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Graph kernel encoding substituents relative positioning

Benoit Gauzere &
Luc Brun &
Didier Villemin.
Chemoinformatics aims to predict molecular properties using informational methods. Computer science's research fields concerned by this domain are machine learning and graph theory. An interesting approach consists in using graph kernels which allow to combine graph theory and machine learning frameworks. Graph kernels allow to define a similarity measure between molecular graphs corresponding to a scalar product in some Hilbert space. Most of existing graph kernels proposed in chemoinformatics do not allow to explicitly encode cyclic information, hence limiting the efficiency of these approaches. In this paper, we propose to define a cyclic representation encoding the relative positioning of substituents around a cycle. We also propose a graph kernel taking into account this information. This contribution has been tested on three classification problems proposed in chemoinformatics.