Neural Information Processing Systems - NIPS05 Workshops

Kernels in Bioinformatics

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

Categories

Top: Computer Science: Bioinformatics
Top: Computer Science: Machine Learning: Kernel Methods

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*Slides*
0:00	Kernels for Protein Sequences
1:43	Protein sequences
2:49	Challenges with protein sequences
5:05	Kernels for protein sequences
8:59	Kernel engineering for protein sequences
11:46	Define a (possibly high-dimensional) feature space of interest
12:10	Physico-chemical kernels
14:35	Substring indexation
19:05	Substring indexation in practice
20:13	Dictionary-based indexation
22:04	Derive a kernel from a generative model
22:17	Probabilistic models for sequences
23:28	Fisher kernel
24:47	Fisher kernel in practice
25:01	Mutual information kernels
26:30	The context-tree kernel
27:15	The context-tree kernel (cont.)
28:10	Marginalized kernels
29:36	Marginalized kernels in practice
30:39	Derive a kernel from a similarity measure
30:50	Sequence alignment
31:22	Alignment score
31:25	Local alignment kernel
32:37	LA kernel in practice
32:57	Difference in performance
33:49	Conclusions

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