A word $u$ is a subsequence of another word $w$ if $u$ can be obtained from $w$ by deleting some of its letters. The word $w$ with alph$(w)=Σ$ is called $k$-subsequence universal if the set of subsequences of length $k$ of $w$ contains all possible words of length $k$ over $Σ$. We propose a series of efficient algorithms computing the minimal number of edit operations (insertion, deletion, substitution) one needs to apply to a given word in order to reach the set of $k$-subsequence universal words.
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are equivalent; the state of the art running time is (almost) quadratic and this is tight under plausible fine-grained complexity assumptions. But for approximation algorithms the picture is different: there is a long line of works with improved approximation factors for Edit Distance, but for LCS (with binary strings) only a trivial $1/2$-approximation was known. In…
String similarity, longest common subsequence and shortest edit scripts are the triplets of problem that related to each other. There are different algorithms exist to generate edit script by solving longest common subsequence problem. This paper proposes an algorithm that uses string similarity problem to generate shortest edit script. For this we use the famous Levenshtein distance algorithm, which computes a numerical value that represents similarity between the strings from 0 to n, where n is the length of longest input string, and produce the shortest edit script which contains instructio…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model, this model allows one to have streaming access to one string and random access to the other string. Our first main contribution is a systematic study of space lower bounds for ED and LCS in the asymmetric streaming model. Previously, there are no explicitly stated results in this context, although some lower bounds about LCS can be inferred from the lower boun…
We consider subsequences with gap constraints, i.e., length-k subsequences p that can be embedded into a string w such that the induced gaps (i.e., the factors of w between the positions to which p is mapped to) satisfy given gap constraints $gc = (C_1, C_2, ..., C_{k-1})$; we call p a gc-subsequence of w. In the case where the gap constraints gc are defined by lower and upper length bounds $C_i = (L^-_i, L^+_i) \in \mathbb{N}^2$ and/or regular languages $C_i \in REG$, we prove tight (conditional on the orthogonal vectors (OV) hypothesis) complexity bounds for checking whether a given p is a g…
We give cell-probe bounds for the computation of edit distance, Hamming distance, convolution and longest common subsequence in a stream. In this model, a fixed string of $n$ symbols is given and one $δ$-bit symbol arrives at a time in a stream. After each symbol arrives, the distance between the fixed string and a suffix of most recent symbols of the stream is reported. The cell-probe model is perhaps the strongest model of computation for showing data structure lower bounds, subsuming in particular the popular word-RAM model. * We first give an $Ω((δ\log n)/(w+\log\log n))$ lower bound for t…
The similarity between a pair of time series, i.e., sequences of indexed values in time order, is often estimated by the dynamic time warping (DTW) distance, instead of any in the well-studied family of measures including the longest common subsequence (LCS) length and the edit distance. Although it may seem as if the DTW and the LCS(-like) measures are essentially different, we reveal that the DTW distance can be represented by the longest increasing subsequence (LIS) length of a sequence of integers, which is the LCS length between the integer sequence and itself sorted. For a given pair of …
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple $O(n^2)$ dynamic programming algorithms, and despite much effort no algorithms with significantly better running time are known. We prove that, even restricted to binary strings or one-dimensional curves, respectively, these measures do not have strongly subquadratic time algorithms, i.e., no algorithms with running time $O(n^{2-\varepsilon})$ for any $\varepsilo…
The edit distance (ED) and longest common subsequence (LCS) are two fundamental problems which quantify how similar two strings are to one another. In this paper, we consider these problems in the asymmetric streaming model introduced by Andoni et al. (FOCS'10) and Saks and Seshadhri (SODA'13). In this model we have random access to one string and streaming access the other string. Our main contribution is a constant factor approximation algorithm for ED with the memory of $\tilde O(n^δ)$ for any constant $δ> 0$. In addition to this, we present an upper bound of $\tilde O_ε(\sqrt{n})$ on the m…
A common approach to implementing similarity search applications is the usage of distance functions, where small distances indicate high similarity. In the case of metric distance functions, metric index structures can be used to accelerate nearest neighbor queries. On the other hand, many applications ask for approximate subsequences or subsets, e.g. searching for a similar partial sequence of a gene, for a similar scene in a movie, or for a similar object in a picture which is represented by a set of multidimensional features. Metric index structures such as the M-Tree cannot be utilized for…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share. We designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s-|n-m|)min(m,n,s)+m+n) and linear space, where …
We consider the problem of preprocessing two strings $S$ and $T$, of lengths $m$ and $n$, respectively, in order to be able to efficiently answer the following queries: Given positions $i,j$ in $S$ and positions $a,b$ in $T$, return the optimal alignment of $S[i \mathinner{.\,.} j]$ and $T[a \mathinner{.\,.} b]$. Let $N=mn$. We present an oracle with preprocessing time $N^{1+o(1)}$ and space $N^{1+o(1)}$ that answers queries in $\log^{2+o(1)}N$ time. In other words, we show that we can query the alignment of every two substrings in almost the same time it takes to compute just the alignment of…
Calculating the length of a longest common subsequence (LCS) of two strings $A$ and $B$ of length $n$ and $m$ is a classic research topic, with many worst-case oriented results known. We present two algorithms for LCS length calculation with respectively $O(mn \log\log n / \log^2 n)$ and $O(mn / \log^2 n + r)$ time complexity, the latter working for $r = o(mn / (\log n \log\log n))$, where $r$ is the number of matches in the dynamic programming matrix. We also describe conditions for a given problem sufficient to apply our techniques, with several concrete examples presented, namely the edit d…
A recent and active line of work achieves tight lower bounds for fundamental problems under the Strong Exponential Time Hypothesis (SETH). A celebrated result of Backurs and Indyk (STOC'15) proves that the Edit Distance of two sequences of length n cannot be computed in strongly subquadratic time under SETH. The result was extended by follow-up works to simpler looking problems like finding the Longest Common Subsequence (LCS). SETH is a very strong assumption, asserting that even linear size CNF formulas cannot be analyzed for satisfiability with an exponential speedup over exhaustive search.…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to quantify the gain in time complexity when the underlying data is highly compressible. We consider grammar compression, which unifies many practically relevant compression schemes. For two strings of total length $N$ and total compressed size $n$, it is known that the edit distance and a longest common subsequence (LCS) can be computed exactly in time $\tilde{O}(…
Approximating the length of the longest increasing sequence (LIS) of an array is a well-studied problem. We study this problem in the data stream model, where the algorithm is allowed to make a single left-to-right pass through the array and the key resource to be minimized is the amount of additional memory used. We present an algorithm which, for any $δ> 0$, given streaming access to an array of length $n$ provides a $(1+δ)$-multiplicative approximation to the \emph{distance to monotonicity} ($n$ minus the length of the LIS), and uses only $O((\log^2 n)/δ)$ space. The previous best known app…
University of Washington（华盛顿大学）；Princeton University（普林斯顿大学）；University of California, San Diego（加州大学圣迭戈分校）
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the string). We consider the relaxed problem of approximate reconstruction. Here, the goal is to output a string that is close to the original one in edit distance while using much fewer traces than is needed for exact reconstruction. We present several algorithms that can approximately reconstruct strings that belong to certain classes, where the estimate is wit…
