References
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Diederich, J. (2008). Rule Extraction from Support Vector Machines, Studies in Computational Intelligence, Vol. 80, Springer, Berlin/Heidelberg.
- 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.
- 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.
- 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.
- Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs, 3rd Edn., Springer-Verlag, London.
- 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.
- 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.
- Quinlan, J.R. (1986). Induction of decision trees, Machine Learning 1(1): 81-106.
- Quinlan, J.R. (1993). C4.5: Programs for Machine Learning, Morgan Kaufmann Publishers, San Francisco, CA.
- R¨atsch, G. and Sonnenburg, S. (2004). Accurate Splice Site Detection for Caenorhabditis Elegans, MIT Press, Cambridge, MA.
- R¨atsch, G., Sonnenburg, S. and Sch¨olkopf, B. (2005). RASE: Recognition of alternatively spliced exons in C. elegans, Bioinformatics 21(Suppl 1): i369-i377.
- 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.
- 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.
- 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.
- Sonnenburg, S. (2009). Machine Learning for Genomic Sequence Analysis, Ph.D. thesis, Technischen Universit¨at Berlin, Berlin.
- Sonnenburg, S., Schweikert, G., Philips, P., Behr, J. and R¨atsch, G. (2007). Accurate splice site prediction using support vector machines, BMC Bioinformatics 8(Suppl 10): S7.
- 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.