Related papers: Motif matching using gapped patterns
Efficient pattern matching is fundamental for practical term rewrite engines. By preprocessing the given patterns into a finite deterministic automaton the matching patterns can be decided in a single traversal of the relevant parts of the…
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,…
Pattern matching in time series data streams is considered to be an essential data mining problem that still stays challenging for many practical scenarios. Different factors such as noise, varying amplitude scale or shift, signal stretches…
Various grammar compression algorithms have been proposed in the last decade. A grammar compression is a restricted CFG deriving the string deterministically. An efficient grammar compression develops a smaller CFG by finding duplicated…
The generalized function matching (GFM) problem has been intensively studied starting with [Ehrenfeucht and Rozenberg, 1979]. Given a pattern p and a text t, the goal is to find a mapping from the letters of p to non-empty substrings of t,…
We present a novel approach for finding multiple noisily embedded template graphs in a very large background graph. Our method builds upon the graph-matching-matched-filter technique proposed in Sussman et al., with the discovery of…
In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…
A hypergraph is a generalization of a graph, in which a hyperedge can connect multiple vertices, modeling complex relationships involving multiple vertices simultaneously. Hypergraph pattern matching, which is to find all isomorphic…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Sequential pattern mining (SPM) with gap constraints (or repetitive SPM or tandem repeat discovery in bioinformatics) can find frequent repetitive subsequences satisfying gap constraints, which are called positive sequential patterns with…
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…
The classical pattern matching paradigm is that of seeking occurrences of one string - the pattern, in another - the text, where both strings are drawn from an alphabet set $\Sigma$. Assuming the text length is $n$ and the pattern length is…
In his 1987 paper entitled "Generalized String Matching", Abrahamson introduced {\em pattern matching with character classes} and provided the first efficient algorithm to solve it. The best known solution to date is due to Linhart and…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…
Matching, a task to optimally assign limited resources under constraints, is a fundamental technology for society. The task potentially has various objectives, conditions, and constraints; however, the efficient neural network architecture…
Pattern matching is a widely used technique in functional languages, especially those in the ML and Haskell traditions, where it is at the core of the semantics. In languages in the Lisp tradition, in contrast, pattern matching it typically…
In this work, we address the problem of approximate pattern matching with wildcards. Given a pattern $P$ of length $m$ containing $D$ wildcards, a text $T$ of length $n$, and an integer $k$, our objective is to identify all fragments of $T$…
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…