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Molecular substructure mining is currently an intensively studied research area. In this paper we present an implementation of an algorithm for finding frequent substructures in a set of molecules, which may also be used to find substructures that discriminate well between a focus and a complement group. In addition to the basic algorithm, we discuss advanced pruning techniques, demonstrating their effectiveness with experiments on two publicly available molecular data sets, and briefly mention some other extensions.
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Borgelt et al. (2005) studied this question.
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