Abstract

We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with nodes being Labeled). This problem is motivated by the study of information retrieval for bio-chemical and molecular databases. Suppose we define the distance between two CUAL graphs G1 and G2 to be the weighted number of edit operations (insert node, delete node and relabel node) to transform G1 to G2. By reduction from exact cover by 3-sets, one can show that finding the distance between two CUAL graphs is NP-complete. In view of the hardness of the problem, we propose a constrained distance metric, called the degree-2 distance, by requiring that any node to be inserted (deleted) have no more than 2 neighbors. With this metric, we present an efficient algorithm to solve the problem. The algorithm runs in time O(N_1 N_2 D²) for general weighting edit operations and in time O(N_1 N_2 D √D log D) for integral weighting edit operations, where N_i, i = 1, 2, is the number of nodes in G_i, D = min{d_1, d_2} and d_i is the maximum degree of G_i.

Citations