Using Operator Equalisation for Prediction of Drug Toxicity with Genetic Programming

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Predicting the toxicity of new potential drugs is a fundamental step in the drug design process. Recent contributions have shown that, even though Genetic Programming is a promising method for this task, the problem of predicting the toxicity of molecular compounds is complex and difficult to Solve. In particular, when executed for predicting drug toxicity, Genetic Programming undergoes the well-known phenomenon of bloat, i.e. the growth in code size during the evolutionary process without a corresponding improvement in fitness. We hypothesize that this might cause overfitting and thus prevent the method from discovering simpler and potentially more general solutions. For this reason, in this paper we investigate two recently defined variants of the operator equalization bloat control method for Genetic Programming. We show that these two methods are bloat free also when executed oil this complex problem. Nevertheless, overfitting still remains an issue. Thus, contradicting the generalized idea that bloat and overfitting are strongly related, we argue that the two phenomena are independent from each other and that eliminating bloat does not necessarily eliminate overfitting.
Original languageUnknown
Title of host publicationProgress in Artificial Intelligence, Proceedings
EditorsLS Lopes, N Lau, P Mariano, LM Rocha
Place of PublicationBerlin
ISBN (Print)0302-9743 978-3-642-04685-8
Publication statusPublished - 1 Jan 2009

Publication series

NameLecture Notes in Artificial Intelligence
PublisherSpringer-Verlag Berlin

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