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Christian Widmer, Nora Toussaint, Yasemin Altun, Oliver Kohlbacher, and Gunnar Rätsch (2010)
Novel Machine Learning Methods for MHC Class I Binding Prediction
In: Proc. Pattern Recognition in Bioinformatics, Springer. Lecture Notes in Computer Science.
MHC class I molecules are key players in the human immune system.
They bind small peptides derived from intracellular proteins and present them
on the cell surface for surveillance by the immune system.
Prediction of such MHC class I binding peptides is a vital step in
the design of peptide-based vaccines and therefore one of the major problems in
computational immunology. Thousands of different types of MHC class I molecules exist,
each displaying a distinct binding specificity. The lack of sufficient training data
for the majority of these molecules hinders the application of Machine Learning
to this problem.
We propose two approaches to improve the predictive power of kernel-based Machine Learning methods
for MHC class I binding prediction: First, a modification of the Weighted Degree string kernel that
allows for the incorporation of amino acid properties. Second, we propose an enhanced Multitask
kernel and an optimization procedure to fine-tune its kernel parameters.
The combination of both approaches yields improved performance, which we demonstrate on the
IEDB benchmark data set.
