Related papers: Motif matching using gapped patterns
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
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…
Many tasks in natural language processing, ranging from machine translation to question answering, can be reduced to the problem of matching two sentences or more generally two short texts. We propose a new approach to the problem, called…
Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
Subgraph matching is a compute-intensive problem that asks to enumerate all the isomorphic embeddings of a query graph within a data graph. This problem is generally solved with backtracking, which recursively evolves every possible partial…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
We put forth a new string matching algorithm which matches the pattern from neither the left nor the right end, instead a special position. Comparing with the Knuth-Morris-Pratt algorithm and the Boyer-Moore algorithm, the new algorithm is…
We propose a novel measure for template matching named Deformable Diversity Similarity -- based on the diversity of feature matches between a target image window and the template. We rely on both local appearance and geometric information…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify variable…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
Exact substring matching is a common task in many software applications. Despite the existence of several algorithms for finding whether or not a pattern string is present in a target string, the most common implementation is a na\"ive,…
Word embedding models offer continuous vector representations that can capture rich contextual semantics based on their word co-occurrence patterns. While these word vectors can provide very effective features used in many NLP tasks such as…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
A novel template matching algorithm that can incorporate the concept of deformable parts, is presented in this paper. Unlike the deformable part model (DPM) employed in object recognition, the proposed template-matching approach called…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…