Related papers: Fast Circular Pattern Matching
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…
The NP-complete Permutation Pattern Matching problem asks whether a $k$-permutation $P$ is contained in a $n$-permutation $T$ as a pattern. This is the case if there exists an order-preserving embedding of $P$ into $T$. In this paper, we…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
Traditional Von Neumann computing is falling apart in the era of exploding data volumes as the overhead of data transfer becomes forbidding. Instead, it is more energy-efficient to fuse compute capability with memory where the data reside.…
With the aggressive scaling of VLSI technology, the explosion of layout patterns creates a critical bottleneck for DFM applications like OPC. Pattern clustering is essential to reduce data complexity, yet existing methods struggle with…
For over a decade now we have been witnessing the success of {\em massive parallel computation} (MPC) frameworks, such as MapReduce, Hadoop, Dryad, or Spark. One of the reasons for their success is the fact that these frameworks are able to…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
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…
Given a string $P$ of length $m$, a longer string $T$ of length $n>m$, and two integers $l\geq 0$ and $r\geq 0$, the context of $P$ in $T$ is the set of all string pairs $(L,R)$, with $|L|=l$ and $|R|=r$, such that the string $LPR$ occurs…
Electromagnetic scattering and absorption by material particles is a fundamental physical problem with a broad range of applications, going from laboratory experiments, biology and material sciences, all the way up to environmental studies…
Many problems in computer science and applied mathematics require rounding a vector $\mathbf{w}$ of fractional values lying in the interval $[0,1]$ to a binary vector $\mathbf{x}$ so that, for a given matrix $\mathbf{A}$,…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some improvements in closing the gaps between the known lower bounds…
Matrices are two-dimensional data structures allowing one to conceptually organize information. For example, adjacency matrices are useful to store the links of a network; correlation matrices are simple ways to arrange gene co-expression…
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…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns…