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Submodular functions have many applications. Matchings have many applications. The bitext word alignment problem can be modeled as the problem of maximizing a nonnegative, monotone, submodular function constrained to matchings in a complete…
We present a new streaming algorithm for the $k$-Mismatch problem, one of the most basic problems in pattern matching. Given a pattern and a text, the task is to find all substrings of the text that are at the Hamming distance at most $k$…
We study the problem of edit similarity joins, where given a set of strings and a threshold value $K$, we want to output all pairs of strings whose edit distances are at most $K$. Edit similarity join is a fundamental problem in data…
The goal in {\em reconfiguration problems} is to compute a {\em gradual transformation} between two feasible solutions of a problem such that all intermediate solutions are also feasible. In the {\em Matching Reconfiguration Problem} (MRP),…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
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…
We consider the problem of sorting $n$ elements in the case of \emph{persistent} comparison errors. In this model (Braverman and Mossel, SODA'08), each comparison between two elements can be wrong with some fixed (small) probability $p$,…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great…
Grammar-based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. Given a grammar, the random access…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
The Dyck language, which consists of well-balanced sequences of parentheses, is one of the most fundamental context-free languages. The Dyck edit distance quantifies the number of edits (character insertions, deletions, and substitutions)…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
Given two strings $A[1..n]$ and $B[1..m]$, and a set of operations allowed to edit the strings, the edit distance between $A$ and $B$ is the minimum number of operations required to transform $A$ into $B$. Sequentially, a standard Dynamic…
This paper focuses on style transfer on the basis of non-parallel text. This is an instance of a broad family of problems including machine translation, decipherment, and sentiment modification. The key challenge is to separate the content…
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…