Search results for "Applied Mathematics"
showing 10 items of 4379 documents
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
2015
This is a post-peer-review, pre-copyedit version of an article published in IEEE - ACM Transactions on Computational Biology and Bioinformatics. The final authenticated version is available online at: http://dx.doi.org/10.1109/TCBB.2015.2389958 [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. Computational methods to detect epistasis therefore suffer from prohibitively lon…
A Meshfree Solver for the MEG Forward Problem
2015
Noninvasive estimation of brain activity via magnetoencephalography (MEG) involves an inverse problem whose solution requires an accurate and fast forward solver. To this end, we propose the Method of Fundamental Solutions (MFS) as a meshfree alternative to the Boundary Element Method (BEM). The solution of the MEG forward problem is obtained, via the Method of Particular Solutions (MPS), by numerically solving a boundary value problem for the electric scalar potential, derived from the quasi-stationary approximation of Maxwell’s equations. The magnetic field is then computed by the Biot-Savart law. Numerical experiments have been carried out in a realistic single-shell head geometry. The p…
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
A multi-domain approach for smoothed particle hydrodynamics simulations of highly complex flows
2018
Abstract An efficient and accurate method is proposed to solve the incompressible flow momentum and continuity equations in computational domains partitioned into subdomains in the framework of the smoothed particle hydrodynamics method. The procedure does not require any overlap of the subdomains, which would result in the increase of the computational effort. Perfectly matching solutions are obtained at the surfaces separating neighboring blocks. The block interfaces can be both planar and curved surfaces allowing to easily decompose even geometrically complex domains. The smoothing length of the kernel function is maintained constant in each subdomain, while changing between blocks where…
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2019
Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…
Out-of-Band Signaling Scheme for High Speed Wireless LANs
2007
In recent years, the physical layer data rate provided by 802.11 Wireless LANs has dramatically increased thanks to significant advances in the modulation and coding techniques employed. However, previous studies show that the 802.11 MAC operation, namely the distributed coordination function (DCF), represents a limiting factor: the throughput efficiency drops as the channel bit rate increases, and a throughput upper limit does indeed exist when the channel bit rate goes to infinite high. These findings indicate that the performance of the DCF protocol will not be efficiently improved by merely increasing the channel bit rate. This paper shows that the DCF performance may significantly bene…
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.
2015
De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clusterin…
Least-squares community extraction in feature-rich networks using similarity data
2021
We explore a doubly-greedy approach to the issue of community detection in feature-rich networks. According to this approach, both the network and feature data are straightforwardly recovered from the underlying unknown non-overlapping communities, supplied with a center in the feature space and intensity weight(s) over the network each. Our least-squares additive criterion allows us to search for communities one-by-one and to find each community by adding entities one by one. A focus of this paper is that the feature-space data part is converted into a similarity matrix format. The similarity/link values can be used in either of two modes: (a) as measured in the same scale so that one may …
Wireless ECG and cardiac monitoring systems: State of the art, available commercial devices and useful electronic components
2021
Abstract Wireless ElectroCardioGram (ECG) systems are employed in manifold application fields: tele-monitoring, sport applications, support to ageing people at home, fetal ECG, wearable devices and ambulatory monitoring. The presence of cables often hinders user’s free movements, alongside clinicians’ routine operations. Therefore, wireless ECG systems are desirable. This paper aims at reviewing the solutions described in the literature, besides commercially available devices and electronic components useful to setup laboratory prototypes. Several systems have been developed, different in terms of the adopted technology; when approaching the development of a wireless ECG system, some import…
Measuring the weather’s impact on MAC layer over 2.4GHz outdoor radio links
2015
The weather s impact on the performance of a radio link at the 2.4 GHz ISM (Industry, Scientific and Medical) band had not been yet studied in great detail up to now as it is generally believed that the ultra-high frequency band is not significantly affected by weather conditions. However, our study shows significant correlations between meteorological variables and control frame errors at MAC (Medium Access Control) layer of the IEEE 802.11b/g standard. This study is performed over an outdoor radio link setting which has been monitored for several months. Moreover, we check if link distance and so modulation scheme and data rate are also decisive features of such impact. Our real scenario …