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Algorithms for detecting optimal hereditary structures in graphs, with application to clique relaxations

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Abstract

Given a simple undirected graph, the problem of finding a maximum subset of vertices satisfying a nontrivial, interesting property Π that is hereditary on induced subgraphs, is known to be NP-hard. Many well-known graph properties meet the above conditions, making the problem widely applicable. This paper proposes a general purpose exact algorithmic framework to solve this problem and investigates key algorithm design and implementation issues that are helpful in tailoring the general framework for specific graph properties. The performance of the algorithms so derived for the maximum s-plex and the maximum s-defective clique problems, which arise in network-based data mining applications, is assessed through a computational study.

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References

  1. Abello, J., Pardalos, P.M., Resende, M.G.C.: On maximum clique problems in very large graphs. In: Abello, J., Vitter, J. (eds.) External Memory Algorithms and Visualization. DIMACS Series on Discrete Mathematics and Theoretical Computer Science, vol. 50, pp. 119–130. American Mathematical Society, Providence (1999)

    Google Scholar 

  2. Applegate, D., Johnson, D.S.: dfmax.c [c program, second dimacs implementation challenge]. http://dimacs.rutgers.edu/pub/challenge/graph/solvers/

  3. Babel, L.: Finding maximum cliques in arbitrary and in special graphs. Computing 46(4), 321–341 (1991)

    Article  MathSciNet  MATH  Google Scholar 

  4. Bader, J.S., Chaudhuri, A., Rothberg, J.M., Chant, J.: Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22(1), 78–85 (2004)

    Article  Google Scholar 

  5. Balas, E., Xue, J.: Weighted and unweighted maximum clique algorithms with upper bounds from fractional coloring. Algorithmica 15, 397–412 (1996)

    Article  MathSciNet  MATH  Google Scholar 

  6. Balas, E., Yu, C.: Finding a maximum clique in an arbitrary graph. SIAM J. Comput. 15, 1054–1068 (1986)

    Article  MathSciNet  MATH  Google Scholar 

  7. Balasundaram, B.: Graph theoretic generalizations of clique: optimization and extensions. PhD thesis, Texas A&M University, College Station, Texas, USA (2007)

  8. Balasundaram, B., Butenko, S., Hicks, I.V.: Clique relaxations in social network analysis: the maximum k-plex problem. Oper. Res. 59(1), 133–142 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  9. Balasundaram, B., Butenko, S., Trukhanov, S.: Novel approaches for analyzing biological networks. J. Comb. Optim. 10(1), 23–39 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  10. Balasundaram, B., Mahdavi Pajouh, F.: Graph theoretic clique relaxations and applications. In: Pardalos, P.M., Du, D.-Z., Graham, R. (eds.) Handbook of Combinatorial Optimization, 2nd edn. Springer, Berlin (2013). doi:10.1007/978-1-4419-7997-1_9

    Google Scholar 

  11. Boginski, V., Butenko, S., Pardalos, P.: Mining market data: a network approach. Comput. Oper. Res. 33, 3171–3184 (2006)

    Article  MATH  Google Scholar 

  12. Boginski, V., Butenko, S., Pardalos, P.M.: On structural properties of the market graph. In: Nagurney, A. (ed.) Innovation in Financial and Economic Networks. Edward Elgar, London (2003)

    Google Scholar 

  13. Bomze, I.M., Budinich, M., Pardalos, P.M., Pelillo, M.: The maximum clique problem. In: Du, D.-Z., Pardalos, P.M. (eds.) Handbook of Combinatorial Optimization, pp. 1–74. Kluwer Academic, Dordrecht (1999)

    Chapter  Google Scholar 

  14. Bron, C., Kerbosch, J.: Algorithm 457: finding all cliques on an undirected graph. Commun. ACM 16, 575–577 (1973)

    Article  MATH  Google Scholar 

  15. Brouwer, A., Shearer, J., Sloane, N., Smith, W.: A new table of constant weight codes. IEEE Trans. Inf. Theory 36, 1334–1380 (1990)

