Mean-Field Approximations to the Longest Common Subsequence Problem
Abstract
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other pairs with probability 1/S, representing the size of the alphabet. This model is analogous to a mean field version of the LCS problem, which can be solved with a cavity approach (Eur. Phys. J. B 7-2(1999),pp. 293-308). We refine here this approximation by incorporating in a systematic way correlations among the matches in the cavity calculation. We obtain a series of closer and closer approximations to the LCS problem, which we quantify in the large limit, both with a perturbative approach and by Monte-Carlo simulations. We find that, as it happens in the expansion around mean-field for other disordered systems, the corrections to our approximations depend upon long-ranged correlation effects which render the large expansion non-perturbative.
Cite
@article{arxiv.cond-mat/9810119,
title = {Mean-Field Approximations to the Longest Common Subsequence Problem},
author = {J. Boutet de Monvel},
journal= {arXiv preprint arXiv:cond-mat/9810119},
year = {2016}
}
Comments
5 pages, 2 figures, remanied version, more details given in section IV