Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from networking and information theory through cryptography and even genetic engineering and linguistics. We present three perspectives on this problem: a graph theoretic framework due to Pevzner, an automata theoretic approach from our previous work, and a new insight that yields a time-optimal streaming algorithm for determining whether a string of @math characters over the alphabet @math can be uniquely decoded from its two-character shingles. Our algorithm achieves an overall time complexity @math and space complexity @math . As an application, we demonstrate how this algorithm can be extended to larger shingles for efficient string reconciliation.
The problem of determining the minimum number of edits (insertions or deletions) required to transform one string into another has a long history in the literature @cite_23 @cite_30 . Orlitsky @cite_5 shows that the amount of communication @math to reconcile two strings @math and @math (of lengths @math and @math respectively) that are known to be at most @math -edits apart is at most [ C_ (x,y) f(y) + 3 f(y) + + 13, ] for [ ( |y|+ ) f(y) ( |y|+ ) + 3 ( ), ] although he leaves an efficient one-way protocol as an open question.
@cite_30 @cite_5 @cite_23
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The edit distance between two character strings can be defined as the minimum cost of a sequence of editing operations which transforms one string into the other. The operations we admit are deleting, inserting and replacing one symbol at a time, with possibly different costs for each of these operations. The problem of finding the longest common subsequence of two strings is a special case of the problem of computing edit distances. We describe an algorithm for computing the edit distance between two strings of length n and m, n ⪖ m, which requires O(n · max(1, mlog n)) steps whenever the costs of edit operations are integral multiples of a single positive real number and the alphabet for the strings is finite. These conditions are necessary for the algorithm to achieve the time bound. We prove the first nontrivial communication complexity lower bound for the problem of estimating the edit distance (aka Levenshtein distance) between two strings. To the best of our knowledge, this is the first computational setting in which the complexity of estimating the edit distance is provably larger than that of Hamming distance. Our lower bound exhibits a trade-off between approximation and communication, asserting, for example, that protocols with @math bits of communication can obtain only approximation @math , where @math is the length of the input strings. This case of @math communication is of particular importance since it captures constant-size sketches as well as embeddings into spaces like @math and squared- @math , two prevailing algorithmic approaches for dealing with edit distance. Indeed, the known nontrivial communication upper bounds are all derived from embeddings into @math . By excluding low-communication protocols for edit distance, we rule out a strictly richer class of algorithms than previous results. Furthermore, our lower bound holds not only for strings over a binary alphabet but also for strings that are permutations (aka the Ulam metric). For this case, our bound nearly matches an upper bound known via embedding the Ulam metric into @math . Our proof uses a new technique that relies on Fourier analysis in a rather elementary way. We initiate the study of the smoothed complexity of sequence alignment, by proposing a semi-random model of edit distance between two input strings, generated as follows: First, an adversary chooses two binary strings of length d and a longest common subsequence A of them. Then, every character is perturbed independently with probability p, except that A is perturbed in exactly the same way inside the two strings. We design two efficient algorithms that compute the edit distance on smoothed instances up to a constant factor approximation. The first algorithm runs in near-linear time, namely d 1+e for any fixed e > 0. The second one runs in time sublinear in d, assuming the edit distance is not too small. These approximation and runtime guarantees are significantly better than the bounds that were known for worst-case inputs. Our technical contribution is twofold. First, we rely on finding matches between substrings in the two strings, where two substrings are considered a match if their edit distance is relatively small, a prevailing technique in commonly used heuristics, such as PatternHunter of [2002]. Second, we effectively reduce the smoothed edit distance to a simpler variant of (worst-case) edit distance, namely, edit distance on permutations (a.k.a. Ulam's metric). We are thus able to build on algorithms developed for the Ulam metric, whose much better algorithmic guarantees usually do not carry over to general edit distance. This paper studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and nonbinary sequences from synchronization (insertion deletion-correcting) codes. These sequences have been corrupted by a fixed number of symbol insertions (larger than the minimum edit distance of the code), yielding a number of distinct traces to be used for reconstruction. We wish to know the minimum number of traces needed for exact reconstruction. This is a general version of a problem tackled by Levenshtein for uncoded sequences. We introduce an exact formula for the maximum number of common supersequences shared by sequences at a certain edit distance, yielding an upper bound on the number of distinct traces necessary to guarantee exact reconstruction. Without specific knowledge of the code words, this upper bound is tight. We apply our results to the famous single deletion insertion-correcting Varshamov–Tenengolts (VT) codes and show that a significant number of VT code word pairs achieve the worst case number of outputs needed for exact reconstruction. We also consider extensions to other channels, such as adversarial deletion and insertion deletion channels and probabilistic channels.