English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  An Automated Combination of Kernels for Predicting Protein Subcellular Localization

Zien, A., & Ong, C. (2007). An Automated Combination of Kernels for Predicting Protein Subcellular Localization. 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:
Zien, A1, Author           
Ong, CS1, Author           
Affiliations:
1Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              

Content

show
hide
Free keywords: -
 Abstract: Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions.We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We utilize an extension of the multiclass support vector machine (SVM)method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets, and show that we perform better than the current state of the art. Furthermore, our method provides some insights as to which features are most useful for determining subcellular localization, which are in agreement with biological reasoning.

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