Related papers: String Matching in ${\tilde O}(\sqrt{n}+\sqrt{m})$…
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…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Important papers have appeared recently on the problem of indexing binary strings for jumbled pattern matching, and further lowering the time bounds in terms of the input size would now be a breakthrough with broad implications. We can…
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…
For every $\epsilon>0$, we give an $\exp(\tilde{O}(\sqrt{n}/\epsilon^2))$-time algorithm for the $1$ vs $1-\epsilon$ \emph{Best Separable State (BSS)} problem of distinguishing, given an $n^2\times n^2$ matrix $\mathcal{M}$ corresponding to…
The circuit-level implementation of a quantum string-matching algorithm, which matches a search string (pattern) of length $M$ inside a longer text of length $N$, has already been demonstrated in the literature to outperform its classical…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
In a previous paper we generalized the Knuth-Morris-Pratt (KMP) pattern matching algorithm and defined a non-conventional kind of RAM, the MP--RAMs (RAMS equipped with extra operations), and designed an O(n) on-line algorithm for solving…
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…
We revisit the complexity of building, given a two-dimensional string of size $n$, an indexing structure that allows locating all $k$ occurrences of a two-dimensional pattern of size $m$. While a structure of size $\mathcal{O}(n)$ with…
We give an O(sqrt n log n)-query quantum algorithm for evaluating size-n AND-OR formulas. Its running time is poly-logarithmically greater after efficient preprocessing. Unlike previous approaches, the algorithm is based on a quantum walk…
We give an $\mathcal{O}(n \log n)$-time, $\mathcal{O}(n)$-space algorithm for factoring a string into the minimum number of palindromic substrings. That is, given a string $S [1..n]$, in $\mathcal{O}(n \log n)$ time our algorithm returns…
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…
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…
We show how to search N items arranged on a $\sqrt{N}\times\sqrt{N}$ grid in time $O(\sqrt N \log N)$, using a discrete time quantum walk. This result for the first time exhibits a significant difference between discrete time and continuous…
We study space and time efficient quantum algorithms for two graph problems -- deciding whether an $n$-vertex graph is a forest, and whether it is bipartite. Via a reduction to the s-t connectivity problem, we describe quantum algorithms…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
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…