Abstract
The problem of finding a maximum clique or enumerating all maximal cliques is very important and has been explored in several excellent survey papers. Here, we focus our attention on the step-by-step examination of a series of branch-and-bound depth-first search algorithms: Basics, MCQ, MCR, MCS, and MCT. Subsequently, as with the depth-first search as above, we present our algorithm, CLIQUES, for enumerating all maximal cliques. Finally, we describe some of the applications of the algorithms and their variants in bioinformatics, data mining, and other fields.
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References
Akutsu, T., Hayashida, M., Bahadur, D.K.C., Tomita, E., Suzuki, J., Horimoto, K.: Dynamic programming and clique based approaches for protein threading with profiles and constraints. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. E89–A, 1215–1222 (2006)
Andrade, D.V., Resende, M.G.C., Werneck, R.F.: Fast local search for the maximum independent set problem. J. Heuristics 18, 525–547 (2012)
Bahadur, D.K.C., Akutsu, T., Tomita, E., Seki, T., Fujiyama, A.: Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm. Genome Inf. 13, 143–152 (2002)
Bahadur, D.K.C., Tomita, E., Suzuki, J., Akutsu, T.: Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach. J. Bioinform. Comput. Biol. 3, 103–126 (2005)
Bahadur, D.K.C., Tomita, E., Suzuki, J., Horimoto, K., Akutsu, T.: Protein threading with profiles and distance constraints using clique based algorithms. J. Bioinform. Comput. Biol. 4, 19–42 (2006)
Batsyn, M., Goldengorin, B., Maslov, E., Pardalos, P.M.: Improvements to MCS algorithm for the maximum clique problem. J. Comb. Optim. 27, 397–416 (2014)
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, Supplement vol. A, pp. 1–74. Kluwer Academic Publishers (1999)
Bron, C., Kerbosch, J.: Algorithm 457, finding all cliques of an undirected graph. Commun. ACM 16, 575–577 (1973)
Brown, J.B., Bahadur, D.K.C., Tomita, E., Akutsu, T.: Multiple methods for protein side chain packing using maximum weight cliques. Genome Inf. 17, 3–12 (2006)
Butenko, S., Wilhelm, W.E.: Clique-detection models in computational biochemistry and genomics - invited review-. Eur. J. Oper. Res. 173, 1–17 (2006)
Carraghan, R., Pardalos, P.M.: An exact algorithm for the maximum clique problem. Oper. Res. Lett. 9, 375–382 (1990)
Eppstein, D., Löffler, M., Strash, D.: Listing all maximal cliques in large sparse real-world graphs. J. Exp. Algorithmics 18, 3.1:1–3.1:21 (2013)
Fujii, T., Tomita, E.: On efficient algorithms for finding a maximum clique. Technical report IECE, AL81-113, pp. 25–34 (1982)
Fukagawa, D., Tamura, T., Takasu, A., Tomita, E., Akutsu, T.: A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structure. BMC Bioinform. 12(S–1), S:13 (2011)
Hatta, T., Tomita, E., Ito, H., Wakatsuki, M.: An improved branch-and-bound algorithm for finding a maximum clique. In: Proceedings of the Summer LA Symposium, no. 9, pp. 1–8 (2015)
Hotta, K., Tomita, E., Takahashi, H.: A view-invariant human face detection method based on maximum cliques. Trans. IPSJ 44(SIG14(TOM9)), 57–70 (2003)
Johnson, D.S., Trick, M.A. (eds.): Cliques, Coloring, and Satisfiability. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 26. American Mathematical Society (1996)
Karp, R.: Reducibility among combinatorial problems. In: Miller, R.E., Thatcher, J.W. (eds.) Comlexity of Computer Computations, pp. 85–103. Plenum Press, New York (1972)
Katayama, K., Hamamoto, A., Narihisa, H.: An effective local search for the maximum clique problem. Inf. Process. Lett. 95, 503–511 (2005)
Kobayashi, S., Kondo, T., Okuda, K., Tomita, E.: Extracting globally structure free sequences by local structure freeness. In: Chen, J., Reif, J. (eds.) Proceedings of Ninth International Meeting on DNA Based Computers, p. 206 (2003)
Kohata, Y., Nishijima, T., Tomita, E., Fujihashi, C., Takahashi, H.: Efficient algorithms for finding a maximum clique. Technical report IEICE, COM89-113, pp. 1–8 (1990)
