Stochastic local search for large-scale instances of the haplotype inference problem by pure parsimony

Journal of Algorithms

Volumn 63, Issue 1-3, 2008, Pages 55-69

  Di Gaspero, Luca ^a   Roli, Andrea ^b  

^a UNIVERSITY OF UDINE   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Bioinformatics; Haplotype inference; Metaheuristics

Indexed keywords

BASIC (PROGRAMMING LANGUAGE); BENCHMARKING; BIOINFORMATICS; BOOLEAN FUNCTIONS; COMBINATORIAL MATHEMATICS; COMBINATORIAL OPTIMIZATION; GENETIC PROGRAMMING; HEURISTIC PROGRAMMING; INTEGER PROGRAMMING; LINEAR PROGRAMMING; LINEARIZATION; MATHEMATICAL PROGRAMMING; NONLINEAR PROGRAMMING; STOCHASTIC PROGRAMMING;

CERTAIN HYPOTHESES; CHALLENGING PROBLEM; COMBINATORIAL OPTIMIZATION TECHNIQUES; COMBINATORIAL PROBLEMS; DESIGN ISSUES; EXACT METHODS; EXECUTION TIME; GENETIC VARIANTS; GREEDY HEURISTIC; HAPLOTYPE INFERENCE; INTEGER LINEAR PROGRAMMING; LOCAL SEARCH METAHEURISTICS; METAHEURISTICS; PSEUDO-BOOLEAN; SEMI-DEFINITE PROGRAMMING; SOLUTION QUALITY; STOCHASTIC LOCAL SEARCH;

HEURISTIC METHODS;

EID: 49449099403     PISSN: 01966774     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jalgor.2008.02.004     Document Type: Article

References (20)

1. Birattari M., Stützle T., Paquete L., and Varrentrapp K. A racing algorithm for configuring metaheuristics. Proc. Genetic and Evolutionary Computation Conference, GECCO 2002 (2002), Morgan Kaufmann, New York 11-18
2. Blum C., and Roli A. Metaheuristics in combinatorial optimization: Overview and conceptual comparison. ACM Comput. Surveys 35 3 (2003) 268-308
3. Brown D.G., and Harrower I.M. Integer programming approaches to haplotype inference by pure parsimony. IEEE/ACM Trans. Comput. Biology Bioinform. 3 2 (2006) 141-154
4. Clark A.G. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biology Evol. 7 (1990) 111-122
5. L. Di Gaspero, A. Roli, A preliminary analysis on metaheuristics methods applied to the haplotype inference problem, Technical report DEIS-LIA-07-006, University of Bologna, Italy, lIA Ser. 84, 2007
6. Di Gaspero L., and Schaerf A. EasyLocal++: An object-oriented framework for flexible design of local search algorithms. Softw. Pract. Exper. 33 8 (2003) 733-765
7. Graça A., Marques-Silva J., Lynce I., and Oliveira A.L. Efficient haplotype inference with pseudo-boolean optimization. In: Anai H., Horimoto K., and Kutsia T. (Eds). Proc. Algebraic Biology, Second International Conference, AB 2007. Castle of Hagenberg, Austria, July 2-4, 2007. Lecture Notes in Comput. Sci. vol. 4545 (2007), Springer, Berlin 125-139
8. Gusfield D. Haplotype inference by pure parsimony. In: Baeza-Yates R.A., Chávez E., and Crochemore M. (Eds). Combinatorial Pattern Matching, CPM 2003, Proc. 14th Annual Symposium. Lecture Notes in Comput. Sci. vol. 2676 (2003), Springer, Berlin 144-155
9. Halldórsson B.V., Bafna V., Edwards N., Lippert R., Yooseph S., and Istrail S. A survey of computational methods for determining haplotypes. In: Istrail S., Waterman M.S., and Clark A.G. (Eds). Computational Methods for SNPs and Haplotype Inference. Lecture Notes in Comput. Sci. vol. 2983 (2002), Springer, Berlin 26-47
10. Hoos H.H., and Stützle T. Stochastic Local Search Foundations and Applications (2005), Morgan Kaufmann, San Francisco, CA
11. Huang Y.-T., Chao K.-M., and Chen T. An approximation algorithm for haplotype inference by maximum parsimony. In: Haddad H., Liebrock L.M., Omicini A., and Wainwright R.L. (Eds). Proceedings 2005 ACM Symposium on Applied Computing, SAC 2005 (2005), ACM 146-150
12. Kalpakis K., and Namjoshi P. Haplotype phasing using semidefinite programming. BIBE (2005), IEEE Comput. Soc. 145-152
13. Lancia G., Pinotti M.C., and Rizzi R. Haplotyping populations by pure parsimony: Complexity of exact and approximation algorithms. INFORMS J. Comput. 16 4 (2004) 348-359
14. Lynce I., and Marques-Silva J. Efficient haplotype inference with boolean satisfiability. Proc. 21st National Conference on Artificial Intelligence and 18th Innovative Applications of Artificial Intelligence Conference (2006), AAAI Press, Menlo Park, CA
15. Lynce I., and Marques-Silva J. SAT in bioinformatics: Making the case with haplotype inference. In: Biere A., and Gomes C.P. (Eds). SAT. Lecture Notes in Comput. Sci. vol. 4121 (2006), Springer, Berlin 136-141
16. Prestwich S., and Roli A. Symmetry breaking and local search spaces. Proc. CPAIOR 2005. Lecture Notes in Comput. Sci. vol. 3524 (2005), Springer, Berlin
17. Resende M.G.C., and Ribeiro C.C. Greedy randomized adaptive search procedures. In: Glover F., and Kocheberger G.A. (Eds). Handbook of Metaheuristics. Internat. Ser. Oper. Res. Manag. Sci. vol. 57 (2003), Kluwer Academic Publ., Norwell, MA 219-249
18. A. Roli, Symmetry-breaking and local search: A case study, in: SymCon'04, 4th International Workshop on Symmetry and Constraint Satisfaction Problems, 2004
19. The International HapMap Consortium. The international HapMap project. Nature 426 (2003) 789-796
20. Wang R.-S., Zhang X.-S., and Sheng L. Haplotype inference by pure parsimony via genetic algorithm. In: Zhang X.-S., Liu D.-G., and Wu L.-Y. (Eds). Operations Research and Its Applications: Fifth International Symposium, ISORA'05. Tibet, China, August 8-13. Lecture Notes Oper. Res. vol. 5 (2005), Beijing World Publ., Beijing 308-318