Abstract
Genetic programming (GP) based data fusion and AdaBoost can both improve in vitro prediction of Cytochrome P450 activity by combining artificial neural networks (ANN). Pharmaceutical drug design data provided by high throughput screening (HTS) is used to train many base ANN classifiers. In data mining (KDD) we must avoid over fitting. The ensembles do extrapolate from the training data to other unseen molecules. I.e. they predict inhibition of a P450 enzyme by compounds unlike the chemicals used to train them. Thus the models might provide in silico screens of virtual chemicals as well as physical ones from Glaxo SmithKline (GSK)’s cheminformatics database. The receiver operating characteristics (ROC) of boosted and evolved ensemble are given.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Peter J. Angeline. Multiple interacting programs: A representation for evolving complex behaviors. Cybernetics and Systems, 29(8):779–806, November 1998.
Ken Binmore. Fun and Games. D. C. Heath, Lexington, MA, USA, 1990.
Leo Breiman. Bagging predictors. Machine Learning, 24:123–140, 1996.
Chawla et al., 2002._N. V. Chawla, K. W. Bowyer, L. O. Hall, and W. P. Kegelmeyer. SMOTE: synthetic minority over-sampling technique. Journal of Artificial Intelligence Research, 16:321–357, 2002.
Yoav Freund and Robert E. Schapire. Experiments with a new boosting algorithm. In Machine Learning: Proceedings of the thirteenth International Conference, pages 148–156. Morgan Kaufmann, 1996.
Chris Gathercole and Peter Ross. Dynamic training subset selection for supervised learning in genetic programming. In Yuval Davidor, Hans-Paul Schwefel, and Reinhard Männer, editors, Parallel Problem Solving from Nature III, volume 866 of LNCS, pages 312–321, Jerusalem, 9-14 October 1994. Springer-Verlag.
Ajith H. Gunatilaka and Brian A. Baertlein. Featurelevel and decision level fusion of noncoincidently sampled sensors for land mine detection. IEEE Transactions on Pattern Analysis and Machine Intelligence, 23(6):577–589, June 2001.
Jacobs et al., 1991._Robert A. Jacobs, Michael I. Jordon, Steven J. Nowlan, and Geoffrey E. Hinton. Adaptive mixtures of local experts. Neural Computation, 3:79–87, 1991.
Gareth Jones. Genetic and evolutionary algorithms. In Paul von Rague, editor, Encyclopedia of Computational Chemistry. John Wiley and Sons, 1998.
Josef Kittler and Fabio Roli, editors. Second International Conference on Multiple Classifier Systems, volume 2096 of LNCS, Cambridge, 2–4 July 2001. Springer Verlag.
Arthur K. Kordon and Guido F. Smits. Soft sensor development using genetic programming. In Lee Spector et al., editors, Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), pages 1346–1351, San Francisco, California, USA, 7-11 July 2001. Morgan Kaufmann.
M. A. Kupinski and M. A. Anastasio. Multiobjective genetic optimization of diagnostic classifiers with implications for generating receiver operating characteristic curves. IEEE Transactions on Medical Imaging, 18(8):675–685, Aug 1999.
Kupinski et al., 2000._Matthew A. Kupinski, Mark A. Anastasio, and Maryellem L. Giger. Multiobjective genetic optimization of diagnostic classifiers used in the computerized detection of mass lesions in mammography. In Kenneth M. Hanson, editor, SPIE Medical Imaging Conference, volume 3979, San Diego, California, 2000.
W. B. Langdon and B. F. Buxton. Genetic programming for combining classifiers. In Lee Spector et al., editors, Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), pages 66–73, San Francisco, California, USA, 7-11 July 2001. Morgan Kaufmann.
W. B. Langdon and B. F. Buxton. Genetic programming for improved receiver operating characteristics. In Josef Kittler and Fabio Roli, editors, Second International Conference on Multiple Classifier System, volume 2096 of LNCS, pages 68–77, Cambridge, 2-4 July 2001. Springer Verlag.
William B. Langdon and Bernard F. Buxton. Evolving receiver operating characteristics for data fusion. In Julian F. Miller et al., editors, Genetic Programming, Proceedings of EuroGP’2001, volume 2038 of LNCS, pages 87–96, Lake Como, Italy, 18-20 April 2001. Springer-Verlag.
Langdon et al., 1999._William B. Langdon, Terry Soule, Riccardo Poli, and James A. Foster. The evolution of size and shape. In Lee Spector, William B. Langdon, UnaMay O’Reilly, and Peter J. Angeline, editors, Advances in Genetic Programming 3, chapter 8, pages 163–190. MIT Press, 1999.
Langdon et al., 2001._W. B. Langdon, S. J. Barrett, and B. F. Buxton. Genetic programming for combining neural networks for drug discovery. In Rajkumar Roy et al., editors, Soft Computing and Industry Recent Applications, pages 597–608. Springer-Verlag, 10-24 September 2001. Published 2002.
Langdon et al., 2002._William B. Langdon, S. J. Barrett, and B. F. Buxton. Combining decision trees and neural networks for drug discovery. In James A. Foster et al., editors, Genetic Programming, Proceedings of the 5th European Conference, EuroGP 2002, volume 2278 of LNCS, pages 60–70, Kinsale, Ireland, 3-5 April 2002. Springer-Verlag.
William B. Langdon. Genetic Programming and Data Structures. Kluwer, 1998.
William B. Langdon. Size fair and homologous tree genetic programming crossovers. Genetic Programming and Evolvable Machines, 1(1/2):95–119, April 2000.
David W. Opitz and Jude W. Shavlik. Actively searching for an effective neural-network ensemble. Connection Science, 8(3–4):337–353, 1996.
Foster Provost and Tom Fawcett. Robust classification for imprecise environments. Machine Learning, 42(3):203–231, March 2001.
Holger Schwenk and Yoshua Bengio. Boosting neural networks. Neural Computation, 12(8):1869–1887, 2000.
Scott et al., 1998._M. J. J. Scott, M. Niranjan, and R. W. Prager. Realisable classifiers: Improving operating performance on variable cost problems. In Paul H. Lewis and Mark S. Nixon, editors, Proceedings of the Ninth British Machine Vision Conference, volume 1, pages 304–315, University of Southampton, UK, 14-17 September 1998.
Terence Soule. Voting teams: A cooperative approach to non-typical problems using genetic programming. In Wolfgang Banzhaf et al., editors, Proceedings of the Genetic and Evolutionary Computation Conference, volume 1, pages 916–922, Orlando, Florida, USA, 13-17 July 1999. Morgan Kaufmann.
Swets et al., 2000._John A. Swets, Robyn M. Dawes, and John Monahan. Better decisions through science. Scientific American, 283(4):70–75, October 2000.
Peter D. Turney. Cost-sensitive classification: Empirical evaluation of a hybrid genetic decision tree induction algorithm. Journal of Artificial Intelligence Research, 2:369–409, 1995.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Langdon, W.B., Barrett, S.J., Buxton, B.F. (2003). Comparison of AdaBoost and Genetic Programming for Combining Neural Networks for Drug Discovery. In: Cagnoni, S., et al. Applications of Evolutionary Computing. EvoWorkshops 2003. Lecture Notes in Computer Science, vol 2611. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36605-9_9
Download citation
DOI: https://doi.org/10.1007/3-540-36605-9_9
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-00976-4
Online ISBN: 978-3-540-36605-8
eBook Packages: Springer Book Archive