A sublinear algorithm for weakly approximating edit distance

We show how to determine whether the edit distance between two given strings is small in sublinear time. Specifically, we present a test which, given two n-character strings A and B, runs in time o(n) and with high probability returns " CLOSE " if their edit distance is O(n Α ), and " FAR " if their edit distance is Ω(n), where Α is a fixed parameter less than 1. Our algorithm for testing the edit distance works by recursively subdividing the strings A and B into smaller substrings and looking for pairs of substrings in A, B with small edit distance. To do this, we query both strings at random places using a special technique for economizing on the samples which does not pick the samples independently and provides better query and overall complexity. As a result, our test runs in time Õ(n max(Α/2, 2Α - 1\) ) for any fixed Α < 1. Our algorithm thus provides a trade-off between accuracy and efficiency that is particularly useful when the input data is very large.We also show a lower bound of Ω(n Α/2 ) on the query complexity of every algorithm that distinguishes pairs of strings with edit distance at most n Α from those with edit distance at least n/6.

Authors

• Tugkan Batu
• Funda Ergün
• Joe Kilian
• Avner Magen
• Sofya Raskhodnikova
• Ronitt Rubinfeld
• Rahul Sami

Keywords

• string matching
• approximation
• sublinear algorithms