A probabilistic framework for mismatch and profile string kernels

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Description/Abstract

There has recently been numerous applications of kernel methods in the field of bioinformatics. In particular, the problem of protein homology has served as a benchmark for the performance of many new kernels which operate directly on strings (such as amino-acid sequences). Several new kernels have been developed and successfully applied to this type of data, including spectrum, string, mismatch, and profile kernels. In this paper we introduce a general probabilistic framework for string kernels which uses the fisher-kernel approach and includes spectrum, mismatch and profile kernels, among others, as special cases. The use of a probabilistic model however provides additional flexibility both in definition and for the re-weighting of features through feature selection methods, prior knowledge or semi-supervised approaches which use data repositories such as BLAST. We give details of the framework and also give preliminary experimental results which show the applicability of the technique.