Related papers: Reconstructing Strings from Substrings with Quantu…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
In the oracle identification problem we have oracle access to bits of an unknown string $x$ of length $n$, with the promise that it belongs to a known set $C\subseteq\{0,1\}^n$. The goal is to identify $x$ using as few queries to the oracle…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
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…
Let us consider the Multiple String Matching Problem. In this problem, we consider a long string, denoted by $t$, of length $n$. This string is referred to as a text. We also consider a sequence of $m$ strings, denoted by $S$, which we…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
Lexicographically minimal string rotation is a fundamental problem in string processing that has recently garnered significant attention in quantum computing. Near-optimal quantum algorithms have been proposed for solving this problem,…
In this paper, we consider the secret-string-learning problem in the teacher-student setting: the teacher has a secret string $s\in {{\{0,1\}}^{n}}$, and the student wants to learn the secret $s$ by question-answer interactions with the…
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…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
We propose a quantum algorithm for closest pattern matching which allows us to search for as many distinct patterns as we wish in a given string (database), requiring a query function per symbol of the pattern alphabet. This represents a…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…