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A New Model for Classifying DNA Code Inspired by Neural Networks and FSA

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Advances in Knowledge Acquisition and Management (PKAW 2006)

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Abstract

This paper introduces a new model of classifiers CL(V,E,ℓ,r) designed for classifying DNA sequences and combining the flexibility of neural networks and the generality of finite state automata. Our careful and thorough verification demonstrates that the classifiers CL(V,E,ℓ,r) are general enough and will be capable of solving all classification tasks for any given DNA dataset. We develop a minimisation algorithm for these classifiers and include several open questions which could benefit from contributions of various researchers throughout the world.

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References

  1. Baldi, P., Brunak, S.: Bioinformatics: The Machine Learning Approach. MIT Press, Cambridge (2001)

    MATH  Google Scholar 

  2. Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms. The MIT Press, Cambridge (2001)

    MATH  Google Scholar 

  3. Dazeley, R.P., Kang, B.H.: Weighted MCRDR: deriving information about relationships between classifications. In: MCRDR, AI 2003: Advances in Artificial Intelligence, Perth, Australia, pp. 245–255 (2003)

    Google Scholar 

  4. Dazeley, R.P., Kang, B.H.: An online classification and prediction hybrid system for knowledge discovery in databases. In: Proc. AISAT 2004, The 2nd Internat. Conf. Artificial Intelligence in Science and Technology, Hobart, Tasmania, pp. 114–119 (2004)

    Google Scholar 

  5. Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G.: Biological Sequence Analysis. Cambridge University Press, Cambridge (1999)

    Google Scholar 

  6. Eilenberg, S.: Automata, Languages, and Machines, vol. A,B. Academic Press, New York (1974)

    MATH  Google Scholar 

  7. Gallian, J.A.: Graph labeling. Electronic J. Combinatorics, Dynamic Survey DS6, 148 (January 20, 2005), http://www.combinatorics.org

  8. Gusfield, D.: Algorithms on Strings, Trees, and Sequences. In: Computer Science and Computational Biology, Cambridge University Press, Cambridge (1997)

    Google Scholar 

  9. Holub, J., Iliopoulos, C.S., Melichar, B., Mouchard, L.: Distributed string matching using finite automata, Combinatorial Algorithms. In: AWOCA 1999, Perth, pp. 114–127 (1999)

    Google Scholar 

  10. Jones, N.C., Pevzner, P.A.: An Introduction to Bioinformatics Algorithms. MIT Press, Cambridge (2004), http://www.bioalgorithms.info/

    Google Scholar 

  11. Kang, B.H.: Pacific Knowledge Acquisition Workshop, Auckland, New Zealand (2004)

    Google Scholar 

  12. Kelarev, A.V.: Ring Constructions and Applications. World Scientific, Singapore (2002)

    MATH  Google Scholar 

  13. Kelarev, A.V.: Graph Algebras and Automata. Marcel Dekker, New York (2003)

    MATH  Google Scholar 

  14. Kelarev, A.V., Miller, M., Sokratova, O.V.: Directed graphs and closure properties for languages. In: Baskoro, E.T. (ed.) Proc.12 Australasian Workshop on Combinatorial Algorithms, Putri Gunung Hotel, Lembang, Bandung, Indonesia, July 14–17, pp. 118–125 (2001)

    Google Scholar 

  15. Kelarev, A.V., Miller, M., Sokratova, O.V.: Languages recognized by two-sided automata of graphs. Proc. Estonian Akademy of Science 54(1), 46–54 (2005)

    MATH  MathSciNet  Google Scholar 

  16. Kelarev, A.V., Sokratova, O.V.: Languages recognized by a class of finite automata. Acta Cybernetica 15, 45–52 (2001)

    MATH  MathSciNet  Google Scholar 

  17. Kelarev, A.V., Sokratova, O.V.: Directed graphs and syntactic algebras of tree languages. J. Automata, Languages & Combinatorics 6(3), 305–311 (2001)

    MATH  MathSciNet  Google Scholar 

  18. Kelarev, A.V., Sokratova, O.V.: Two algorithms for languages recognized by graph algebras. Internat. J. Computer Math. 79(12), 1317–1327 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  19. Kelarev, A.V., Sokratova, O.V.: On congruences of automata defined by directed graphs. Theoret. Computer Science 301, 31–43 (2003)

    Article  MATH  MathSciNet  Google Scholar 

  20. Kelarev, A.V., Trotter, P.G.: A combinatorial property of automata, languages and their syntactic monoids. In: Proceedings of the Internat. Conf. Words, Languages and Combinatorics III, Kyoto, Japan, pp. 228–239 (2003)

