Abstract
We examine some common threads between biological sequence analysis and AI methods, and propose a model of human language processing inspired in biological sequence replication and nucleotide bindings. It can express and implement both analysis and synthesis in the same stroke, much as biological mechanisms can analyse a string plus synthesize it elsewhere, e.g. for repairing damaged DNA substrings.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Barranco-Mendoza, A.: Stochastic and Heuristic Modelling for Analysis of the Growth of Pre-Invasive Lesions and for a Multidisciplinary Approach to Early Cancer Diagnosis. Ph.D. Thesis, Simon Fraser University, Burnaby, BC (2005)
Bavarian, M., Dahl, V.: Constraint-Based Methods for Biological Sequence Analysis. Journal of Universal Computing Science 12(11), 1500–1520 (2006)
Barranco-Mendoza, A., Persaoud, D.R., Dahl, V.: A property-based model for lung cancer diagnosis. RECOMB poster, 27–31 (2004)
Christiansen, H.: CHR as Grammar Formalism, a First Report. In: Apt, K.R., Bartak, R., Monfroy, E., Rossi, F. (eds.) Sixth Annual Workshop of the ERCIM Working Group on Constraints, Prague (2001)
Fruhwirth, T.: Theory and Practice of Constraint Handling Rules. In: Stuckey, P., Marriot, K. (eds.) Journal of Logic Pro., Special Issue on Constraint Logic Programming 37(1-3), 95–138 (1998)
King, R.D.: Applying inductive logic programming to predicting gene function. AI Mag. 25(1), 57–68 (2004)
King, R.D., Muggleton, S., Lewis, R.A., Sternberg, M.J.E.: Drug design by machine learning. Proc. Natl. Acad. Sci. 89, 11322–11326 (1992)
Muggleton, S., King, R.D., Sternberg, M.J.E.: Protein secondary structure prediction using logic-based machine learning. Protein Eng. 5, 647–657 (1992)
Rawling, C.J., Taylor, W.R., Nyakairo, J., Fox, J., Sternberg, M.J.E.: Reasoning about protein topology using the logic programming language PROLOG. J. Mol. Bio. 3(4), 151–157 (1985)
Searls, D.B.: The computational linguistics of biological sequences. In: Artificial intelligence and molecular biology, pp. 47–120. American Association for Artificial Intelligence (1993)
Woods, W.A.: An experimental parsing system for transition network grammars. In: Rustin, R. (ed.) Natural Language Processing, pp. 145–149. Algorithmics Press, New York (1973)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Dahl, V., Maharshak, E. (2009). DNA Replication as a Model for Computational Linguistics. In: Mira, J., Ferrández, J.M., Álvarez, J.R., de la Paz, F., Toledo, F.J. (eds) Methods and Models in Artificial and Natural Computation. A Homage to Professor Mira’s Scientific Legacy. IWINAC 2009. Lecture Notes in Computer Science, vol 5601. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02264-7_36
Download citation
DOI: https://doi.org/10.1007/978-3-642-02264-7_36
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02263-0
Online ISBN: 978-3-642-02264-7
eBook Packages: Computer ScienceComputer Science (R0)