Hybrid randomised neighbourhoods improve stochastic local search for DNA code design

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2671, Issue , 2003, Pages 418-433

  Tulpan, Dan C ^a   Hoos, Holger H ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; CODES (SYMBOLS); DESIGN; DNA; LOCAL SEARCH (OPTIMIZATION); STOCHASTIC SYSTEMS; ALGORITHMS; COMBINATORIAL MATHEMATICS; COMPUTATIONAL METHODS; CONSTRAINT THEORY; GENETIC ENGINEERING; MUTAGENESIS; NANOSTRUCTURED MATERIALS; STOCHASTIC PROGRAMMING;

BIOMOLECULAR COMPUTATION; CANDIDATE SETS; DNA STRANDS; LONG-RANGE CONNECTION; MOLECULAR TAGGING; NEIGHBOURHOOD; SEARCH SPACES; STOCHASTIC LOCAL SEARCHES;

GENE ENCODING; DNA SEQUENCES;

BIOMOLECULAR COMPUTATION; COMBINATORIAL CONSTRAINTS; DNA STRANDS; NANOSTRUCTURE DESIGN;

EID: 7044249181     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-44886-1_31     Document Type: Conference Paper

References (19)

1. R. S. Braich, C. Johnson, P.W. K. Rothemund, D. Hwang, N. Chelyapov, and L. M. Adleman, “Solution of a satisfiability problem on a gel-based DNA computer”, Preliminary Proc. Sixth International Meeting on DNA BasedC omputers, Leiden, The Netherlands, June, 2000.
2. S. Brenner and R. A. Lerner, “Encoded combinatorial chemistry”, Proc. Natl. Acad. Sci. USA, Vol 89, pages 5381–5383, June 1992.
3. R. Deaton, R.C. Murphy, M. Garzon, D. R. Franceschetti, and S. E Stevens Jr., “Gooden codings for DNA-based solutions to combinatorial problems,” Proc. DNA BasedCom puters II, DIMACS Workshop June 10-12, 1996, L. F. Landweber andE.B. Baum, Editors, DIMACS Series in Discrete Mathematics andT heoretical Computer Science, Vol. 44, pages 247–258, 1999.
4. R. Deaton, M. Garzon, R.C. Murphy, J. A. Rose, D.R. Franceschetti, and S.E. Stevens Jr., “Genetic search of reliable encodings for DNA-based computation,” Koza, John R., Goldberg, DavidE., Fogel, DavidB., andR iolo, Rick L. (editors), Proceedings of the First Annual Conference on Genetic Programming 1996.
5. A.A. El Gamal, L.A. Hemachandra, I. Shperling, and V.K. Wei, “Using simulated annealing to design good codes,” IEEE Transactions on Information Theory, Vol. IT-33, No. 1, January 1987.
6. D. Faulhammer, A.R. Cukras, R. J. Lipton, and L. F. Landweber, “Molecular computation: RNA solutions to chess problems,” Proc. Natl. Acad. Sci. USA, 97: 1385-1389, 2000.
7. U. Feldkamp, W. Banzhaf, H. Rauhe, “A DNA sequence compiler,” Poster presentedat the 6th International Meeting on DNA Based Computers, Leiden, June, 2000. See also http://ls11-www.cs.uni-dortmund.de/molcomp/Publications/publications.html (visitedN ovember 11, 2000).
8. A.G. Frutos, Q. Liu, A. J. Thiel, A.M. W. Sanner, A.E. Condon, L.M. Smith, and R. M. Corn, “Demonstration of a wordd esign strategy for DNA computing on surfaces,” Nucleic Acids Research, Vol. 25, No. 23, pages 4748-4757, December 1997.
9. A. J. Hartemink, D.K. Gifford, and J. Khodor, “Automated constraint-based nucleotide sequence selection for DNA computation,” 4th Annual DIMACS Workshop on DNA-BasedCom puters, Philadelphia, Pennsylvania, June 1998.
10. I. S. Honkala, and P.R. J. Ostergard, “Code design,” In Local Search In Combinatorial Optimization (E. Aarts andJ. K. Lenstra, eds.), Wiley-Interscience Series in Discrete Mathematics andO ptimization, 1997.
11. H. H. Hoos, “Stochastic Local Search - Methods, Models, Applications”, infix- Verlag, Sankt Augustin, Germany, ISBN 3-89601-215-0, 1999.
12. H.H. Hoos and T. Stützle, “Evaluating Las Vegas Algorithms — Pitfalls and Remedies,” In Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence (UAI-98), pages 238-245, 1998.
13. M. Li, H-J. Lee, A. E. Condon, and R. M. Corn, “DNA WordD esign Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays,” Langmuir, 18, pages 805-812, 2002.
14. A. Marathe, A. Condon, and R. Corn, “On combinatorial DNA word design,” J. Computational Biology, 8:3, pages 201-220, 2001.
15. Programmable DNA web site, http://ls11-www.cs.uni-dortmund.de/molcomp/Downloads/downloads.html. VisitedN ovember 11, 2000.
16. J.H. Reif, T.H. LaBean, and N. C. Seeman, “Challenges and Applications for Self-AssembledD NA Nanostructures”, Proc. Sixth Inter.l Workshop on DNABased Computers, Leiden, The Neth., June, 2000. DIMACS Ed. by A. Condon andG. Rozenberg, Lecture Notes in CS, Springer-Verlag, Berlin Heidelberg, vol. 2054, pages 173-198, 2001.
17. D. C. Tulpan, H.H. Hoos, A. Condon, “Stochastic Local Search Algorithms for DNA WordD esign”, DNA 8 Conference, Japan, March 2002.
18. B. Yurke, A. J. Tuberfield, A.P. Mills Jr, F.C. Simmel and J. L. Neumann, “A DNA-fuelledm olecular machine made of DNA.” Nature 406, pages 605-608, 2000.
19. B-T. Zhang and S-Y. Shin, “Molecular algorithms for efficient andreliab le DNA computing,” Proc. 3rdA nnual Genetic Programming Conference, Editedb y J.R. Koza, K. Deb, M. Doringo, D. B. Fogel, M. Garzon, H. Iba, andR.L. Riolo, Morgan Kaufmann, pages 735-742, 1998