Related papers: PHONI: Streamed Matching Statistics with Multi-Gen…
The pattern matching problem with swaps is to find all occurrences of a pattern in a text while allowing the pattern to swap adjacent symbols. The goal is to design fast matching algorithm that takes advantage of the bit parallelism of…
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. In the last two…
One of the most fundamental tasks in data science is to assist a user with unknown preferences in finding high-utility tuples within a large database. To accurately elicit the unknown user preferences, a widely-adopted way is by asking the…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Finding patterns in large highly connected datasets is critical for value discovery in business development and scientific research. This work focuses on the problem of subgraph matching on streaming graphs, which provides utility in a…
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…
Big data problems frequently require processing datasets in a streaming fashion, either because all data are available at once but collectively are larger than available memory or because the data intrinsically arrive one data point at a…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
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…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
We present a new streaming algorithm for the $k$-Mismatch problem, one of the most basic problems in pattern matching. Given a pattern and a text, the task is to find all substrings of the text that are at the Hamming distance at most $k$…
A central problem in data streams is to characterize which functions of an underlying frequency vector can be approximated efficiently. Recently there has been considerable effort in extending this problem to that of estimating functions of…
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…
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,…
Permutation patterns and pattern avoidance are central, well-studied concepts in combinatorics and computer science. Given two permutations $\tau$ and $\pi$, the pattern matching problem (PPM) asks whether $\tau$ contains $\pi$. This…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
We investigate the problem of deterministic pattern matching in multiple streams. In this model, one symbol arrives at a time and is associated with one of s streaming texts. The task at each time step is to report if there is a new match…
With the explosion of the size of digital dataset, the limiting factor for decomposition algorithms is the \emph{number of passes} over the input, as the input is often stored out-of-core or even off-site. Moreover, we're only interested in…