Abstract
Rough set methods are often employed for reducting decision rules. The specific techniques involving rough sets can be carried out in a computational manner. However, they are quite demanding when it comes computing overhead. In particular, it becomes problematic to compute all minimal length decision rules while dealing with a large number of decision rules. This results in an NP-hard problem. To address this computational challenge, in this study, we propose a method of DNA rough-set computing composed of computational DNA molecular techniques used for decision rule reducts. This method can be effectively employed to alleviate the computational complexity of the problem.
This book chapter has been prepared on a basis of the results of the paper, entitled “A DNA-based algorithm for minimizing decision rules: a rough sets approach” to be published in IEEE Transactions on NanoBioscience at the end of 2011.
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
Adleman, L.M.: Computing with DNA: The manipulation of DNA to solve mathematical problems is redefining what is meant by computation. Scientific American 279(2), 34–41 (1998)
Burlage, R.S., Atlas, R., Stahl, D., Geesey, G., Sayler, G.: Techniques in microbial ecology, pp. 299–311. Oxford University Press Inc. (1998)
Burton, Z.F., Kaguni, J.M.: Experiments in molecularbiology: Biochemical applications, pp. 11–20. Academic Press (1997)
Cooper, N.G., Berg, P.: The human genome project: Deciphering the blueprint of heredity, pp. 48–54. University Science Books (1994)
Fitch, J.P.: An engineering introduction to biotechnology, pp. 43–60. SPIE Press (2002)
Goedken, E.R., Levitus, M., Johnson, A., Bustamante, C., O’Donnell, M., Kuriyan, J.: Fluorescence measurements on the E. coli DNA polymerase clamp loader: Implications for conformational changes during ATP and clamp binding. Journal of Molecular Biology 336(5), 1047–1059 (2004)
Greene, J.J., Rao, V.B.: Recombinant DNA principles and methodologies, pp. 126–134. Marcel Dekker Inc. (1996)
Grzymała-Busse, J.W.: A comparison of tree strategies to rule induction from data with numerical attributes. Electronic Notes in Theoretical Computer Science 82(4), 132–140 (2003)
Hartl, D.L., Jones, E.W.: Essential genetics: A genomics perspective, 3rd edn., pp. 90–412. Jones and Bartlett Publishers Inc. (2002)
Hartl, D.L., Jones, E.W.: Genetics: Analysis of genes and genomes, 7th edn., pp. 431–445. Jones and Bartlett Publishers Inc. (2009)
Jorgensen, W.L., Madura, J.D.: Temperature and size dependence for Monte Carlo simulation of TIP4P water. Molecular Physics: An International Journal at the Interface between Chemistry and Physics 56(6), 1381–1392 (1985)
Kari, L., Paun, G., Rozenberg, G., Salomaa, A., Yu, S.: DNA computing, sticker systems, and universality. Acta Informatica 35(5), 401–420 (1998)
Kleinberg, J., Tardos, E.: Algorithm design, pp. 29–207. Pearson Education Inc. (2006)
Matejtschuk, P.: Affinity separations: A practical approach, pp. 2–38. Oxford University Press Inc. (1997)
McPherson, M.J., Quirke, P., Taylor, G.R.: PCR 1: A practical approach, pp. 1–14. Oxford University Press Inc. (1991)
Micklos, D.A., Freyer, G.A., Crotty, D.A.: DNA science: A first course, 2nd edn., pp. 30–182. Cold Spring Harbor Laboratory Press (2003)
Nicholl, D.S.T.: An introduction to genetic engineering, 2nd edn. Studies in Biology, pp. 43–51. Cambridge University Press (2002)
Pawlak, Z.: Rough sets. International Journal of Computer and Information Sciences 11(5), 341–356 (1982)
Pawlak, Z.: Rough classification. International Journal of Man-Machine Studies 20(5), 469–483 (1984)
Pawlak, Z., Wong, S.K.M., Ziarko, W.: Rough sets: Probabilistic versus deterministic approach. International Journal of Man-Machine Studies 29(1), 81–95 (1988)
Pedrycz, W., Chen, S.-C., Rubin, S.H., Lee, G.: Risk evaluation through decision-support architectures in threat assessment and countering terrorism. Applied Soft Computing 11(1), 621–631 (2011)
Pedrycz, W., Russo, B., Succi, G.: A model of job satisfaction for collaborative development processes. Journal of Systems and Software 84(5), 739–752 (2011)
Peters, J.F., Skowron, A.: Zdzisław Pawlak life and work (1926-2006). Information Sciences 177, 1–2 (2007)
Polkowski, L.: Advances in soft computing: Rough sets, pp. 18–45. Physica-Verlag, Heidelberg (2002)
Polkowski, L., Skowron, A.: Rough Sets in Knowledge Discovery 1. Methodology and Applications, pp. 201–250. Physica-Verlag, Heidelberg (1998)
Rabinow, P.: Making PCR: A story of biotechnology, pp. 1–17. The University of Chicago Press, Chicago (1996)
Skowron, A., Rauszer, C.: The discernibility matrices and functions in information systems. In: Słowiński, R. (ed.) Intelligent Decision Support: Handbook of Application and Advances of the Rough Sets Theory, pp. 331–362. Kluwer Academic Publishers, Dordrecht (1992)
Shan, N., Ziarko, W.: Data-based acquisition and incremental modification of classification rules. Computational Intelligence 11(2), 357–370 (1995)
Skowron, A., Stepaniuk, J., Swiniarski, R.: Approximation spaces in rough-granular computing. Fundamenta Informaticae 100(1-4), 141–157 (2010)
Skowron, A., Wasilewski, P.: Information Systems in Modeling Interactive Computations on Granules. In: Szczuka, M., Kryszkiewicz, M., Ramanna, S., Jensen, R., Hu, Q. (eds.) RSCTC 2010. LNCS(LNAI), vol. 6086, pp. 730–739. Springer, Heidelberg (2010)
Słowiński, R. (ed.): Intelligent Decision Support. Handbook of Application and Advances of The Rough Sets Theory, pp. 363–372. Kluwer Academic Publishers, Dordrecht (1992)
Tyagi, R.: Understanding molecular biology, pp. 174–213. Discovery Publishing House Pvt. Ltd. (2009)
Watada, J., Wang, S., Pedrycz, W.: Building confidence-interval-based fuzzy random regression models. IEEE Transactions on Fuzzy System 17(6), 1273–1283 (2009)
Watson, J.D., Crick, F.H.C.: Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171(4356), 737–738 (1953)
Watson, J.D., Myers, R.M., Caudy, A.A., Witkowski, J.A.: Recombinant DNA: Genes and genomes - a short course, 3rd edn., pp. 5–25. W.H. Freeman and Company (2007)
Ziarko, W.: Variable precision rough set model. Journal of Computer and System Sciences 46(1), 39–59 (1993)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Kim, I., Watada, J., Pedrycz, W. (2013). DNA Rough-Set Computing in the Development of Decision Rule Reducts. In: Skowron, A., Suraj, Z. (eds) Rough Sets and Intelligent Systems - Professor Zdzisław Pawlak in Memoriam. Intelligent Systems Reference Library, vol 42. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30344-9_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-30344-9_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-30343-2
Online ISBN: 978-3-642-30344-9
eBook Packages: EngineeringEngineering (R0)