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Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…
We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that…
In this paper, we present a novel neural graph matching approach applied to document comparison. Document comparison is a common task in the legal and financial industries. In some cases, the most important differences may be the addition…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
Artificial Neural Networks (ANN) comprise important symmetry properties, which can influence the performance of Monte Carlo methods in Neuroevolution. The problem of the symmetries is also known as the competing conventions problem or…
In this paper we consider graph algorithms in models of computation where the space usage (random accessible storage, in addition to the read only input) is sublinear in the number of edges $m$ and the access to input data is constrained.…
Machine-translated text plays an important role in modern life by smoothing communication from various communities using different languages. However, unnatural translation may lead to misunderstanding, a detector is thus needed to avoid…
Comparison and evaluation of graph-based representations of sentence meaning is a challenge because competing representations of the same sentence may have different number of nodes, and it is not obvious which nodes should be compared to…
The task of calculating similarities between strings held by different organizations without revealing these strings is an increasingly important problem in areas such as health informatics, national censuses, genomics, and fraud detection.…
The graph is one of the most widely used mathematical structures in engineering and science because of its representational power and inherent ability to demonstrate the relationship between objects. The objective of this work is to…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
We consider the Stochastic Matching problem, which is motivated by applications in kidney exchange and online dating. In this problem, we are given an undirected graph. Each edge is assigned a known, independent probability of existence and…