Related papers: String Matching: Communication, Circuits, and Lear…
We investigate the randomized and quantum communication complexity of the Hamming Distance problem, which is to determine if the Hamming distance between two n-bit strings is no less than a threshold d. We prove a quantum lower bound of…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
We define the ``shift-match number'' for a binary string and we compute the probability of occurrence of a given string as a subsequence in longer strings in terms of its shift-match number. We thus prove that the string matching…
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…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
Citation matching is a challenging task due to different problems such as the variety of citation styles, mistakes in reference strings and the quality of identified reference segments. The classic citation matching configuration used in…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
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…
In this work, we study longest common substring, pattern matching, and wildcard pattern matching in the asymmetric streaming model. In this streaming model, we have random access to one string and streaming access to the other one. We…
In the Dictionary-based String Matching (DSM) problem, a retrieval system has access to a source sequence and stores the position of a certain number of strings in a posting table. When a user inquires the position of a string, the…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
We investigate the longest common substring problem for encoded sequences and its asymptotic behaviour. The main result is a strong law of large numbers for a re-scaled version of this quantity, which presents an explicit relation with the…
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…
As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to…