    Google Scholar 

  21. Lee, K.H., Kay, J., Kang, B.H.: Keyword association network: a statistical multi-term indexing approach for document categorization. In: Proc. Fifth Australasian Document Computing Symposium, Brisbane, Australia, pp. 9–16 (2000)

    Google Scholar 

  22. Lee, K., Kay, J., Kang, B.H.: KAN and RinSCut: lazy linear classifier and rank-in-score threshold in similarity-based text categorization. In: Proc. ICML-2002 Workshop on Text Learning, University of New South Wales, Sydney, Australia, pp. 36–43 (2002)

    Google Scholar 

  23. Lee, K.H., Kay, J., Kang, B.H., Rosebrock, U.: A Comparative Study on Statistical Machine Learning Algorithms and Thresholding Strategies for Automatic Text Categorization. In: Ishizuka, M., Sattar, A. (eds.) PRICAI 2002. LNCS (LNAI), vol. 2417, pp. 444–453. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  24. Lee, K.H., Kang, B.H.: A new framework for uncertainty sampling: exploiting uncertain and positive-certain examples in similarity-based text classification. In: Proc. Internat. Conf. on Information Technology: Coding and Computing (ITCC 2004), Las Vegas, Nevada, p. 12 (2004)

    Google Scholar 

  25. Luger, G.F.: Artificial Intelligence. Structures and Strategies for Complex Problem Solving. Addison-Wesley, Reading (2005)

    Google Scholar 

  26. Mount, D.: Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory (2001), http://www.bioinformaticsonline.org/

  27. Park, S.S., Kim, Y., Park, G., Kang, B.H., Compton, P.: Automated information mediator for HTML and XML Based Web information delivery service. In: Proc. 18th Australian Joint Conf. on Artificial Intelligence, Sydney, pp. 401–404 (2005)

    Google Scholar 

  28. Park, G.S., Kim, Y.S., Kang, B.H.: Synamic mobile content adaptation according to various delivery contexts. J. Security Engineering 2, 202–208 (2005)

    Google Scholar 

  29. Park, G.S., Kim, Y.T., Kim, Y., Kang, B.H.: SOAP message processing performance enhancement by simplifying system architecture. J. Security Engineering 2, 163–170 (2005)

    Google Scholar 

  30. Park, G.S., Park, S., Kim, Y., Kang, B.H.: Intelligent web document classification using incrementally changing training data Set. J. Security Engineering 2, 186–191 (2005)

    Google Scholar 

  31. Păun, G., Salomaa, A.: New Trends in Formal Languages. Springer, Berlin (1997)

    Google Scholar 

  32. Petrovskiy, M.: Probability Estimation in Error Correcting Output Coding Framework Using Game Theory. In: Zhang, S., Jarvis, R. (eds.) AI 2005. LNCS (LNAI), vol. 3809, pp. 186–196. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  33. Pin, J.E. (ed.): LITP 1988. LNCS, vol. 386. Springer, Heidelberg (1989)

    MATH  Google Scholar 

  34. Rozenberg, G., Salomaa, A.: Handbook of Formal Languages. In: Word, Language, Grammar, vol. 1, Springer, Berlin (1997)

    Google Scholar 

  35. Smyth, B.: Computing Patterns in Strings. Addison-Wesley, Reading (2003)

    Google Scholar 

  36. Tuga, M., Miller, M.: Δ-Optimum Exclusive Sum Labeling of Certain Graphs with Radius One. In: Akiyama, J., Baskoro, E.T., Kano, M. (eds.) IJCCGGT 2003. LNCS, vol. 3330, pp. 216–225. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  37. Sugeng, K.A., Miller, M., Slamin, Bača, M.: ( a, d)-Edge-Antimagic Total Labelings of Caterpillars. In: Akiyama, J., Baskoro, E.T., Kano, M. (eds.) IJCCGGT 2003. LNCS, vol. 3330, pp. 169–180. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  38. van Leeuwen, J.: Handbook of Theoretical Computer Science. In: Algorithms and Complexity, vol. A,B, Elsevier, Amsterdam (1990)

    Google Scholar 

  39. Witten, I.H., Frank, E.: Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations. Morgan Kaufmann, San Francisco (2005)

    Google Scholar 

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Kang, B., Kelarev, A., Sale, A., Williams, R. (2006). A New Model for Classifying DNA Code Inspired by Neural Networks and FSA. In: Hoffmann, A., Kang, Bh., Richards, D., Tsumoto, S. (eds) Advances in Knowledge Acquisition and Management. PKAW 2006. Lecture Notes in Computer Science(), vol 4303. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11961239_17

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  • DOI: https://doi.org/10.1007/11961239_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68955-3

  • Online ISBN: 978-3-540-68957-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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