Related papers: Efficient Parallel Output-Sensitive Edit Distance
In this paper we present two versions of a parallel finger structure FS on p processors that supports searches, insertions and deletions, and has a finger at each end. This is to our knowledge the first implementation of a parallel search…
The minimum distance of a code is an important concept in information theory. Hence, computing the minimum distance of a code with a minimum computational cost is a crucial process to many problems in this area. In this paper, we present…
In this paper, we study the single-source shortest-path (SSSP) problem with positive edge weights, which is a notoriously hard problem in the parallel context. In practice, the $\Delta$-stepping algorithm proposed by Meyer and Sanders has…
Graph edit distance (GED) is an important similarity measure adopted in a similarity-based analysis between two graphs, and computing GED is a primitive operator in graph database analysis. Partially due to the NP-hardness, the existing…
We introduce fast-decodable indexing schemes for edit distance which can be used to speed up edit distance computations to near-linear time if one of the strings is indexed by an indexing string $I$. In particular, for every length $n$ and…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. In this paper we…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
Edit distance is an important measure of string similarity. It counts the number of insertions, deletions and substitutions one has to make to a string $x$ to get a string $y$. In this paper we design an almost linear-size sketching scheme…
For parallel breadth first search (BFS) algorithm on large-scale distributed memory systems, communication often costs significantly more than arithmetic and limits the scalability of the algorithm. In this paper we sufficiently reduce the…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…
We consider the problem of solving integer programs of the form $\min \{\,c^\intercal x\ \colon\ Ax=b, x\geq 0\}$, where $A$ is a multistage stochastic matrix in the following sense: the primal treedepth of $A$ is bounded by a parameter…
For $n$-vertex $m$-edge graphs with integer polynomially-bounded costs and capacities, we provide a randomized parallel algorithm for the minimum cost flow problem with $\tilde O(m+n^ {1.5})$ work and $\tilde O(\sqrt{n})$ depth. On…
Dynamic time warping distance (DTW) is a widely used distance measure between time series. The best known algorithms for computing DTW run in near quadratic time, and conditional lower bounds prohibit the existence of significantly faster…
We consider approximate circular pattern matching (CPM, in short) under the Hamming and edit distance, in which we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a threshold $k>0$, and we are to report all starting positions…
Although several self-indexes for highly repetitive text collections exist, developing an index and search algorithm with editing operations remains a challenge. Edit distance with moves (EDM) is a string-to-string distance measure that…
Parallel sentence extraction is a task addressing the data sparsity problem found in multilingual natural language processing applications. We propose an end-to-end deep neural network approach to detect translational equivalence between…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
We study the problem of estimating the edit distance between two $n$-character strings. While exact computation in the worst case is believed to require near-quadratic time, previous work showed that in certain regimes it is possible to…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…