Kernels in Bioinformatics

Posted in Science on August 01, 2008


Kernels in Bioinformatics

Lecture slides:

  • Protein sequences
  • Challenges with protein sequences
  • Kernels for protein sequences
  • Kernel engineering for protein sequences
  • Define a (possibly high-dimensional) feature space of interest
  • Physico-chemical kernels
  • Substring indexation
  • Substring indexation in practice
  • Dictionary-based indexation
  • Derive a kernel from a generative model
  • Probabilistic models for sequences
  • Fisher kernel
  • Fisher kernel in practice
  • Mutual information kernels
  • The context-tree kernel
  • The context-tree kernel (cont.)
  • Marginalized kernels
  • Marginalized kernels in practice
  • Derive a kernel from a similarity measure
  • Sequence alignment
  • Alignment score
  • Local alignment kernel
  • LA kernel in practice
  • Difference in performance
  • Conclusions

Author: Jean-Philippe Vert, Ecole des Mines de Paris - Paris Tech

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Tags: Science, Lectures, Computer Science, Machine Learning, VideoLectures.Net, Bioinformatics, Kernel Methods