Large-scale Protein-Protein Interaction prediction using novel kernel methods
by Xue-wen Chen, Bing Han, Jianwen Fang, Ryan J. Haasl
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 2, No. 2, 2008

Abstract: Knowledge of Protein-Protein Interactions (PPIs) can give us new insights into molecular mechanisms and properties of the cell. In this paper, we propose a novel domain-based kernel method to predict PPIs. A new kernel that measures the similarity between protein pairs based on a new feature representation is developed and applied to a large scale PPI database. Experimental results demonstrate its effectiveness. Furthermore, we evaluate the problem of cross-species PPI prediction and the effect of the number of negative samples on the performance of PPI predictions, which are two fundamental problems in most in silico PPI methods.

Online publication date: Sat, 28-Jun-2008

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