Related papers: Counting common substrings effectively
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more…
In this note, we first introduce a new problem called the longest common subsequence and substring problem. Let $X$ and $Y$ be two strings over an alphabet $\Sigma$. The longest common subsequence and substring problem for $X$ and $Y$ is to…
Analyzing patterns in data streams generated by network traffic, sensor networks, or satellite feeds is a challenge for systems in which the available storage is limited. In addition, real data is noisy, which makes designing data stream…
The following paper presents a method of comparing two sets of vectors. The method can be applied in all tasks, where it is necessary to measure the closeness of two objects presented as sets of vectors. It may be applicable when we compare…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
The fundamental problem of similarity studies, in the frame of data-mining, is to examine and detect similar items in articles, papers, books, with huge sizes. In this paper, we are interested in the probabilistic, and the statistical and…
We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…
Dense subgraph extraction is a fundamental problem in graph analysis and data mining, aimed at identifying cohesive and densely connected substructures within a given graph. It plays a crucial role in various domains, including social…
Computing subgraph frequencies is a fundamental task that lies at the core of several network analysis methodologies, such as network motifs and graphlet-based metrics, which have been widely used to categorize and compare networks from…
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…
Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of…
In this paper we introduce a dynamic programming algorithm to perform linear text segmentation by global minimization of a segmentation cost function which consists of: (a) within-segment word similarity and (b) prior information about…
It is discussed and surveyed a numerical method proposed before, that alternative to the usual compression method, provides an approximation to the algorithmic (Kolmogorov) complexity, particularly useful for short strings for which…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
We consider an efficient two-party protocol for securely computing the similarity of strings w.r.t. an extended edit distance measure. Here, two parties possessing strings $x$ and $y$, respectively, want to jointly compute an approximate…
A closed string $u$ is either of length one or contains a border that occurs only as a prefix and as a suffix in $u$ and nowhere else within $u$. In this paper, we present fast $\mathcal{O}(n\log n)$ time algorithms to compute all…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…