Related papers: Quantum Pattern Matching in Generalised Degenerate…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
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 pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
We consider the problem of computing the q-gram profile of a string \str of size $N$ compressed by a context-free grammar with $n$ production rules. We present an algorithm that runs in $O(N-\alpha)$ expected time and uses $O(n+q+\kq)$…
The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…
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…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
We propose a quantum string comparison method whose main building blocks are a specially designed oracle construction followed by Grover's search algorithm. The purpose of the oracle is to compare all alphabets of the string in parallel.…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
The equation for QCD string proposed earlier is reviewed. This equation appears when we examine the gonihedric string model and the corresponding transfer matrix. Arguing that string equation should have a generalized Dirac form we found…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary $\mathcal{D}$ in fragments of a given string $T$ of length $n$. The dictionary is internal in the sense that each pattern in…
Suppose that three kinds of quantum systems are given in some unknown states $\ket f^{\otimes N}$, $\ket{g_1}^{\otimes K}$, and $\ket{g_2}^{\otimes K}$, and we want to decide which \textit{template} state $\ket{g_1}$ or $\ket{g_2}$, each…
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…