Related papers: A Three-Stage Algorithm for the Closest String Pro…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary $D$ of $d$ strings of total length $n$ over an alphabet of size $\sigma$. Given…
In this paper, we propose new techniques for solving geometric optimization problems involving interpoint distances of a point set in the plane. Given a set $P$ of $n$ points in the plane and an integer $1 \leq k \leq \binom{n}{2}$, the…
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…
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…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
Genome annotation is an important issue in biology which has long been addressed with gene prediction methods and manual experiments requiring biological expertise. The expanding Next Generation Sequencing technologies and their enhanced…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…
Given a redundant dictionary $\Phi$, represented by an $M \times N$ matrix ($\Phi \in \mathbb{R}^{M \times N}$) and a target signal $y \in \mathbb{R}^M$, the \emph{sparse approximation problem} asks to find an approximate representation of…
Weighted Hamming distance, as a similarity measure between binary codes and binary queries, provides superior accuracy in search tasks than Hamming distance. However, how to efficiently and accurately find $K$ binary codes that have the…
In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We…
We consider the problem of finding optimal piecewise constant approximations of one-dimensional signals. These approximations should consist of a specified number of segments (samples) and minimise the mean squared error to the original…
In CPM 2017, Amir et al. introduce a problem, named \emph{approximate string cover} (\textbf{ACP}), motivated by many aplications including coding and automata theory, formal language theory, combinatorics and molecular biology. A…
Divide and Conquer is a well known algorithmic procedure for solving many kinds of problem. In this procedure, the problem is partitioned into two parts until the problem is trivially solvable. Finding the distance of the closest pair is an…
Anytime heuristic search algorithms try to find a (potentially suboptimal) solution as quickly as possible and then work to find better and better solutions until an optimal solution is obtained or time is exhausted. The most widely-known…
In this paper we propose an algorithm for the approximate k-Nearest-Neighbors problem. According to the existing researches, there are two kinds of approximation criterion. One is the distance criteria, and the other is the recall criteria.…