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Pairwise rational kernels obtained by automaton operations. (English) Zbl 1302.68178

Holzer, Markus (ed.) et al., Implementation and application of automata. 19th international conference, CIAA 2014, Giessen, Germany, July 30 – August 2, 2014. Proceedings. Berlin: Springer (ISBN 978-3-319-08845-7/pbk). Lecture Notes in Computer Science 8587, 332-345 (2014).
Summary: Pairwise rational kernels (PRKs) are the combination of pairwise kernels, which handle similarities between two pairs of entities, and rational kernels, which are based on finite-state transducer for manipulating sequence data. PRKs have been already used in bioinformatics problems, such as metabolic network prediction, to reduce computational costs in terms of storage and processing.
In this paper, we propose new pairwise rational kernels based on automaton and transducer operations. In this case, we define new operations over pairs of automata to obtain new rational kernels. We develop experiments using these new PRKs to predict metabolic networks. As a result, we obtain better accuracy and execution times when we compare them with previous kernels.
For the entire collection see [Zbl 1293.68026].

MSC:

68Q45 Formal languages and automata
92C42 Systems biology, networks

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