Konc, J., Janežič, D.: An improved branch and bound algorithm for the maximum clique problem. MATCH Commun. Math. Comput. Chem. 58, 569–590 (2007)
Li, C.M., Quan, Z.: Combining graph structure exploitation and propositional reasoning for the maximum clique problem. In: Proceedings of IEEE ICTAI, pp. 344–351 (2010)
Makino, K., Uno, T.: New algorithms for enumerating all maximal cliques. In: Hagerup, T., Katajainen, J. (eds.) SWAT 2004. LNCS, vol. 3111, pp. 260–272. Springer, Heidelberg (2004). doi:10.1007/978-3-540-27810-8_23
Maslov, E., Batsyn, M., Pardalos, P.M.: Speeding up branch and bound algorithms for solving the maximum clique problem. J. Glob. Optim. 59, 1–21 (2014)
Matsunaga, T., Yonemori, C., Tomita, E., Muramatsu, M.: Clique-based data mining for related genes in a biomedical database. BMC Bioinform. 10, 205 (2009)
Moon, J.W., Moser, L.: On cliques in graphs. Israel J. Math. 3, 23–28 (1965)
Mori, T., Tamura, T., Fukagawa, D., Takasu, A., Tomita, E., Akutsu, T.: A clique-based method using dynamic programming for computing edit distance between unordered trees. J. Comput. Biol. 19, 1089–1104 (2012)
Nagai, M., Tabuchi, T., Tomita, E., Takahashi, H.: An experimental evaluation of some algorithms for finding a maximum clique. In: Conference Records of the National Convention of IEICE 1988, p. D-348 (1988)
Nakui, Y., Nishino, T., Tomita, E., Nakamura, T.: On the minimization of the quantum circuit depth based on a maximum clique with maximum vertex weight. Technical report RIMS, 1325, Kyoto University, pp. 45–50 (2003)
Okubo, Y., Haraguchi, M., Tomita, E.: Structural change pattern mining based on constrained maximal k-plex search. In: Ganascia, J.-G., Lenca, P., Petit, J.-M. (eds.) DS 2012. LNCS (LNAI), vol. 7569, pp. 284–298. Springer, Heidelberg (2012). doi:10.1007/978-3-642-33492-4_23
Okubo, Y., Haraguchi, M., Tomita, E.: Relational change pattern mining based on modularity difference. In: Ramanna, S., Lingras, P., Sombattheera, C., Krishna, A. (eds.) MIWAI 2013. LNCS (LNAI), vol. 8271, pp. 187–198. Springer, Heidelberg (2013). doi:10.1007/978-3-642-44949-9_18
Okubo, Y., Haraguchi, M., Tomita, E.: Enumerating maximal isolated cliques based on vertex-dependent connection lower bound. In: Perner, P. (ed.) MLDM 2016. LNCS (LNAI), vol. 9729, pp. 569–583. Springer, Heidelberg (2016)
Pardalos, P.M., Xue, J.: The maximum clique problem. J. Glob. Optim. 4, 301–328 (1994)
Pattillo, J., Youssef, N., Butenko, S.: Clique relaxation models in social network analysis. In: Thai, M.T., Pardalos, P.M. (eds.) Handbook of Optimization in Complex Networks: Communication and Social Networks. Springer Optimization and Its Applications, vol. 58, pp. 143–162. Springer, Heidelberg (2012)
Segundo, P.S., Nikolaev, A., Batsyn, M.: Infra-chromatic bound for exact maximum clique search. Comput. Oper. Res. 64, 293–303 (2015)
Shindo, M., Tomita, E., Maruyama, Y.: An efficient algorithm for finding a maximum clique. Technical report IECE, CAS86-5, pp. 33–40 (1986)
Shindo, M., Tomita, E.: A simple algorithm for finding a maximum clique and its worst-case time complexity. Syst. Comput. Jpn. 21, 1–13 (1990). Wiley
Sutani, Y., Higashi, T., Tomita, E., Takahashi, S., Nakatani, H.: A faster branch-and-bound algorithm for finding a maximum clique. Technical report IPSJ, 2006-AL-108, pp. 79–86 (2006)
Tarjan, R.E., Trojanowski, A.E.: Finding a maximum independent set. SIAM J. Comput. 6(3), 537–546 (1977)
Tomita, E., Yamada, M.: An algorithm for finding a maximum complete subgraph. In: Conference Records of the National Convention of IECE 1978, p. 8 (1978)
Tomita, E., Tanaka, A., Takahashi, H.: The worst-case time complexity for finding all the cliques. Technical report, University of Electro-Communications, UEC-TR-C5(2) (1988). (Reference [238] in [34], Reference [308] in [7]). http://id.nii.ac.jp/1438/00001898/
