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Ensemble Modeling for Bio-medical Applications

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Part of the book series: Studies in Computational Intelligence ((SCI,volume 180))

Abstract

In this paper we propose to use ensembles of models constructed using methods of Statistical Learning. The input data for model construction consists of real measurements taken in physical system under consideration. Further we propose a program toolbox which allows the construction of single models as well as heterogenous ensembles of linear and nonlinear models types. Several well performing model types, among which are ridge regression, k-nearest neighbor models and neural networks have been implemented. Ensembles of heterogenous models typically yield a better generalization performance than homogenous ensembles. Additionally given are methods for model validation and assessment as well as adaptor classes performing transparent feature selection or random subspace training on large number of input variables. The toolbox is implemented in Matlab and C++ and available under the GPL. Several applications of the described methods and the numerical toolbox itself are described. These include ECG modeling, classification of activity in drug design and ...

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References

  1. Krogh, A., Vedelsby, J.: Neural network ensembles, cross validation, and active learning. In: Tesauro, G., Touretzky, D., Leen, T. (eds.) Advances in Neural Information Processing Systems, vol. 7, pp. 231–238. MIT Press, Cambridge (1995), citeseer.ist.psu.edu/krogh95neural.html

    Google Scholar 

  2. Perrone, M.P., Cooper, L.N.: When Networks Disagree: Ensemble Methods for Hybrid Neural Networks. In: Mammone, R.J. (ed.) Neural Networks for Speech and Image Processing, pp. 126–142. Chapman and Hall, Boca Raton (1993)

    Google Scholar 

  3. Hansen, L., Salamon, P.: Neural Network Ensembles. IEEE Trans. on Pattern Analysis and Machine Intelligence 12(10), 993–1001 (1990)

    Article  Google Scholar 

  4. Naftaly, U., Intrator, N., Horn, D.: Optimal ensemble averaging of neural networks. Network, Comp. Neural Sys. 8, 283–296 (1997)

    Article  MATH  Google Scholar 

  5. Breiman, L., Friedman, J.H., Olshen, R.A., Stone, C.J.: Classification and Regression Trees. Wadsworth International Group, Belmont (1984)

    MATH  Google Scholar 

  6. Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning. Springer Series in Statistics. Springer, Heidelberg (2001)

    MATH  Google Scholar 

  7. Krogh, A., Sollich, P.: Statistical mechanics of ensemble learning. Physical Review E 55(1), 811–825 (1997)

    Article  Google Scholar 

  8. Breiman, L.: Bagging predictors. Machine Learning 24(2), 123–140 (1996), citeseer.ist.psu.edu/breiman96bagging.html

    MATH  MathSciNet  Google Scholar 

  9. Merkwirth, C., Ogorzalek, M., Wichard, J.: Stochastic gradient descent training of ensembles of dt-cnn classifiers for digit recognition. In: Proceedings of the European Conference on Circuit Theory and Design ECCTD 2003, Kraków, Poland, vol. 2, pp. 337–341 (September 2003)

    Google Scholar 

  10. Wichard, J., Ogorzałek, M.: Iterated time series prediction with ensemble models. In: Proceedings of the 23rd International Conference on Modelling Identification and Control (2004)

    Google Scholar 

  11. Suykens, J., Vandewalle, J. (eds.): Nonlinear Modeling - Advanced Black–Box Techniques. Kluwer Academic Publishers, Dordrecht (1998)

    Google Scholar 

  12. Cohen, S., Intrator, N.: A hybrid projection based and radial basis function architecture. In: Kittler, J., Roli, F. (eds.) MCS 2000. LNCS, vol. 1857, pp. 147–155. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  13. Merkwirth, C., Lengauer, T.: Automatic generation of complementary descriptors with molecular graph networks (2004)

    Google Scholar 

  14. Weislow, O., Kiser, R., Fine, D., Bader, J., Shoemaker, R., Boyd, M.: New soluble formazan assay for hiv-1 cytopathic effects: application to high flux screening of synthetic and natural products for aids antiviral activity. J. Nat. Cancer Inst. 81, 577–586 (1989)

    Article  Google Scholar 

  15. Deshpande, M., Kuramochi, M., Karypis, G.: Frequent sub-structure-based approaches for classifying chemical compounds. In: Proceedings of the Third IEEE International Conference on Data Mining ICDM 2003, Melbourne, Florida, pp. 35–42 (November 2003)

    Google Scholar 

  16. Wilton, D., Willett, P., Lawson, K., Mullier, G.: Comparison of ranking methods for virtual screening in lead-discovery programs. J. Chem. Inf. Comput. Sci. 43, 469–474 (2003)

    Google Scholar 

  17. Rothfuss, A., Steger-Hartmann, T., Heinrich, N., Wichard, J.: Computational prediction of the chromosome-damaging potential of chemicals. Chemical Research in Toxicology 19(10), 1313–1319 (2006)

    Article  Google Scholar 

  18. Kirkland, D., Aardema, M., Henderson, L., Muller, L.: Evaluation of the ability of a battery of three in vitro genotoxicity tests to discriminate rodent carcinogens and non-carcinogens. Mutat. Res. 584, 1–256 (2005)

    Google Scholar 

  19. Snyder, R.D., Pearl, G.S., Mandakas, G., Choy, W.N., Goodsaid, F., Rosenblum, I.Y.: Assessment of the sensitivity of the computational programs DEREK, TOPKAT and MCASE in the prediction of the genotoxicity of pharmaceutical molecules. EnViron. Mol. Mutagen. 43, 143–158 (2004)

    Article  Google Scholar 

  20. Todeschini, R.: Dragon Software, http://www.talete.mi.it/dragon_exp.htm

  21. Breiman, L.: Arcing classifiers. The Annals of Statistics 26(3), 801–849 (1998), http://citeseer.nj.nec.com/breiman98arcing.html

    Article  MATH  MathSciNet  Google Scholar 

  22. Serra, J.R., Thompson, E.D., Jurs, P.C.: Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure. Chem. Res. Toxicol. 16, 153–163 (2003)

    Article  Google Scholar 

  23. Li, H., Ung, C., Yap, C., Xue, Y., Li, Z., Cao, Z., Chen, Y.: Prediction of genotoxicity of chemical compounds by statistical learning methods. Chem. Res. Toxicol. 18, 1071–1080 (2005)

    Article  Google Scholar 

  24. McNames, J.: Innovations in Local Modeling for Time Series Prediction, Ph.D. Thesis, Stanford University (1999)

    Google Scholar 

  25. Norgaard, M.: Neural Network Based System Identification Toolbox, Tech. Report. 00-E-891, Department of Automation, Technical University of Denmark (2000), http://www.iau.dtu.dk/research/control/nnsysid.html

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Merkwirth, C., Wichard, J., Ogorzałek, M.J. (2009). Ensemble Modeling for Bio-medical Applications. In: Mitkowski, W., Kacprzyk, J. (eds) Modelling Dynamics in Processes and Systems. Studies in Computational Intelligence, vol 180. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92203-2_9

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  • DOI: https://doi.org/10.1007/978-3-540-92203-2_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-92202-5

  • Online ISBN: 978-3-540-92203-2

  • eBook Packages: EngineeringEngineering (R0)

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