Code for String Kernels

This page provides information on downloading the string kernel code for spectrum/mismatch kernel [1,2] and profile kernel [3]. Code for other variants [4] of the string kernels will be available at a later date. The code for the spectrum/mismatch kernel and profile kernel are packaged together with sample data files and the motif extraction software (specifically for the profile kernel). The PSIBLAST profile for 7329 sequences (using 5 iterations) has been included, as well as the 54 experimental setup for the profile kernel experiments. You can design your own experiments and create your own set of profiles. Included are also license files and a number of README files which will facilitate your using of the software.

Note: A version of SPIDER is included in the distribution. The SVM training/testing requires MATLAB to work with SPIDER. For more information about spider, please see http://www.kyb.tuebingen.mpg.de/bs/people/spider/.

Release Notes: Please fill in the following form. Your information is used solely for gathering statistics about the usage of the string kernel code and will not be given out to anybody nor used by us for any other purposes.

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References

[1] C. Leslie, E. Eskin, and W. Noble. Spectrum kernel: A string kernel for SVM protein classification. Proceedings of the Pacific Symposium on Biocomputing, January 2-7, 2002. pp. 474-485.
[2] C. Leslie, E. Eskin, A. Cohen, J. Weston, and W. Noble. Mismatch String Kernels for Discriminative Protein Classification. Bioinformatics, 20:4, pp. 467-476, 2004.
[3] R. Kuang, E. Ie, K. Wang, K. Wang, M. Siddiqi, Y. Freund and C. Leslie. Profile-based string kernels for remote homology detection and motif extraction. Accepted, Proceedings of the IEEE Computational Systems Bioninformatics 2004, Stanford, August, 2004.
[4] C. Leslie and R. Kuang. Fast Kernels for Inexact String Matching. Proceedings of the Conference on Learning Theory and Kernel Workshop, 2003.
Tze Way Eugene Ie
Last modified: Sat Sep 25 16:41:20 EDT 2004