Abstract
Computational intelligence poses several possibilities in Bioinformatics, particularly by generating low-cost, low-precision, good solutions. Rough sets promise to open up an important dimension in this direction. The present article surveys the role of artificial neural networks, fuzzy sets and genetic algorithms, with particular emphasis on rough sets, in Bioinformatics. Since the work entails processing huge amounts of incomplete or ambiguous biological data, the knowledge reduction capability of rough sets, learning ability of neural networks, uncertainty handling capacity of fuzzy sets and searching potential of genetic algorithms are synergistically utilized.
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
Baldi, P., Brunak, S.: Bioinformatics: The Machine Learning Approach. Adaptive Computation and Machine Learning, The MIT Press, Cambridge (2001)
Special Issue on Bioinformatics. IEEE Computer 35 (2002)
Special Issue on Bioinformatics, Part I: Advances and Challenges. Proceedings of the IEEE 90 (2002)
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215, 403–410 (1990)
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25, 3389–3402 (1997)
Zadeh, L.A.: Fuzzy logic, neural networks, and soft computing. Communications of the ACM 37, 77–84 (1994)
Mitra, S., Acharya, T.: Data Mining: Multimedia, Soft Computing, and Bioinformatics. John Wiley, New York (2003)
Haykin, S.: Neural Networks: A Comprehensive Foundation. Macmillan College Publishing Co. Inc, New York (1994)
Goldberg, D.E.: Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, Reading (1989)
Qian, N., Sejnowski, T.: Predicting the secondary structure of globular proteins using neural network models. Journal of Molecular Biology 202, 865–884 (1988)
Rost, B., Sander, C.: Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology 232, 584–599 (1993)
Riis, S.K., Krogh, A.: Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. Journal of Computational Biology 3, 163–183 (1996)
Herrero, J., Valencia, A., Dopazo, J.: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17, 126–136 (2001)
Cho, S.B., Ryu, J.: Classifying gene expression data of cancer using classifier ensemble with mutually exclusive features. Proceedings of the IEEE 90, 1744–1753 (2002)
Fogel, G., Corne, D. (eds.): Evolutionary Computation in Bioinformatics. Morgan Kaufmann, San Francisco (2002)
Schulze-Kremer, S.: Genetic algorithms for protein tertiary structure prediction. In: Männer, R., Manderick, B. (eds.) Parallel Problem Solving from Nature II, pp. 391–400. North Holland, Amsterdam (1992)
Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor, R.: Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology 267, 727–748 (1997)
Deb, K., Raji Reddy, A.: Reliable classification of two-class cancer data using evolutionary algorithms. BioSystems 72, 111–129 (2003)
Mitra, S.: An evolutionary rough partitive clustering. Pattern Recognition Letters 25, 1439–1449 (2004)
Torkkola, K., Gardner, R.M., Kaysser-Kranich, T., Ma, C.: Self-organizing maps in mining gene expression data. Information Sciences 139, 79–96 (2001)
Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Smitrovsky, E., Lander, E.S., Golub, T.R.: Interpreting patterns of gene expression with self-organizing maps: Methods and applications to hematopoietic differentiation. In: Proceedings of National Academy of Sciences, USA 96, 2907–2912 (1999)
Futschik, M.E., Reeve, A., Kasabov, N.: Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissue. Artificial Intelligence in Medicine 28, 165–189 (2003)
Uberbacher, E.C., Xu, Y., Mural, R.J.: Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol 266, 259–281 (1996)
Larsen, N.I., Engelbrecht, J., Brunak, S.: Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal. Nucleic Acids Res 23, 1223–1230 (1995)
Pedersen, A.G., Nielsen, H.: Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis. Ismb 5, 226–233 (1997)
Towell, G.G., Shavlik, J.W.: Knowledge-based artificial neural networks. Artificial Intelligence 70, 119–165 (1994)
Opitz, D.W., Shavlik, J.W.: Connectionist theory refinement: Genetically searching the space of network topologies. Journal of Artificial Intelligence Research 6, 177–209 (1997)