Tomita, E., Kohata, Y., Takahashi, H.: A simple algorithm for finding a maximum clique. Technical report, University of Electro-Communications, UEC-TR-C5(1) (1988). (Reference [239] in [34], Reference [309] in [7]). http://id.nii.ac.jp/1438/00001899/
Tomita, E., Mitsuma, S., Takahashi, H.: Two algorithms for finding a near-maximum clique. Technical report, University of Electro-Communications, UEC-TR-C1 (1988). (Reference [240] in [34], Reference [310] in [7]). http://id.nii.ac.jp/1438/00001900/
Tomita, E., Seki, T.: An efficient branch-and-bound algorithm for finding a maximum clique. In: Calude, C.S., Dinneen, M.J., Vajnovszki, V. (eds.) DMTCS 2003. LNCS, vol. 2731, pp. 278–289. Springer, Heidelberg (2003)
Tomita, E., Tanaka, A., Takahashi, H.: The worst-case time complexity for generating all maximal cliques and computational experiments. Theoret. Comput. Sci. 363, 28–42 (2006). (Special Issue on COCOON 2004)
Tomita, E., Kameda, T.: An efficient branch-and-bound algorithm for finding a maximum clique with computational experiments. J. Glob. Optim. 37, 95–111 (2007). J. Glob. Optim. 44, 311 (2009)
Tomita, E., Sutani, Y., Higashi, T., Takahashi, S., Wakatsuki, M.: A simple and faster branch-and-bound algorithm for finding a maximum clique. In: Rahman, M.S., Fujita, S. (eds.) WALCOM 2010. LNCS, vol. 5942, pp. 191–203. Springer, Heidelberg (2010). doi:10.1007/978-3-642-11440-3_18
Tomita, E., Akutsu, T., Matsunaga, T.: Efficient algorithms for finding maximum and maximal cliques: Effective tools for bioinformatics. In: Laskovski, A.N. (ed.) Biomedical Engineering, Trends in Electronics, Communications and Software, pp. 625–640. InTech, Rijeka (2011). http://cdn.intechopen.com/pdfs-wm/12929.pdf
Tomita, E., Sutani, Y., Higashi, T., Wakatsuki, M.: A simple and faster branch-and-bound algorithm for finding a maximum clique with computational experiments. IEICE Trans. Inf. Syst. E96–D, 1286–1298 (2013). http://id.nii.ac.jp/1438/00000287/
Tomita, E.: Clique enumeration. In: Kao, M.-Y. (ed.) Encyclopedia of Algorithms, 2nd edn, pp. 313–317. Springer, Heidelberg (2016)
Tomita, E., Yoshida, K., Hatta, T., Nagao, A., Ito, H., Wakatsuki, M.: A much faster branch-and-bound algorithm for finding a maximum clique. In: Zhu, D., Bereg, S. (eds.) FAW 2016. LNCS, vol. 9711, pp. 215–226. Springer, Heidelberg (2016)
Tsukiyama, S., Ide, M., Ariyoshi, H., Shirakawa, I.: A new algorithm for generating all the maximal independent sets. SIAM J. Comput. 6, 505–517 (1977)
Wu, Q., Hao, J.K.: A review on algorithms for maximum clique problems - invited review-. Eur. J. Oper. Res. 242, 693–709 (2015)
Yonemori, C., Matsunaga, T., Sekine, J., Tomita, E.: A structural analysis of enterprise relationship using cliques. DBSJ J. 7, 55–60 (2009)
Zhai, H., Haraguchi, M., Okubo, Y., Tomita, E.: Enumerating maximal clique sets with pseudo-clique constraint. In: Japkowicz, N., Matwin, S. (eds.) DS 2015. LNCS (LNAI), vol. 9356, pp. 324–339. Springer, Heidelberg (2015). doi:10.1007/978-3-319-24282-8_28
Zhai, H., Haraguchi, M., Okubo, Y., Tomita, E.: A fast and complete algorithm for enumerating pseudo-cliques in large graphs. Int. J. Data Sci. Anal. 2, 145–158 (2016). Springer
Acknowledgments
The author would like to express his sincere gratitude to H. Ito, T. Akutsu, M. Haraguchi, Y. Okubo, T. Nishino, H. Takahashi and many others for their fruitful joint work and kind help. This work was supported by JSPS KAKENHI Grant Numbers JP16300001, JP19300040, JP19500010, JP21300047, JP22500009, JP25330009, Kayamori Foundation of Informational Science Advancement, Funai Foundation for Information Technologies, and others.
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Tomita, E. (2017). Efficient Algorithms for Finding Maximum and Maximal Cliques and Their Applications. In: Poon, SH., Rahman, M., Yen, HC. (eds) WALCOM: Algorithms and Computation. WALCOM 2017. Lecture Notes in Computer Science(), vol 10167. Springer, Cham. https://doi.org/10.1007/978-3-319-53925-6_1
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