub.html • Kernel class in Winter (Welling) ICS 273 B.

  4. Organization and References • 9/27: Organization. Introduction to Kernels. Kernel Tutorial. (Pierre + Liva). General refs: Learning with Kernels Support Vector Machines, Regularization, Optimization and Beyond written by Bernhard Schölkopf and Alex Smola (MIT Press, Cambridge, MA, 2002). http://www.kernel-machines.org/ • 10/4: Kernel Tutorial. Applications to Sequences. (Liva) G. Refs: Lanckriet et al: A statisitical framework for data fusion available at http://noble.gs.washington.edu/papers/lanckriet_statistical.pdf . And one or two of these: • Profile-based string kernels for remote homology detection and motif extraction, R. Kuang, E. Ie, K. Wang, K. Wang, M. Siddiqi, Y. Freund, C. Leslie. Computational Systems Biology Conference, 2004. In press • Mismatch String Kernels for Discriminative Protein Classification, C. Leslie, E. Eskin, A. Cohen, J. Weston, and W. Noble. [Journal version of NIPS 2002 paper.] Bioinformatics 20(4):467-76 (2004). • Mismatch String Kernels for SVM Protein Classification, C. Leslie, E. Eskin, J. Weston, and W. Noble. Neural Information Processing Systems 2002 (NIPS 2002), Vancouver, December 9-14, 2002.

  5. 10/11: Alternative to Kernels. Recursive Neural Networks. Applications to Protein Structure Prediction (Pierre). • 10/18: Kernel Tutorial. Applications to Graphs, Molecular Structures, Chemistry. (Liva//papers in Baldi’s group) • 10/25: Students (need volunteers) will presenting SVMs (or for instance kernel PCA, or both). • A tutorial on support vector machines for pattern recognition. Data Mining and Knowledge Discovery, 2(2):955-974, 1998. CJC Burges, http://citeseer.ist.psu.edu/burges98tutorial.html • Nonlinear component analysis as a kernel eigenvalue problem. B. Schoelkopf, A.J. Smola, and K.-R. Muller. Neural Computation, 10:1299-1319, 1998. http://citeseer.ist.psu.edu/sch98nonlinear.html • 11/1:Combining Classifiers. Combining Kernels. (Liva) • Kernel and computational biology. * G. Lanckriet et al: A statisitical framework for data fusion available at http://noble.gs.washington.edu/papers/lanckriet_statistical.pdf • 11/8, 11/15, 11/22, 11/29, 12/6:open-ended [please propose something by October 4. Or else will be assigned.

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