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Sigurd Vogler, Gökcen Savasci, Martin Ludwig, Christian Ochsenfeld
We introduce a new ansatz to compute hyperfine coupling constants of selected nuclei at the level of second-order Møller-Plesset perturbation (MP2) and double-hybrid density functional theory with reduced computational effort, opening the route to the analyis of hyperfine coupling constants of large molecular structures. Our approach is based on a reformulation of the canonical MP2 term in atomic orbitals, thus exploiting the locality of electron correlation. We show that a perturbation-including integral screening reduces the scaling behavior of the number of significant two-electron integrals to sublinear...
May 15, 2018: Journal of Chemical Theory and Computation
Ernst Joachim Houtgast, Vlad-Mihai Sima, Koen Bertels, Zaid Al-Ars
We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main BWA-MEM computational functions, onto an accelerator. Sequencers typically output reads with a length of 150 base pairs. However, read length is expected to increase in the near future...
April 12, 2018: Computational Biology and Chemistry
Mert Tuzer, Abdulkadir Yazıcı, Rüştü Türkay, Michael Boyman, Burak Acar
PURPOSE: To develop a medical ultrasound (US) simulation method using T1-weighted magnetic resonance images (MRI) as the input that offers a compromise between low-cost ray-based and high-cost realistic wave-based simulations. METHODS: The proposed method uses a novel multi-ray image formation approach with a virtual phased array transducer probe. A domain model is built from input MR images. Multiple virtual acoustic rays are emerged from each element of the linear transducer array...
May 4, 2018: International Journal of Computer Assisted Radiology and Surgery
Jing Huang, Justin A Lemkul, Peter K Eastman, Alexander D MacKerell
Presented is the implementation of the Drude force field in the open-source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms...
May 4, 2018: Journal of Computational Chemistry
Xiaoyong Pan, Hong-Bin Shen
Motivation: RNA-binding proteins (RBPs) take over 5∼10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using pattern learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs...
May 2, 2018: Bioinformatics
Boaz Jessie Jackin, Shinpei Watanabe, Kanemitsu Ootsu, Takeshi Ohkawa, Takashi Yokota, Yoshio Hayasaki, Toyohiko Yatagai, Takanobu Baba
A parallel computation method for large-size Fresnel computer-generated hologram (CGH) is reported. The method was introduced by us in an earlier report as a technique for calculating Fourier CGH from 2D object data. In this paper we extend the method to compute Fresnel CGH from 3D object data. The scale of the computation problem is also expanded to 2 gigapixels, making it closer to real application requirements. The significant feature of the reported method is its ability to avoid communication overhead and thereby fully utilize the computing power of parallel devices...
April 20, 2018: Applied Optics
Rafael Gadea-Gironés, Ricardo Colom-Palero, Vicente Herrero-Bosch
In the optimization of deep neural networks (DNNs) via evolutionary algorithms (EAs) and the implementation of the training necessary for the creation of the objective function, there is often a trade-off between efficiency and flexibility. Pure software solutions implemented on general-purpose processors tend to be slow because they do not take advantage of the inherent parallelism of these devices, whereas hardware realizations based on heterogeneous platforms (combining central processing units (CPUs), graphics processing units (GPUs) and/or field-programmable gate arrays (FPGAs)) are designed based on different solutions using methodologies supported by different languages and using very different implementation criteria...
April 30, 2018: Sensors
Nuttiiya Seekhao, Caroline Shung, Joseph JaJa, Luc Mongeau, Nicole Y K Li-Jessen
Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs...
2018: Frontiers in Physiology
Haifeng Wang, Hanchuan Peng, Yuchou Chang, Dong Liang
Image reconstruction in magnetic resonance imaging (MRI) clinical applications has become increasingly more complicated. However, diagnostic and treatment require very fast computational procedure. Modern competitive platforms of graphics processing unit (GPU) have been used to make high-performance parallel computations available, and attractive to common consumers for computing massively parallel reconstruction problems at commodity price. GPUs have also become more and more important for reconstruction computations, especially when deep learning starts to be applied into MRI reconstruction...
March 2018: Quantitative Imaging in Medicine and Surgery
Raúl García-Calvo, J L Guisado, Fernando Diaz-Del-Rio, Antonio Córdoba, Francisco Jiménez-Morales
Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task...
