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Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
In this letter, we consider a problem of reconstructing an unknown discrete signal taking values in a finite alphabet from incomplete linear measurements. The difficulty of this problem is that the computational complexity of the…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
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…
In grammar-based compression a string is represented by a context-free grammar, also called a straight-line program (SLP), that generates only that string. We refine a recent balancing result stating that one can transform an SLP of size…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
A palindromic substring $T[i.. j]$ of a string $T$ is said to be a shortest unique palindromic substring (SUPS) in $T$ for an interval $[p, q]$ if $T[i.. j]$ is a shortest palindromic substring such that $T[i.. j]$ occurs only once in $T$,…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is sent through a probabilistic \emph{deletion channel} which independently deletes each bit with probability $\delta$ and concatenates the surviving…
Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter,…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…