The Compressed Overlap Index

Abstract: For analysing text algorithms, for computing superstrings, or for testing random number generators, one needs to compute all overlaps between any pairs of words in a given set. The positions of overlaps of a word onto itself, or of two words, are needed to compute the absence probability of a word in a random text, or the numbers of common words shared by two random texts. In all these contexts, one needs to compute or to query overlaps between pairs of words in a given set. For this sake, we designed COvI, a compressed overlap index that supports multiple queries on overlaps: like computing the correlation of two words, or listing pairs of words whose longest overlap is maximal among all possible pairs. COvI stores overlaps in a hierarchical and non-redundant manner. We propose an implementation that can handle datasets of millions of words and still answer queries efficiently. Comparison with a baseline solution - called FullAC - relying on the Aho-Corasick automaton shows that COvI provides significant advantages. For similar construction times, COvI requires half the memory FullAC, and still solves complex queries much faster.