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Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs

Daniel Junger, Christian Hundt, Jorge Gonzalez-Dominguez, Bertil Schmidt

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Tags: Algorithms, Bioinformatics, Clustering, Computer science, CUDA, Filtering, nVidia, nVidia GeForce GTX Titan X

September 3, 2016 by hgpu

Iterative Hard Thresholding for Model Selection in Genome-Wide Association Studies

Kevin L. Keys, Gary K. Chen, Kenneth Lange

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Tags: Bioinformatics, Genetics, Machine learning, nVidia, OpenCL, Package, Statistics, Tesla C2050

August 8, 2016 by hgpu

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

Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters

Yongchao Liu, Tony Pan, Srinivas Aluru

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Tags: Algorithms, Bioinformatics, Computer science, Intel Xeon Phi, OpenMP

May 7, 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

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

Density-based parallel skin lesion border detection with webCL

James Lemon, Sinan Kockara, Tansel Halic, Mutlu Mete

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Tags: Algorithms, Bioinformatics, Clustering, Heterogeneous systems, Image processing, Java, OpenCL

October 16, 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

Accelerating DNA Sequence Analysis using Intel Xeon Phi

Suejb Memeti, Sabri Pllana

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Tags: Bioinformatics, Computer science, Intel Xeon Phi, OpenMP, Performance

July 1, 2015 by hgpu

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla K20

June 30, 2015 by hgpu

Concurrent Task Execution on the Intel Xeon Phi

Yucheng Zhu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Intel Xeon Phi, nVidia, OpenMP, Sequence alignment, Smith-Waterman algorithm, Tesla K20, Thesis

June 22, 2015 by hgpu

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

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high performance computing on graphics processing units: hgpu.org

Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs

Iterative Hard Thresholding for Model Selection in Genome-Wide Association Studies

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

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

Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters

A Massively Parallel Algorithm for Cell Classification Using CUDA

Pairwise Sequence Alignment with Gaps with GPU

Density-based parallel skin lesion border detection with webCL

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Accelerating DNA Sequence Analysis using Intel Xeon Phi

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Concurrent Task Execution on the Intel Xeon Phi

Recent source codes

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Ginkgo: high-performance linear algebra library for manycore systems

AlphaFold2

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