1. introduction. edit distance levenshtein distance.pdfVIP

APPROXIMATING EDIT DISTANCE IN NEAR-LINEAR TIME∗ ALEXANDR ANDONI† AND KRZYSZTOF ONAK‡ Abstract. We show how to compute the edit distance between two strings of length n up to a √ ˜ factor of 2O( log n) in n1+o(1) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time, improving on the state-of-the-art n1/3+o(1) approximation. √ ˜ Previously, approximation of 2O( log n) was known only for embedding edit distance into 1 , and it is not known if that embedding can be computed in less than quadratic time. Key words. approximation algorithms, edit distance, metric embeddings AMS subject classifications. 68Q25, 68R15, 68W20, 68W25, 68W40 1. Introduction. The edit distance (or Levenshtein distance) between two strings is the number of insertions, deletions, and substitutions needed to transform one string into the other [19]. This distance is of fundamental importance in several fields such as computational biology and text processing/searching, and consequently, problems involving edit distance were studied extensively (cf. [22], [12], and references therein). In computational biology, for instance, edit distance and its slight variants are the most elementary measures of dissimilarity for genomic data, and thus improvements on edit distance algorithms have the potential of major impact. The basic problem is to compute the edit distance between two strings of length n 2 9] over some alphabet. The text-book dynamic programming runs in O(n ) time (cf. [ and references therein). This was only slightly improved by Masek and Paterson [20] 2 2