Related papers: Quantum Pattern Matching in Generalised Degenerate…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
Various grammar compression algorithms have been proposed in the last decade. A grammar compression is a restricted CFG deriving the string deterministically. An efficient grammar compression develops a smaller CFG by finding duplicated…
Quantum searching for one of $N$ marked items in an unsorted database of $n$ items is solved in $\mathcal{O}(\sqrt{n/N})$ steps using Grover's algorithm. Using nonlinear quantum dynamics with a Gross-Pitaevskii type quadratic nonlinearity,…
The Hamming distance is ubiquitous in computing. Its computation gets expensive when one needs to compare a string against many strings. Quantum computers (QCs) may speed up the comparison. In this paper, we extend an existing algorithm for…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
In this paper we propose a new, more appropriate definition of regular and indeterminate strings. A regular string is one that is "isomorphic" to a string whose entries all consist of a single letter, but which nevertheless may itself…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
The spectral theory of quantum graphs is related via an exact trace formula with the spectrum of the lengths of periodic orbits (cycles) on the graphs. The latter is a degenerate spectrum, and understanding its structure (i.e.,finding out…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…
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…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
Gradient-based algorithms, popular strategies to optimization problems, are essential for many modern machine-learning techniques. Theoretically, extreme points of certain cost functions can be found iteratively along the directions of the…
We show how, given a straight-line program with $g$ rules for a binary string $B$ of length $n$, in $O(g^{2 / 3} n^{4 / 3})$ time we can build a linear-space index such that, given $m$ and $c$, in O(1) time we can determine whether there is…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
Given a regular expression $R$ and a string $Q$, the regular expression parsing problem is to determine if $Q$ matches $R$ and if so, determine how it matches, e.g., by a mapping of the characters of $Q$ to the characters in $R$. Regular…