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https://www.readbyqxmd.com/read/28208684/a-real-time-high-performance-computation-architecture-for-multiple-moving-target-tracking-based-on-wide-area-motion-imagery-via-cloud-and-graphic-processing-units
#1
Kui Liu, Sixiao Wei, Zhijiang Chen, Bin Jia, Genshe Chen, Haibin Ling, Carolyn Sheaff, Erik Blasch
This paper presents the first attempt at combining Cloud with Graphic Processing Units (GPUs) in a complementary manner within the framework of a real-time high performance computation architecture for the application of detecting and tracking multiple moving targets based on Wide Area Motion Imagery (WAMI). More specifically, the GPU and Cloud Moving Target Tracking (GC-MTT) system applied a front-end web based server to perform the interaction with Hadoop and highly parallelized computation functions based on the Compute Unified Device Architecture (CUDA©)...
February 12, 2017: Sensors
https://www.readbyqxmd.com/read/28198568/compressed-sensing-mri-reconstruction-from-3d-multichannel-data-using-gpus
#2
Ching-Hua Chang, Xiangdong Yu, Jim X Ji
PURPOSE: To accelerate iterative reconstructions of compressed sensing (CS) MRI from 3D multichannel data using graphics processing units (GPUs). METHODS: The sparsity of MRI signals and parallel array receivers can reduce the data acquisition requirements. However, iterative CS reconstructions from data acquired using an array system may take a significantly long time, especially for a large number of parallel channels. This paper presents an efficient method for CS-MRI reconstruction from 3D multichannel data using GPUs...
February 15, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28160511/efficient-gaussian-density-formulation-of-volume-and-surface-areas-of-macromolecules-on-graphical-processing-units
#3
Baofeng Zhang, Denise Kilburg, Peter Eastman, Vijay S Pande, Emilio Gallicchio
We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii...
February 4, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28141583/towards-real-time-photon-monte-carlo-dose-calculation-in-the-cloud
#4
Peter Ziegenhein, Igor Kozin, Cornelis Philippus Kamerling, Uwe Oelfke
Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as GPUs or clusters of central processing units (CPU)-based system. Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations...
January 31, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28140352/initial-development-of-gocmc-a-gpu-oriented-fast-cross-platform-monte-carlo-engine-for-carbon-ion-therapy
#5
Nan Qin, Marco Pinto, Zhen Tian, Georgios Dedes, Arnold Pompos, Steve Jiang, Katia Parodi, Xun Jia
Monte Carlo (MC) simulation is considered as the most accurate method for calculation of absorbed dose and fundamental physics quantities related to biological effects in carbon ion therapy. To improve its computational efficiency, we have developed a GPU-oriented fast MC package named goCMC, for carbon therapy. goCMC simulates particle transport in voxelized geometry with kinetic energy up to 450 MeV/u. Class II condensed history simulation scheme with a continuous slowing down approximation was employed. Energy straggling and multiple scattering were modeled...
January 31, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28129194/securemed-secure-medical-computation-using-gpu-accelerated-homomorphic-encryption-scheme
#6
Alhassan Khedr, Glenn Gulak
Sharing the medical records of individuals among healthcare providers and researchers around the world can accelerate advances in medical research. While the idea seems increasingly practical due to cloud data services, maintaining patient privacy is of paramount importance. Standard encryption algorithms help protect sensitive data from outside attackers but they cannot be used to compute on this sensitive data while being encrypted. Homomorphic Encryption (HE) presents a very useful tool that can compute on encrypted data without the need to decrypt it...
