Efficient Algorithms for Finding Maximum and Maximal Cliques: Effective Tools for Bioinformatics

Many problems can be formulated as graphs where a graph consists of a set of vertices and a set of edges, in which the vertices stand for objects in question and the edges stand for some relations among the objects. A clique is a subgraph in which all pairs of vertices are mutually adjacent. Thus, a maximum clique stands for a maximum collection of objects which are mutually related in some specified criterion. The so called maximum clique problem is one of the original 21 problems shown to be NP-complete by R. Karp (19). Therefore, it is strongly believed that the maximum clique problem is not solvable easily, i.e., it is not solvable in polynomial-time. Nevertheless, much work has been done on this problem, experimentally and theoretically. It attracts much attention especially recently since it has found many practical applications to bioinformatics (see, e.g., (2; 15; 27; 28; 37; 3; 9; 4; 8; 14; 55; 23; 25; 22; 13)) and many others (see, e.g., excellent surveys (34; 5), and (17; 20; 31; 49; 54; 51)). This chapter presents efficient algorithms for finding a maximum clique and maximal cliques as effective tools for bioinformatics, and shows our successful applications of these algorithms to bioinformatics.