2018: Evolutionary Bioinformatics Online
Yiqun Yang, Matthew W Urban, Robert J McGough
Shear wave calculations induced by an acoustic radiation force are very time-consuming on desktop computers, and high-performance graphics processing units (GPUs) achieve dramatic reductions in the computation time for these simulations. The acoustic radiation force is calculated using the fast near field method (FNM) and the angular spectrum approach (ASA), and then the shear waves are calculated in parallel with Green's functions on a GPU. This combination enables rapid evaluation of shear waves for push beams with different spatial samplings and for apertures with different f/#...
April 16, 2018: Physics in Medicine and Biology
Moustafa Alzantot, Yingnan Wang, Zhengshuang Ren, Mani B Srivastava
Mobile devices have become an essential part of our daily lives. By virtue of both their increasing computing power and the recent progress made in AI, mobile devices evolved to act as intelligent assistants in many tasks rather than a mere way of making phone calls. However, popular and commonly used tools and frameworks for machine intelligence are still lacking the ability to make proper use of the available heterogeneous computing resources on mobile devices. In this paper, we study the benefits of utilizing the heterogeneous (CPU and GPU) computing resources available on commodity android devices while running deep learning models...
June 2017: MobiSys ...: the ... International Conference on Mobile Systems, Applications and Services. International Conference on Mobile Systems, Applications, and Services
Rüdiger Göbl, Nassir Navab, Christoph Hennersperger
PURPOSE: Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in special hardware, resulting in limited flexibility of implemented processing steps on such platforms. METHODS: With SUPRA, we propose an open-source pipeline for fully software-defined ultrasound processing for real-time applications to alleviate these problems...
March 28, 2018: International Journal of Computer Assisted Radiology and Surgery
Shanshan Ren, Koen Bertels, Zaid Al-Ars
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm...
2018: Evolutionary Bioinformatics Online
Julia Mascolo-Fortin, Dmitri Matenine, Louis Archambault, Philippe Després
BACKGROUND: Four-dimensional cone beam computed tomography allows for temporally resolved imaging with useful applications in radiotherapy, but raises particular challenges in terms of image quality and computation time. OBJECTIVE: The purpose of this work is to develop a fast and accurate 4D algorithm by adapting a GPU-accelerated ordered subsets convex algorithm (OSC), combined with the total variation minimization regularization technique (TV). METHODS: Different initialization schemes were studied to adapt the OSC-TV algorithm to 4D reconstruction: each respiratory phase was initialized either with a 3D reconstruction or a blank image...
March 15, 2018: Journal of X-ray Science and Technology
Gang Mei, Jiayin Zhang, Nengxiong Xu, Kunyang Zhao
The strategy of Divide-and-Conquer (D&C) is one of the frequently used programming patterns to design efficient algorithms in computer science, which has been parallelized on shared memory systems and distributed memory systems. Tzeng and Owens specifically developed a generic paradigm for parallelizing D&C algorithms on modern Graphics Processing Units (GPUs). In this paper, by following the generic paradigm proposed by Tzeng and Owens, we provide a new and publicly available GPU implementation of the famous D&C algorithm, QuickHull, to give a sample and guide for parallelizing D&C algorithms on the GPU...
January 2018: Heliyon
Thomas Kovac, Tom Haber, Frank Van Reeth, Niel Hens
BACKGROUND: Over the last years, substantial effort has been put into enhancing our arsenal in fighting epidemics from both technological and theoretical perspectives with scientists from different fields teaming up for rapid assessment of potentially urgent situations. This paper focusses on the computational aspects of infectious disease models and applies commonly available graphics processing units (GPUs) for the simulation of these models. However, fully utilizing the resources of both CPUs and GPUs requires a carefully balanced heterogeneous approach...
March 16, 2018: BMC Bioinformatics
Daniel J Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J Andrew McCammon, Ross C Walker
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average...
March 12, 2018: Journal of Computational Chemistry
Wing-Kin Tam, Yang Zhi
BACKGROUND: Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. NEW METHOD: In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs)...
March 9, 2018: Journal of Neuroscience Methods
M Radek, J-G Tenberge, S Hilke, G Wilde, M Peterlechner
Electron microscopy images are interference patterns and can generally not be interpreted in a straight forward manner. Typically, time consuming numerical simulations have to be employed to separate specimen features from imaging artifacts. Directly comparing numerical predictions to experimental results, realistic simulation box sizes and varying imaging parameters are needed. In this work, we introduce an accelerated multislice algorithm, named STEMcl, that is capable of simulating series of large super cells typical for defective and amorphous systems, in addition to parameter series using the massive parallelization accessible in today's commercial PC-hardware, e...
February 16, 2018: Ultramicroscopy
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