Kis: An automated attribute induction method for classification of dna sequences

International Journal of Applied Mathematics and Computer Science

Volumn 22, Issue 3, 2012, Pages 711-721

  Biedrzycki, Rafal ^a   Arabas, Jaroslaw ^a  

^a WARSAW UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

Annotation; Classification; Optimization; Patterns

Indexed keywords

ANNOTATION; COMMON FEATURES; DNA SEQUENCE RECOGNITION; DONOR AND ACCEPTOR; INDUCTION METHOD; PATTERNS; REFERENCE METHOD; SEQUENCE PATTERNS;

ALGORITHMS; CLASSIFICATION (OF INFORMATION); OPTIMIZATION;

DNA SEQUENCES;

EID: 84876726016     PISSN: None     EISSN: 1641876X     Source Type: Journal    
DOI: 10.2478/v10006-012-0053-2     Document Type: Article

References (23)

1. Baten, A.K.M.A., Chang, B.C.H., Halgamuge, S.K. and Li, J. (2006). Splice site identification using probabilistic parameters and SVMclassification, BMC Bioinformatics 7(Suppl 5): S15, DOI:10.1186/1471-2105-7-S5-S15. (Pubitemid 46443016)
2. Berget, S.M., Moore, C. and Sharp, P.A. (1977). Spliced segments at the 5' terminus of adenovirus 2 late mRNA, Proceedings of the National Academy of Sciences 74(8): 3171-3175. (Pubitemid 8180310)
3. Carrasco, R.C. and Oncina, J. (1994). Learning stochastic regular grammars by means of a state merging method, ICGI'94: Proceedings of the Second International Colloquium on Grammatical Inference and Applications, Alicante, Spain, pp. 139-152.
4. Chen, T.-M., Lu, C.-C. and Li,W.-H. (2005). Prediction of splice sites with dependency graphs and their expanded Bayesian networks, Bioinformatics 21(4): 471-482. (Pubitemid 40310234)
5. Davis, J. and Goadrich, M. (2006). The relationship between Precision-Recall and ROC curves, ICML'06: Proceedings of the 23rd International Conference on Machine Learning, Pittsburgh, PA, USA, pp. 233-240.
6. Deshpande, M. and Karypis, G. (2002). Evaluation of techniques for classifying biological sequences, Pacific-Asia Conference on Knowledge Discovery and Data Mining, Taipei, Taiwan, pp. 417-431.
7. Diederich, J. (2008). Rule Extraction from Support Vector Machines, Studies in Computational Intelligence, Vol. 80, Springer, Berlin/Heidelberg.
8. Durbin, R., Eddy, S.R., Krogh, A. and Mitchison, G. (1998). Biological Sequence Analysis-Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge.
9. Elsik, C.G., Worley, K.C., Zhang, L., Milshina, N.V., Jiang, H., Reese, J.T., Childs, K.L., Venkatraman, A., Dickens, C.M., Weinstock, G.M. and Gibbs, R.A. (2006). Community annotation: Procedures, protocols, and supporting tools, Genome Research 16(11): 1329-1333. (Pubitemid 44664674)
10. Kashiwabara, A.Y., Vieira, D.C.G., Machado-Lima, A. and Durham, A.M. (2007). Splice site prediction using stochastic regular grammars, GMR 6(1): 105-115. (Pubitemid 46740506)
11. Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs, 3rd Edn., Springer-Verlag, London.
12. Oncina, J. and Garcia, P. (1992). Inferring regular languages in polynomial update time, in A. Sanfeliu, N. P'erez de la Blanca and E. Vidal (Eds.), Pattern Recognition and Image Analysis, World Scientific Publishing, Singapore, pp. 49-61.
13. Pesole, G., Grillo, G., Larizza, A. and Liuni, S. (2000). The untranslated regions of eukaryotic mRNAs: Structure, function, evolution and bioinformatic tools for their analysis, Briefings in Bioinformatics 1(3): 236-249.
14. Quinlan, J.R. (1986). Induction of decision trees, Machine Learning 1(1): 81-106.
15. Quinlan, J.R. (1993). C4.5: Programs for Machine Learning, Morgan Kaufmann Publishers, San Francisco, CA.
16. Ratsch, G. and Sonnenburg, S. (2004). Accurate Splice Site Detection for Caenorhabditis Elegans, MIT Press, Cambridge, MA.
17. Ratsch, G., Sonnenburg, S. and Scholkopf, B. (2005). RASE: Recognition of alternatively spliced exons in C. elegans, Bioinformatics 21(Suppl 1): i369-i377. (Pubitemid 41794510)
18. Reese, M.G., Eeckman, F.H., Kulp, D. and Haussler, D. (1997). Improved splice site detection in Genie, Journal of Computational Biology 4(3): 311-324.
19. Ron, D., Singer, Y. and Tishby, N. (1996). The power of amnesia: Learning probabilistic automata with variable memory length, Machine Learning 25(2): 117-149. (Pubitemid 126724391)
20. Ron, D., Singer, Y. and Tishby, N. (1998). On the learnability and usage of acyclic probabilistic finite automata, Journal of Computer and System Sciences 56(2): 133-152. (Pubitemid 128415328)
21. Sonnenburg, S. (2009). Machine Learning for Genomic Sequence Analysis, Ph.D. thesis, Technischen Universit?at Berlin, Berlin.
22. Sonnenburg, S., Schweikert, G., Philips, P., Behr, J. and Ratsch, G. (2007). Accurate splice site prediction using support vector machines, BMC Bioinformatics 8(Suppl 10): S7.
23. Tickle, A., Andrews, R., Golea, M. and Diederich, J. (1998). The truth will come to light: Directions and challenges in extracting the knowledge embedded within trained artificial neural networks, IEEE Transactions on Neural Networks 9(6): 1057-1068. (Pubitemid 128742391)