    Article  MathSciNet  MATH  Google Scholar 

  16. Butenko, S., Wilhelm, W.: Clique-detection models in computational biochemistry and genomics. Eur. J. Oper. Res. 173, 1–17 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  17. Carraghan, R., Pardalos, P.: An exact algorithm for the maximum clique problem. Oper. Res. Lett. 9, 375–382 (1990)

    Article  MATH  Google Scholar 

  18. Cowen, L., Goddard, W., Jesurum, C.E.: Defective coloring revisited. J. Graph Theory 24(3), 205–219 (1997)

    Article  MathSciNet  MATH  Google Scholar 

  19. Dimacs. Cliques, Coloring, and Satisfiability: Second Dimacs Implementation Challenge (1995). Online: http://dimacs.rutgers.edu/Challenges/. Accessed March 2007

  20. Dimacs. Graph partitioning and graph clustering: tenth Dimacs implementation challenge (2011). Online: http://www.cc.gatech.edu/dimacs10/index.shtml. Accessed July 2012

  21. Frik, M.: A survey of (m,k)-colorings. In: Gimbel, J., Kennedy, J.W., Quintas, L.V. (eds.) Quo Vadis, Graph Theory? Annals of Discrete Mathematics, vol. 55, pp. 45–58. Elsevier, New York (1993)

    Google Scholar 

  22. Garey, M.R., Johnson, D.S.: Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, New York (1979)

    MATH  Google Scholar 

  23. Hasselberg, J., Pardalos, P.M., Vairaktarakis, G.: Test case generators and computational results for the maximum clique problem. J. Glob. Optim. 3(4), 463–482 (1993)

    Article  MathSciNet  MATH  Google Scholar 

  24. Håstad, J.: Clique is hard to approximate within n 1−ε. Acta Math. 182, 105–142 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  25. Johnson, D.S., Trick, M.A. (eds.): Cliques, Coloring, and Satisfiablility: Second Dimacs Implementation Challenge. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 26. American Mathematical Society, Providence (1996)

    MATH  Google Scholar 

  26. Krishna, P., Chatterjee, M., Vaidya, N.H., Pradhan, D.K.: A cluster-based approach for routing in ad-hoc networks. In: Proceedings of the USENIX Symposium on Location Independent and Mobile Computing, pp. 1–8 (1995)

    Google Scholar 

  27. Leskovec, J.: Stanford network analysis project (2012). http://snap.stanford.edu/data/

  28. Lewis, J.M., Yannakakis, M.: The node-deletion problem for hereditary properties is NP-complete. J. Comput. Syst. Sci. 20(2), 219–230 (1980)

    Article  MathSciNet  MATH  Google Scholar 

  29. Lund, C., Yannakakis, M.: The approximation of maximum subgraph problems. In: Proceedings of the 20th International Colloquium on Automata, Languages and Programming, ICALP ’93, pp. 40–51. Springer, London (1993)

    Chapter  Google Scholar 

  30. McClosky, B.: Independence systems and stable set relaxations. PhD thesis, Rice University (2008)

  31. McClosky, B., Hicks, I.V.: The co-2-plex polytope and integral systems. SIAM J. Discrete Math. 23(3), 1135–1148 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  32. McClosky, B., Hicks, I.V.: Combinatorial algorithms for the maximum k-plex problem. J. Comb. Optim. 23, 29–49 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  33. Moser, H., Niedermeier, R., Sorge, M.: Exact combinatorial algorithms and experiments for finding maximum k-plexes. J. Combin. Optim., 1–27 (2011). doi:10.1007/s10878-011-9391-5

  34. Östergård, P.R.J.: A new algorithm for the maximum-weight clique problem. Electron. Notes Discrete Math. 3, 153–156 (1999)

