We present a string-matching program that runs on the GPU. Our program, Cmatch, achieves a speedup of as much as 35x on a recent GPU over the equivalent CPU-bound version. String matching has a long history in computational biology with roots in finding similar proteins and gene sequences in a database of known sequences. The explosion in sequence data available in the 80s and 90s motivated the...

ExpaRNA’s core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ExpaRNA-P that solves the lifted problem of finding such sets of exact matchings in entire Boltzmann-distributed structure ensembles of two RNAs. Due to a novel kind of structural sparsification, the new algorithm maintains the time and space compl...

One of the main objectives of cloud computing providers is increasing the revenue of their cloud datacenters by accommodating virtual network requests as many as possible. However, arrival and departure of virtual network requests fragment physical network’s resources and reduce the possibility of accepting more virtual network requests. To increase the number of virtual network requests accomm...

Network virtualization allows cloud infrastructure providers to accommodate multiple virtual networks on a single physical network. However, mapping multiple virtual network resources to physical network components, called virtual network embedding (VNE), is known to be non-deterministic polynomial-time hard (NP-hard). Effective virtual network embedding increases the revenue by increasing the ...

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 ∆, the exact string matching problem consists of finding all occurrences of P in T . For this problem, we present algorithms that in O(n∆) time preprocess P to essentially identify sparse(P ), a rarely occurring substring of P , and then use it to find occurr...

This paper proposes a novel algorithm for complete exact patternmatching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improve...

In this paper we present an elegant pixel-based texture synthesis technique which is able to generate visually pleasing results from source textures of both stochastic and structured nature. Inspired by the observation that the most common artefacts which occur when synthesizing textures are high frequency discontinuities, our technique tries to avoid these artefacts by forcing at least one of ...

To start with, having employed transformation wave, some nonlinear partial differential equations have been converted into an ODE. Then, using the infinite series method for equations with similar linear part, the researchers have earned the exact soliton solutions of the selected equations. It is required to state that the infinite series method is a well-organized method for obtaining exact s...

Unlike traditional minutiae-based fingerprint matching approach, which establishes the minutiae correspondence between two fingerprints, in this paper a novel ridge-based fingerprint matching algorithm, which establishes the exact ridge correspondence between two fingerprints is proposed. The ridge correspondence is called ‘exact’ because correspondences between points on ridges are also establ...