The Levelwise Version Space Algorithm and its Application to Molecular Fragment Finding

Luc De Raedt, Stefan Kramer

Abstract:

A tight integration of Mitchell's version space algorithm with Agrawal et al.'s Apriori algorithm is presented. The algorithm can be used to generate patterns that satisfy a variety of constraints on data. Constraints that can be imposed on patterns include the generality relation among patterns and imposing a minimum or a maximum frequency on data sets of interest.

The theoretical framework is applied to an important application in chemo-informatics, i.e. that of finding fragments of interest within a given set of compounds. Fragments are linearly connected substructures of compounds. An implementation as well as preliminary experiments within the application are presented.