Semi-supervised Protein Classification Using Cluster Kernels

A key issue in supervised protein classification is the representation of input sequencesof amino acids. Recent work using string kernels for protein datahas achieved state-of-the-art classification performance. However, suchrepresentations are based only on labeled data -- examples with known 3D structures, organized into structural classes -- while in practice, unlabeled data is far more plentiful. In this work, we develop simpleand scalable cluster kernel techniques for incorporating unlabeled datainto the representation of protein sequences. We show that our methods greatly improve the classification performance of string kernels andoutperform standard approaches for using unlabeled data, such as adding close homologs of the positive examples to the training data. We achieve equal or superior performance to previously presented cluster kernel methods while achieving far greater computational efficiency.