Recurrent Kernel Networks Dexiong Chen Laurent Jacob Inria∗ CNRSy
[email protected] [email protected] Julien Mairal Inria∗
[email protected] Abstract Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data are available, models that allow end-to-end training such as neural networks are often preferred. Links between recurrent neural networks (RNNs) and substring kernels have recently been drawn, by formally showing that RNNs with specific activation functions were points in a reproducing kernel Hilbert space (RKHS). In this paper, we revisit this link by generalizing convolutional kernel networks—originally related to a relaxation of the mismatch kernel—to model gaps in sequences. It results in a new type of recurrent neural network which can be trained end-to-end with backpropagation, or without supervision by using kernel approximation techniques. We experimentally show that our approach is well suited to biological sequences, where it outperforms existing methods for protein classification tasks. 1 Introduction Learning from biological sequences is important for a variety of scientific fields such as evolution [8] or human health [16]. In order to use classical statistical models, a first step is often to map sequences to vectors of fixed size, while retaining relevant features for the considered learning task. For a long time, such features have been extracted from sequence alignment, either against a reference or between each others [3]. The resulting features are appropriate for sequences that are similar enough, but they become ill-defined when sequences are not suited to alignment.