Related papers: A New Algebraic Approach for String Reconstruction…
In the pooled data problem the goal is to efficiently reconstruct a binary signal from additive measurements. Given a signal $\sigma \in \{ 0,1 \}^n$, we can query multiple entries at once and get the total number of non-zero entries in the…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
We study systems of String Equations where block variables need to be assigned strings so that their concatenation gives a specified target string. We investigate this problem under a multivariate complexity framework, searching for…
String diagrams are an increasingly popular algebraic language for the analysis of graphical models of computations across different research fields. Whereas string diagrams have been thoroughly studied as semantic structures, much less…
We relate the computational complexity of finite strings to universal representations of their underlying symmetries. First, Boolean functions are classified using the universal covering topologies of the circuits which enumerate them. A…
The modular subset sum problem consists of deciding, given a modulus $m$, a multiset $S$ of $n$ integers in $0..m-1$, and a target integer $t$, whether there exists a subset of $S$ with elements summing to $t \mod m $, and to report such a…
In this work we introduce a new linear time compression algorithm, called "Re-pair for Trees", which compresses ranked ordered trees using linear straight-line context-free tree grammars. Such grammars generalize straight-line context-free…
Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…
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…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…
We study word reconstruction problems. Improving a previous result by P. Fleischmann, M. Lejeune, F. Manea, D. Nowotka and M. Rigo, we prove that, for any unknown word $w$ of length $n$ over an alphabet of cardinality $k$, $w$ can be…
We consider binary dispatching problem originating from object oriented programming. We want to preprocess a hierarchy of classes and collection of methods so that given a function call in the run-time we are able to retrieve the most…
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…
This paper depicts an algorithm for solving the Decision Boolean Satisfiability Problem using the binary numerical properties of a Special Decision Satisfiability Problem, parallel execution, object oriented, and short termination. The two…
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…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
In the past thirty years, numerous algorithms for building the suffix array of a string have been proposed. In 2021, the notion of suffix array was extended from strings to DFAs, and it was shown that the resulting data structure can be…