    Article  Google Scholar 

  35. Östergård, P.R.J.: A fast algorithm for the maximum clique problem. Discrete Appl. Math. 120, 197–207 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  36. Östergård, P.R.J., Vaskelainen, V.P.: Russian Doll search for the Steiner triple covering problem. Optim. Lett. 5(4), 631–638 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  37. Pattillo, J., Youssef, N., Butenko, S.: On clique relaxation models in network analysis. Eur. J. Oper. Res. 226, 9–18 (2013)

    Article  MathSciNet  Google Scholar 

  38. Ramaswami, R., Parhi, K.K.: Distributed scheduling of broadcasts in a radio network. In: Proceedings of the Eighth Annual Joint Conference of the IEEE Computer and Communications Societies (INFOCOM ’89), vol. 2, pp. 497–504 (1989)

    Chapter  Google Scholar 

  39. Scott, J.: Social Network Analysis: A Handbook, 2nd edn. Sage Publications, London (2000)

    Google Scholar 

  40. Seidman, S.B., Foster, B.L.: A graph theoretic generalization of the clique concept. J. Math. Sociol. 6, 139–154 (1978)

    Article  MathSciNet  MATH  Google Scholar 

  41. Sewell, E.C.: A branch and bound algorithm for the stability number of a sparse graph. INFORMS J. Comput. 10(4), 438–447 (1998)

    Article  MathSciNet  Google Scholar 

  42. Sloane, N.J.A.: Unsolved problems in graph theory arising from the study of codes. Graph Theory Notes N. Y. 18, 11–20 (1989)

    Google Scholar 

  43. Sloane, N.J.A.: Challenge problems: Independent sets in graphs (2000). Online: http://www.research.att.com/~njas/doc/graphs.html. Accessed July 2003

  44. Sloane, N.J.A.: On single-deletion-correcting codes. In: Arasu, K.T., Seress, A. (eds.) Codes and Designs. Ohio State University Mathematical Research Institute Publications, vol. 10, pp. 273–291. Walter de Gruyter, Berlin (2002)

    Google Scholar 

  45. Tomita, E., Kameda, T.: An efficient branch-and-bound algorithm for finding a maximum clique with computational experiments. J. Glob. Optim. 37(1), 95–111 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  46. Vaskelainen, V.: Russian Doll Search algorithms for discrete optimization problems. PhD thesis, Helsinki University of Technology (2010)

  47. Verfaillie, G., Lemaitre, M., Schiex, T.: Russian Doll Search for solving constraint optimization problems. In: Proceedings of the National Conference on Artificial Intelligence, pp. 181–187. Citeseer, Princeton (1996)

    Google Scholar 

  48. Wasserman, S., Faust, K.: Social Network Analysis. Cambridge University Press, New York (1994)

    Google Scholar 

  49. Wood, D.R.: An algorithm for finding a maximum clique in a graph. Oper. Res. Lett. 21(5), 211–217 (1997)

    Article  MathSciNet  MATH  Google Scholar 

  50. Yannakakis, M.: Node-and edge-deletion NP-complete problems. In: STOC ’78: Proceedings of the 10th Annual ACM Symposium on Theory of Computing, pp. 253–264. ACM Press, New York (1978)

    Chapter  Google Scholar 

  51. Yannakakis, M.: The effect of a connectivity requirement on the complexity of maximum subgraph problems. J. ACM 26(4), 618–630 (1979)

    Article  MathSciNet  MATH  Google Scholar 

  52. Yu, H., Paccanaro, A., Trifonov, V., Gerstein, M.: Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7), 823–829 (2006)

    Article  Google Scholar 

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Acknowledgements

We would like to thank the referees for providing useful suggestions, which helped us to significantly improve the paper. This research was supported in part by the US Department of Energy Grant DE-SC0002051 and the US Air Force Office of Scientific Research Grants FA9550-09-1-0154 and FA9550-12-1-0103.

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Correspondence to Sergiy Butenko.

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Trukhanov, S., Balasubramaniam, C., Balasundaram, B. et al. Algorithms for detecting optimal hereditary structures in graphs, with application to clique relaxations. Comput Optim Appl 56, 113–130 (2013). https://doi.org/10.1007/s10589-013-9548-5

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