Finding Optimal Pairs of Patterns

We consider the problem of finding the optimal pair of string patterns for discriminating between two sets of strings, i.e. finding the pair of patterns that is best with respect to some appropriate scoring function that gives higher scores to pattern pairs which occur more in the strings of one set, but less in the other. We present an O(N2 ) time algorithm for finding the optimal pair of substring patterns, where N is the total length of the strings. The algorithm looks for all possible Boolean combination of the patterns, e.g. patterns of the form p ∧ ¬q, which indicates that the pattern pair is considered to match a given string s, if p occurs in s, AND q does NOT occur in s. The same algorithm can be applied to a variant of the problem where we are given a single set of sequences along with a numeric attribute assigned to each sequence, and the problem is to find the optimal pattern pair whose occurrence in the sequences is correlated with this numeric attribute. An efficie...

• Type: Conference
• Year: 2004
• Where: WABI
• Authors: Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
• Keywords: Algorithm, Algorithms, Optimal Pair, Pattern Pair, WABI 2004