English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Positional Oligomer Importance Matrices

Sonnenburg, S., Zien, A., Philips, P., & Rätsch, G. (2007). Positional Oligomer Importance Matrices. Talk presented at NIPS 2007 Workshop on Machine Learning in Computational Biology. Whistler, BC, Canada.

Item is

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Sonnenburg, S1, Author           
Zien, A2, Author           
Philips, P, Author
Rätsch, G2, Author           
Affiliations:
1Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497794              
2Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              

Content

show
hide
Free keywords: -
 Abstract: At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences, above all of DNA and proteins. In many cases, the most accurate classifiers are obtained by training SVMs with complex sequence kernels, for instance for transcription starts or splice sites. However, an often criticized downside of SVMs with complex kernels is that it is very hard for humans to understand the learned decision rules and to derive biological insights from them. To close this gap, we introduce the concept of positional oligomer importance matrices (POIMs) and develop an efficient algorithm for their computation. We demonstrate how they overcome the limitations of sequence logos, and how they can be used to find relevant motifs for different biological phenomena in a straight-forward way. Note that the concept of POIMs is not limited to interpreting SVMs, but is applicable to general k8722;mer based scoring systems.

Details

show
hide
Language(s):
 Dates: 2007-12
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

Event

show
hide
Title: NIPS 2007 Workshop on Machine Learning in Computational Biology
Place of Event: Whistler, BC, Canada
Start-/End Date: -

Legal Case

show

Project information

show

Source

show