January 23, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28109237/atomic-orbital-based-sos-mp2-with-tensor-hypercontraction-ii-local-tensor-hypercontraction
#7
Chenchen Song, Todd J Martínez
In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28087515/h-blast-a-fast-protein-sequence-alignment-toolkit-on-heterogeneous-computers-with-gpus
#8
Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
MOTIVATION: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. RESULTS: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
January 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28049411/accelerating-metagenomic-read-classification-on-cuda-enabled-gpus
#9
Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt
BACKGROUND: Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28048442/su-d-206-02-evaluation-of-partial-storage-of-the-system-matrix-for-cone-beam-computed-tomography-using-a-gpu-platform
#10
D Matenine, G Cote, J Mascolo-Fortin, Y Goussard, P Despres
PURPOSE: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons' trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. METHODS: We propose an optimized implementation of the Siddon's algorithm using graphics processing units (GPUs) with a novel data storage scheme...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047350/su-f-t-256-4d-imrt-planning-using-an-early-prototype-gpu-enabled-eclipse-workstation
#11
A Hagan, A Modiri, M Svatos, A Sawant
PURPOSE: True 4D IMRT planning, based on simultaneous spatiotemporal optimization has been shown to significantly improve plan quality in lung radiotherapy. However, the high computational complexity associated with such planning represents a significant barrier to widespread clinical deployment. We introduce an early prototype GPU-enabled Eclipse workstation for inverse planning. To our knowledge, this is the first GPUintegrated Eclipse system demonstrating the potential for clinical translation of GPU computing on a major commercially-available TPS...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046636/tu-ab-brc-10-modeling-of-radiotherapy-linac-source-terms-using-archer-monte-carlo-code-performance-comparison-of-gpu-and-mic-computing-accelerators
#12
T Liu, H Lin, L Su, C Shi, X Tang, B Bednarz, X Xu
PURPOSE: (1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods. METHODS: The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046368/su-d-206-01-employing-a-novel-consensus-optimization-strategy-to-achieve-iterative-cone-beam-ct-reconstruction-on-a-multi-gpu-platform
#13
B Li, Z Tian, L Zhou, S Jiang, X Jia
PURPOSE: While compressed sensing-based cone-beam CT (CBCT) iterative reconstruction techniques have demonstrated tremendous capability of reconstructing high-quality images from undersampled noisy data, its long computation time still hinders wide application in routine clinic. The purpose of this study is to develop a reconstruction framework that employs modern consensus optimization techniques to achieve CBCT reconstruction on a multi-GPU platform for improved computational efficiency...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046330/su-g-tep1-15-toward-a-novel-gpu-accelerated-deterministic-solution-to-the-linear-boltzmann-transport-equation
#14
R Yang, B Fallone, J St Aubin
PURPOSE: To develop a Graphic Processor Unit (GPU) accelerated deterministic solution to the Linear Boltzmann Transport Equation (LBTE) for accurate dose calculations in radiotherapy (RT). A deterministic solution yields the potential for major speed improvements due to the sparse matrix-vector and vector-vector multiplications and would thus be of benefit to RT. METHODS: In order to leverage the massively parallel architecture of GPUs, the first order LBTE was reformulated as a second order self-adjoint equation using the Least Squares Finite Element Method (LSFEM)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28018839/a-distributed-astra-toolbox
#15
Willem Jan Palenstijn, Jeroen Bédorf, Jan Sijbers, K Joost Batenburg
While iterative reconstruction algorithms for tomography have several advantages compared to standard backprojection methods, the adoption of such algorithms in large-scale imaging facilities is still limited, one of the key obstacles being their high computational load. Although GPU-enabled computing clusters are, in principle, powerful enough to carry out iterative reconstructions on large datasets in reasonable time, creating efficient distributed algorithms has so far remained a complex task, requiring low-level programming to deal with memory management and network communication...
2017: Advanced Structural and Chemical Imaging
https://www.readbyqxmd.com/read/28008220/prefiltering-model-for-homology-detection-algorithms-on-gpu
#16
Germán Retamosa, Luis de Pedro, Ivan González, Javier Tamames
Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27991456/a-new-approach-to-integrate-gpu-based-monte-carlo-simulation-into-inverse-treatment-plan-optimization-for-proton-therapy
#17
Yongbao Li, Zhen Tian, Ting Song, Zhaoxia Wu, Yaqiang Liu, Steve Jiang, Xun Jia
Monte Carlo (MC)-based spot dose calculation is highly desired for inverse treatment planning in proton therapy because of its accuracy. Recent studies on biological optimization have also indicated the use of MC methods to compute relevant quantities of interest, e.g. linear energy transfer. Although GPU-based MC engines have been developed to address inverse optimization problems, their efficiency still needs to be improved. Also, the use of a large number of GPUs in MC calculation is not favorable for clinical applications...
January 7, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27976899/ab-initio-multiple-spawning-photochemical-dynamics-of-dmabn-using-gpus
#18
Basile F E Curchod, Aaron Sisto, Todd J Martínez
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group...
January 3, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27958738/extreme-gradient-boosting-as-a-method-for-quantitative-structure-activity-relationships
#19
Robert P Sheridan, Wei Min Wang, Andy Liaw, Junshui Ma, Eric M Gifford
In the pharmaceutical industry it is common to generate many QSAR models from training sets containing a large number of molecules and a large number of descriptors. The best QSAR methods are those that can generate the most accurate predictions but that are not overly expensive computationally. In this paper we compare eXtreme Gradient Boosting (XGBoost) to random forest and single-task deep neural nets on 30 in-house data sets. While XGBoost has many adjustable parameters, we can define a set of standard parameters at which XGBoost makes predictions, on the average, better than those of random forest and almost as good as those of deep neural nets...
December 27, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/27925252/the-gpu-enabled-divide-expand-consolidate-ri-mp2-method-dec-ri-mp2
#20
Dmytro Bykov, Thomas Kjaergaard
We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller-Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm...
February 5, 2017: Journal of Computational Chemistry
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