Does Preprocessing help in Fast Sequence Comparisons?
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We study edit distance computation with preprocessing: the preprocessing algorithm acts on each string separately, and then the query algorithm takes as input the two preprocessed strings. This model is inspired by scenarios where we would like to compute edit distance between many pairs in the same pool of strings. Our results include: Permutation-LCS: If the LCS between two permutations has length n-k, we can compute it exactly with O(n log(n)) preprocessing and O(k log(n)) query time. Small edit distance: For general strings, if their edit distance is at most k, we can compute it exactly with O(nlog(n)) preprocessing and O(k^2 log(n)) query time. Approximate edit distance: For the most general input, we can approximate the edit distance to within factor (7+o(1)) with preprocessing time Õ(n^2) and query time Õ(n^1.5+o(1)). All of these results significantly improve over the state of the art in edit distance computation without preprocessing. Interestingly, by combining ideas from our algorithms with preprocessing, we provide new improved results for approximating edit distance without preprocessing in subquadratic time.
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