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Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…
The problem of finding a maximum size matching in a graph (known as the maximum matching problem) is one of the most classical problems in computer science. Despite a significant body of work dedicated to the study of this problem in the…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
While neural machine translation (NMT) has achieved state-of-the-art translation performance, it is unable to capture the alignment between the input and output during the translation process. The lack of alignment in NMT models leads to…
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 matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
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…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
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…
Analyzing patterns in data streams generated by network traffic, sensor networks, or satellite feeds is a challenge for systems in which the available storage is limited. In addition, real data is noisy, which makes designing data stream…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…