Related papers: Quantum Algorithm for the Multiple String Matching…
We generalize Karp-Rabin string matching to handle multiple patterns in $\mathcal{O}(n \log n + m)$ time and $\mathcal{O}(s)$ space, where $n$ is the length of the text and $m$ is the total length of the $s$ patterns, returning correct…
The maximal clique problem, to find the maximally sized clique in a given graph, is classically an NP-complete computational problem, which has potential applications ranging from electrical engineering, computational chemistry,…
We prove that any exact quantum algorithm searching an ordered list of N elements requires more than \frac{1}{\pi}(\ln(N)-1) queries to the list. This improves upon the previously best known lower bound of {1/12}\log_2(N) - O(1). Our proof…
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 a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
Quantum computing has the potential to speed up some optimization methods. One can use quantum computers to solve linear systems via Quantum Linear System Algorithms (QLSAs). QLSAs can be used as a subroutine for algorithms that require…
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
A fundamental problem in computer science is to find all the common zeroes of $m$ quadratic polynomials in $n$ unknowns over $\mathbb{F}_2$. The cryptanalysis of several modern ciphers reduces to this problem. Up to now, the best complexity…
Calculating the length of a longest common subsequence (LCS) of two strings $A$ and $B$ of length $n$ and $m$ is a classic research topic, with many worst-case oriented results known. We present two algorithms for LCS length calculation…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
We use a Bayesian approach to optimally solve problems in noisy binary search. We deal with two variants: 1. Each comparison can be erroneous with some probability $1 - p$. 2. At each stage $k$ comparisons can be performed in parallel and a…
We solve the problems of detecting and counting various forms of regularities in a string represented as a Straight Line Program (SLP). Given an SLP of size $n$ that represents a string $s$ of length $N$, our algorithm compute all runs and…
Given two unsorted lists each of length N that have a single common entry, a quantum computer can find that matching element with a work factor of $O(N^{3/4}\log N)$ (measured in quantum memory accesses and accesses to each list). The…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…