Relevant cycle hypergraph representation for molecules

Abstract

Chemoinformatics aims to predict molecule's properties through informational methods. Some methods base their prediction model on the comparison of molecular graphs. Considering such a molecular representation, graph kernels provide a nice framework which allows to combine machine learning techniques with graph theory. Despite the fact that molecular graph encodes all structural information of a molecule, it does not explicitly encode cyclic information. In this paper, we propose a new molecular representation based on a hypergraph which explicitly encodes both cyclic and acyclic information into one molecular representation called relevant cycle hypergraph. In addition, we propose a similarity measure in order to compare relevant cycle hypergraphs and use this molecular representation in a chemoinformatics prediction problem. © 2013 Springer-Verlag.