On network-based kernel methods for protein-protein interactions with applications in protein functions prediction
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Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding (LLE) kernel method, diffusion kernel and laplacian kernel to uncover the relationship between proteins functions and protein-protein interactions (PPI). The author first construct kernels based on PPI networks, then apply support vector machine (SVM) techniques to classify proteins into different functional groups. The 5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chi-square methods. Finally, the authors conduct predictions of functions of some unknown genes and verify the preciseness of our prediction in part by the information of other data source.
Key wordsDiffusion kernel kernel method Laplacian kernel local linear embedding (LLE) kernel protein function prediction support vector machine.
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