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An Enzyme-Inspired Approach to Surmount Barriers in Graph Bisection

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Image Computational Science and Its Applications – ICCSA 2008 (ICCSA 2008)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5072))

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Abstract

Finding optimal solutions in the graph bisection problem is a notoriously hard task. One of the main reasons is the barriers which prevent search algorithms from reaching the optimal solutions. Given an algorithm for finding optimal solutions, the search process can be represented by a Markov chain. Every two neighboring solutions has a connection in the chain with a transition probability. If the algorithm is deterministic, many of the connections are set to the probability zero since they can never be chosen in the algorithm. It thus may happen that there is no path with a positive probability. We suggest a method to open paths with zero or near-zero transition probability by implicitly changing the chain, which we believe will eventually make the search more flexible. Experimental results showed significant improvement over traditional representative partitioning methodologies, the Fiduccia-Mattheyses algorithm and its two-phase variant.

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References

  1. Alpert, C., Kahng, A.B.: A general framework for vertex orderings, with applications to netlist clustering. In: Proceedings of the IEEE/ACM International Conference on Computer-Aided Design, pp. 63–67 (1994)

    Google Scholar 

  2. Alpert, C.J., Kahng, A.B.: Recent directions in netlist partitioning: A survey. Integration, the VLSI Journal 19(1-2), 1–81 (1995)

    Article  MATH  Google Scholar 

  3. Battiti, R., Bertossi, A.: Greedy, prohibition, and reactive heuristics for graph partitioning. IEEE Transactions on Computers 48(4), 361–385 (1999)

    Article  Google Scholar 

  4. Bui, T.N., Heigham, C., Jones, C., Leighton, T.: Improving the performance of the Kernighan-Lin and simulated annealing graph bisection algorithms. In: Proceedings of the 26th ACM/IEEE Design Automation Conference, pp. 775–778 (1989)

    Google Scholar 

  5. Bui, T.N., Moon, B.-R.: Genetic algorithm and graph partitioning. IEEE Transactions on Computers 45(7), 841–855 (1996)

    Article  MATH  MathSciNet  Google Scholar 

  6. Choe, T.-Y., Park, C.-I.: A k-way graph partitioning algorithm based on clustering by eigenvector. In: Proceedings of the Fourth International Conference on Computational Science, pp. 598–601 (2004)

    Google Scholar 

  7. Cong, J., Lim, S.K.: Edge separability-based circuit clustering with application to multilevel circuit partitioning. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 23(3), 346–357 (2004)

    Article  Google Scholar 

  8. Dhillon, I., Guan, Y., Kulis, B.: A fast kernel-based multilevel algorithm for graph clustering. In: Proceedings of the Eleventh ACM SIGKDD International Conference on Knowledge discovery in data mining, pp. 629–634 (2005)

    Google Scholar 

  9. Fiduccia, C., Mattheyses, R.: A linear time heuristics for improving network partitions. In: Proceedings of the 19th ACM/IEEE Design Automation Conference, pp. 175–181 (1982)

    Google Scholar 

  10. Garey, M., Johnson, D.S.: Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, San Francisco (1979)

    MATH  Google Scholar 

  11. Goldberg, D.: Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, Reading (1989)

    MATH  Google Scholar 

  12. Huang, M.L., Nguyen, Q.V.: A fast algorithm for balanced graph clustering. In: Proceedings of the Eleventh International Conference on Information Visualization, pp. 46–52 (2007)

    Google Scholar 

  13. Hwang, I., Kim, Y.-H., Moon, B.-R.: Multi-attractor gene reordering for graph bisection. In: Proceedings of the Eighth Annual Conference on Genetic and Evolutionary Computation, pp. 1209–1216 (2006)

    Google Scholar 

  14. Johnson, D.S., Aragon, C., McGeoch, L., Schevon, C.: Optimization by simulated annealing: An experimental evaluation, Part 1, graph partitioning. Operations Research 37, 865–892 (1989)

    Article  MATH  Google Scholar 

  15. Kernighan, B., Lin, S.: An efficient heuristic procedure for partitioning graphs. Bell Systems Technical Journal 49, 291–307 (1970)

    Google Scholar 

  16. Kim, Y.-H., Moon, B.-R.: Investigation of the fitness landscapes in graph bipartitioning: An empirical study. Journal of Heuristics 10(2), 111–133 (2004)

    Article  Google Scholar 

  17. Kim, Y.-H., Moon, B.-R.: Lock-gain based graph partitioning. Journal of Heuristics 10(1), 37–57 (2004)

    Article  MATH  Google Scholar 

  18. Kirkpatrick, S., Gelatt Jr., C.D., Vecchi, M.P.: Optimization by simulated annealing. Science 220(4598), 671–680 (1983)

    Article  MathSciNet  Google Scholar 

  19. Martin, O.C., Otto, S.W., Felten, E.W.: Large-step Markov chains for the traveling salesman problem. Complex Systems 5(3), 299–326 (1991)

    MATH  MathSciNet  Google Scholar 

  20. Merz, P., Freisleben, B.: Fitness landscapes, memetic algorithms, and greedy operators for graph bipartitioning. Evolutionary Computation 8(1), 61–91 (2000)

    Article  Google Scholar 

  21. Moraglio, A., Kim, Y.-H., Yoon, Y., Moon, B.-R.: Geometric crossovers for multiway graph partitioning. Evolutionary Computation 15(4), 445–474 (2007)

    Article  Google Scholar 

  22. Saha, B., Mitra, P.: Dynamic algorithm for graph clustering using minimum cut tree. In: Proceedings of the Sixth IEEE International Conference on Data Mining Workshops, pp. 667–671 (2006)

    Google Scholar 

  23. Schaeffer, S.E.: Graph clustering. Computer Science Review 1(1), 27–64 (2007)

    Article  MathSciNet  Google Scholar 

  24. Wang, J., Peng, H., Hu, J., Yang, C.: A graph clustering algorithm based on minimum and normalized cut. In: Proceedings of the Seventh International Conference on Computational Science, pp. 497–504 (2007)

    Google Scholar 

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Osvaldo GervasiBeniamino MurganteAntonio LaganàDavid TaniarYoungsong MunMarina L. Gavrilova

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Kim, YH. (2008). An Enzyme-Inspired Approach to Surmount Barriers in Graph Bisection. In: Gervasi, O., Murgante, B., Laganà, A., Taniar, D., Mun, Y., Gavrilova, M.L. (eds) Computational Science and Its Applications – ICCSA 2008. ICCSA 2008. Lecture Notes in Computer Science, vol 5072. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69839-5_63

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