Related papers: Pairwise sequence alignment with block and charact…
In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Given a stream of items each associated with a numerical value, its edit distance to monotonicity is the minimum number of items to remove so that the remaining items are non-decreasing with respect to the numerical value. The space…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
Many modern data analysis algorithms either assume that or are considerably more efficient if the distances between the data points satisfy a metric. These algorithms include metric learning, clustering, and dimensionality reduction.…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of…
Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size…
Many modern data analysis algorithms either assume or are considerably more efficient if the distances between the data points satisfy a metric. These algorithms include metric learning, clustering, and dimension reduction. As real data…
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. Sampled string…
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…
This study aims to publish a novel similarity metric to increase the speed of comparison operations. Also the new metric is suitable for distance-based operations among strings. Most of the simple calculation methods, such as string length…
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 edit distance $ed(X,Y)$ of two strings $X,Y\in \Sigma^*$ is the minimum number of character edits (insertions, deletions, and substitutions) needed to transform $X$ into $Y$. Its weighted counterpart $ed^w(X,Y)$ minimizes the total cost…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
This paper introduces a new type of grammar learning algorithm, inspired by string edit distance (Wagner and Fischer, 1974). The algorithm takes a corpus of flat sentences as input and returns a corpus of labelled, bracketed sentences. The…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…