high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang

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Tags: Bioinformatics, Biology, CUDA, Deep learning, Neural networks, NLP, nVidia, Package, Python, Tesla K20, Text mining

August 1, 2016 by hgpu

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

Marius Erbert, Steffen Rechner, Matthias Muller-Hannemann

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 970, nVidia GeForce GTX Titan, Package

July 26, 2016 by hgpu

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl

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Tags: Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti

July 5, 2016 by hgpu

PROJECTION Algorithm for Motif Finding on GPUs

Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna

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Tags: Algorithms, Biology, Computational biology, CUDA, nVidia

May 26, 2016 by hgpu

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

Kenichi W. Okamoto, Priyanga Amarasekare

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 690, Package

April 3, 2016 by hgpu

A Massively Parallel Algorithm for Cell Classification Using CUDA

Samuel Schmidt

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Tags: Bioinformatics, Biology, CUDA, Machine learning, nVidia, nVidia GeForce GTX 770, RNA, Thesis

March 20, 2016 by hgpu

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

David S. Lawrie

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Tags: Algorithms, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 780 M, nVidia GeForce GTX 980

March 10, 2016 by hgpu

GeNN: a code generation framework for accelerated brain simulations

Esin Yavuz, James Turner, Thomas Nowotny

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Tags: Biology, Code generation, CUDA, Neural networks, Neuroscience, Numerical simulation, nVidia, nVidia Quadro K 2000 M, Package, Tesla C2070, Tesla K40

January 29, 2016 by hgpu

Pairwise Sequence Alignment with Gaps with GPU

Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 650, OpenCL, Sequence alignment

October 27, 2015 by hgpu

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Lev E. Givon, Aurel A. Lazar

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Tags: Biology, Computer science, CUDA, nVidia, OpenMPI, Tesla K20

October 22, 2015 by hgpu

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Particle swarm optimization, Sequence alignment, Tesla C1060

July 24, 2015 by hgpu

Multiple String Matching on a GPU using CUDAs

Charalampos S. Kouzinopoulos, Panagiotis D. Michailidis, Konstantinos G. Margaritis

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 280, String matching

July 10, 2015 by hgpu

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Scaling Deep Learning on GPU and Knights Landing clusters

ParTeCL: parallel testing using OpenCL

DenseNet: Densely Connected Convolutional Networks

Memory-Efficient Implementation of DenseNets

SVMbenchmark: CUDA and OpenCL SVM training benchmark

A Comparison of Support Vector Machines Training GPU-Accelerated Open Source Implementations

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high performance computing on graphics processing units: hgpu.org

Applications

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

PROJECTION Algorithm for Motif Finding on GPUs

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

A Massively Parallel Algorithm for Cell Classification Using CUDA

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

GeNN: a code generation framework for accelerated brain simulations

Pairwise Sequence Alignment with Gaps with GPU

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Multiple String Matching on a GPU using CUDAs

Recent source codes

Scaling Deep Learning on GPU and Knights Landing clusters

Gpufit: GPU-accelerated Levenberg-Marquardt curve fitting in CUDA

GARDENIA: Graph Analytics Repository for Designing Next-Generation Accelerators

GPU-benchmarks

bit-reversal-methods

bifrost: A stream processing framework for high-throughput applications

NEMATUS: Open-Source Neural Machine Translation in Theano

ParTeCL: parallel testing using OpenCL

DenseNet: Densely Connected Convolutional Networks

SVMbenchmark: CUDA and OpenCL SVM training benchmark

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International Conference on Intelligent Autonomous Systems (ICIAS), 2018

International Conference on Robotics and Intelligent System (ICRIS), 2018

International Conference on Image and Graphics Processing (ICIGP), 2018

8th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB), 2018

The 10th International Conference on Computer Modeling and Simulation (ICCMS), 2018