Abstract
This paper proposes a hybrid algorithm that combines characteristics of both Genetic Programming (GP) and Genetic Algorithms (GAs), for discovering motifs in proteins and predicting their functional classes, based on the discovered motifs. In this algorithm, individuals are represented as IF-THEN classification rules. The rule antecedent consists of a combination of motifs automatically extracted from protein sequences. The rule consequent consists of the functional class predicted for a protein whose sequence satisfies the combination of motifs in the rule antecedent. The system can be used in two different ways. First, as a stand-alone classification system, where the evolved classification rules are directly used to predict the functional classes of proteins. Second, the system can be used just as an “attribute construction” method, discovering motifs that are given, as predictor attributes, to another classification algorithm. In this usage of the system, a classical decision tree induction algorithm was used as the classifier. The proposed system was evaluated in these two scenarios and compared with another Genetic Algorithm designed specifically for the discovery of motifs – and therefore used only as an attribute construction algorithm. This comparison was performed by mining an enzyme data set extracted from the Protein Data Bank. The best results were obtained when using the proposed hybrid GP/GA as an attribute construction algorithm and performing the classification (using the constructed attributes) with the decision tree induction algorithm.
This work was partially supported by the Brazilian National Research Council – CNPq, under research grant no. 309262/2007-0 to H.S. Lopes.
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References
Arakaki, A.K., Zhang, Y., Skolnick, J.: Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics 20, 1087–1096 (2004)
Ben-Hur, A., Brutlag, D.: Remote homology detection: a motif based approach. Bioinformatics 19, i26–i33 (2003)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research 28, 235–242 (2000)
Clare, A., King, R.D.: Machine learning of functional class from phenotype data. Bioinformatics 18, 160–166 (2002)
Fayyad, U.M., Piatetsky-Shapiro, G., Smyth, P.: From data mining to knowledge discovery: an overview. In: Fayyad, U.M., et al. (eds.) Advances in Knowledge Discovery and Data Mining, pp. 1–34 (1996)
Goldberg, D.E.: Genetic Algorithms in Search, Optimization & Machine Learning. Addison-Wesley, Reading (1989)
Han, J., Kamber, M.: Data Mining: Concepts and Techniques. Morgan Kaufmann, San Francisco (2001)
Holden, N., Freitas, A.A.: Hierarchical classification of protein function with ensembles of rules and particle swarm optimisation. Soft Computing 13, 259–272 (2009)
King, R.D., Karwath, A., Clare, A., Dehaspe, L.: The Utility of different representations of protein sequence for predicting functional class. Bioinformatics 17, 445–454 (2001)
Koza, J.R.: Genetic Programming: on the Programming of Computers by Means of Natural Selection. MIT Press, Cambridge (1992)
Kretschmann, K., Fleischmann, W., Apweiler, R.: Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on Swiss-Prot. Bioinformatics 17, 920–926 (2001)
Manning, A.M., Brass, A., Goble, C.A., Keane, J.A.: Clustering techniques in biological sequence analysis. In: Proceedings of the 1st European Symposium on Principles of Data Mining and Knowledge Discovery, pp. 315–322 (1997)
Maruo, M.H., Lopes, H.S., Delgado, M.R.B.S.: Self-adapting evolutionary parameters: encoding aspects for combinatorial optimization problems. In: Raidl, G.R., Gottlieb, J. (eds.) EvoCOP 2005. LNCS, vol. 3448, pp. 154–165. Springer, Heidelberg (2005)
Mirkin, B., Ritter, O.: A Feature-based approach to discrimination and prediction of protein folding groups. In: Suhai, S. (ed.) Genomics and Proteomics: Functional and Computational Aspects, pp. 157–177. Kluwer, Dordrecht (2000)
Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247, 536–540 (1995)
Quinlan, J.R.: C4.5: Programs for Machine Learning. Morgan Kaufmann, San Francisco (1993)
Sebban, M., Mokrousov, I., Rastogi, N., Sola, C.: A data mining approach to spacer oligonucleotide typing of mycobacterium tuberculosis. Bioinformatics 18, 235–243 (2002)
Tsunoda, D.F., Lopes, H.S.: Automatic motif discovery in an enzyme database using a genetic algorithm-based approach. Soft Computing 10, 325–330 (2006)
Tsunoda, D.F., Lopes, H.S., Freitas, A.A.: An evolutionary approach for motif discovery and transmembrane protein classification. In: Rothlauf, F., Branke, J., Cagnoni, S., Corne, D.W., Drechsler, R., Jin, Y., Machado, P., Marchiori, E., Romero, J., Smith, G.D., Squillero, G. (eds.) EvoWorkshops 2005. LNCS, vol. 3449, pp. 105–114. Springer, Heidelberg (2005)
Weinert, W.R., Lopes, H.S.: Neural networks for protein classification. Applied Bioinformatics 3, 41–48 (2004)
Weiss, G.M.: Learning with rare cases and small disjuncts. In: Proc. of Twelfth International Conference on Machine Learning, pp. 558–565 (1995)
Witten, I.H., Frank, E.: Data Mining: Practical Machine Learning Tools and Techniques, 2nd edn. Morgan Kaufmann, San Francisco (2005)
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Tsunoda, D.F., Lopes, H.S., Freitas, A.A. (2009). A Hybrid Evolutionary Approach for the Protein Classification Problem. In: Nguyen, N.T., Kowalczyk, R., Chen, SM. (eds) Computational Collective Intelligence. Semantic Web, Social Networks and Multiagent Systems. ICCCI 2009. Lecture Notes in Computer Science(), vol 5796. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04441-0_55
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