Ma, Q., Wang, J.T.L., Shasha, D., Wu, C.H.: DNA sequence classification via an expectation maximization algorithm and neural networks: A case study. IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews 31, 468–475 (2001)
Browne, A., Hudson, B.D., Whitley, D.C., Ford, M.G., Picton, P.: Biological data mining with neural networks: Implementation and application of a flexible decision tree extraction algorithm to genomic problem domains. Neurocomputing 57, 275–293 (2004)
Setiono, R.: Extracting rules from neural networks by pruning and hidden-unit splitting. Neural Computation 9, 205–225 (1997)
Hanke, J., Reich, J.G.: Kohonen map as a visualization tool for the analysis of protein sequences: Multiple alignments, domains and segments of secondary structures. Comput Applic Biosci 6, 447–454 (1996)
Cai, Y.D., Yu, H., Chou, K.C.: Artificial neural network method for predicting HIV protease cleavage sites in protein. J. Protein Chem. 17, 607–615 (1998)
Cai, Y.D., Yu, H., Chou, K.C.: Prediction of beta-turns. J. Protein Chem. 17, 363–376 (1998)
Ferran, E.A., Pflugfelder, B., Ferrara, P.: Self-organized neural maps of human protein sequences. Protein Sci. 3, 507–521 (1994)
Wang, H.C., Dopazo, J., de la Fraga, L.G., Zhu, Y.P., Carazo, J.M.: Self-organizing tree-growing network for the classification of protein sequences. Protein Sci. 7, 2613–2622 (1998)
Wang, H.C., Dopazo, J., Carazo, J.M.: Self-organizing tree-growing network for classifying amino acids. Bioinformatics 14, 376–377 (1998)
Chou, P., Fasmann, G.: Prediction of the secondary structure of proteins from their amino acid sequence. Advances in Enzymology 47, 45–148 (1978)
Bohr, H., Bohr, J., Brunak, S., Cotterill, R.M.J., Fredholm, H.: A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Letters 261, 43–46 (1990)
Lund, O., Frimand, K., Gorodkin, J., Bohr, H., Bohr, J., Hansen, J., Brunak, S.: Protein distance constraints predicted by neural networks and probability distance functions. Protein Eng. 10, 1241–1248 (1997)
Notredame, C., Higgins, D.G.: SAGA: Sequence alignment by genetic algorithm. Ucleic Acids Research 24, 1515–1524 (1996)
Notredame, C., Holm, L., Higgins, D.G.: COFFEE: An objective function for multiple sequence alignments. Bioinformatics 14, 407–422 (1998)
Deb, K., Agarwal, S., Pratap, A., Meyarivan, T.: A fast elitist non-dominated sorting genetic algorithm for multi-objective optimization: NSGA-II. In: Proceedings of the Parallel Problem Solving from Nature VI Conferences, pp. 849–858 (2000)
Pawlak, Z.: Rough Sets, Theoretical Aspects of Reasoning about Data. Kluwer Academic, Dordrecht (1991)
Skowron, A., Rauszer, C.: The discernibility matrices and functions in information systems. In: Slowiński, R. (ed.) Intelligent Decision Support, Handbook of Applications and Advances of the Rough Sets Theory, pp. 331–362. Kluwer Academic, Dordrecht (1992)
Midelfart, H., Lægreid, A., Komorowski, J.: Classification of gene expression data in an ontology. In: Crespo, J.L., Maojo, V., Martin, F. (eds.) ISMDA 2001. LNCS, vol. 2199, pp. 186–194. Springer, Heidelberg (2001)
Midelfart, H., Komorowski, J., Nørsett, K., Yadetie, F., Sandvik, A.K., Lægreid, A.: Learning rough set classifiers from gene expressions and clinical data. Fundamenta Informaticae 53, 155–183 (2002)
Lingras, P., West, C.: Interval set clustering of Web users with rough k-means. Technical Report No. 2002-002, Dept. of Mathematics and Computer Science, St. Mary’s University, Halifax, Canada (2002)
Wroblewski, J.: Finding minimal reducts using genetic algorithms. Technical Report 16/95, Warsaw Institute of Technology - Institute of Computer Science, Poland (1995)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mitra, S. (2005). Computational Intelligence in Bioinformatics. In: Peters, J.F., Skowron, A. (eds) Transactions on Rough Sets III. Lecture Notes in Computer Science, vol 3400. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11427834_6
Download citation
DOI: https://doi.org/10.1007/11427834_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25998-5
Online ISBN: 978-3-540-31850-7
eBook Packages: Computer ScienceComputer Science (R0)