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An Automated Combination of Kernels for Predicting Protein Subcellular Localization


Conference Paper


Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions. While many predictive computational tools have been proposed, they tend to have complicated architectures and require many design decisions from the developer. Here we utilize the multiclass support vector machine (m-SVM) method to directly solve protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. We further propose a general class of protein sequence kernels which considers all motifs, including motifs with gaps. Instead of heuristically selecting one or a few kernels from this family, we utilize a recent extension of SVMs that optimizes over multiple kernels simultaneously. This way, we automatically search over families of possible amino acid motifs. We compare our automated approach to three other predictors on four different datasets, and show that we perform better than the current state of the art. Further, our method provides some insights as to which sequence motifs are most useful for determining subcellular ocalization, which are in agreement with biological reasoning.

Author(s): Ong, CS. and Zien, A.
Book Title: WABI 2008
Journal: Algorithms in Bioinformatics: 8th International Workshop (WABI 2008)
Pages: 186-197
Year: 2008
Month: September
Day: 0
Editors: Crandall, K. A., J. Lagergren
Publisher: Springer

Department(s): Empirical Inference
Bibtex Type: Conference Paper (inproceedings)

DOI: 10.1007/978-3-540-87361-7_16
Event Name: 8th Workshop on Algorithms in Bioinformatics
Event Place: Karlsruhe, Germany

Address: Berlin, Germany
Digital: 0
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

Links: PDF


  title = {An Automated Combination of Kernels for Predicting Protein Subcellular Localization},
  author = {Ong, CS. and Zien, A.},
  journal = {Algorithms in Bioinformatics: 8th International Workshop (WABI 2008)},
  booktitle = {WABI 2008},
  pages = {186-197},
  editors = {Crandall, K. A., J. Lagergren},
  publisher = {Springer},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  address = {Berlin, Germany},
  month = sep,
  year = {2008},
  month_numeric = {9}