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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

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

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

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

Quan Zhou, Wenlin Chen, Shiji Song, Jacob R. Gardner, Kilian Q. Weinberger, Yixin Chen

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Tags: Algorithms, Biology, CUDA, Genetics, Machine learning, Neuroscience, nVidia, nVidia GeForce GTX Titan, Statistics

September 9, 2014 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, Graph theory, nVidia, Path problems, Tesla C2050, Thesis

July 3, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

Pairwise Sequence Alignment for Very Long Sequences on GPUs

J. Li, S. Ranka, S. Sahni

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Tags: CUDA, Genetics, nVidia, nVidia Tesla C2050, Sequence alignment, Smith-Waterman algorithm

April 2, 2014 by hgpu

Applying GPU Dynamic Parallelism to High-Performance Normalization of Gene Expressions

R.P. Souto, C. Osthoff, A.T.R. de Vasconcelos, D.A. Augusto, P.L. da Silva Dias, A. Rodriguez, O. Trelles, M. Ujaldon

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Tags: CUDA, Genetics, nVidia, Sorting, Tesla K20c

March 22, 2014 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, nVidia, Path problems, Tesla C2050, Tesla C2090, Thesis

December 16, 2013 by hgpu

CFMDS: CUDA-based fast multidimensional scaling for genome-scale data

Sungin Park, Soo-Yong Shin, Kyu-Baek Hwang

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Tags: Bioinformatics, Biology, CUDA, Genetics, Multidimensional scaling, nVidia, Package

June 21, 2013 by hgpu

GPU based Eulerian Assembly of Genomes

Syed Faraz Mahmood

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800, Thesis

March 7, 2013 by hgpu

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Tony Kam-Thong

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Tags: Biology, CUDA, Genetics, Machine learning, nVidia, nVidia GeForce GTX 295, nVidia GeForce GTX 580, Package, Thesis

September 16, 2012 by hgpu

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

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high performance computing on graphics processing units: hgpu.org

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

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

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Pairwise Sequence Alignment for Very Long Sequences on GPUs

Applying GPU Dynamic Parallelism to High-Performance Normalization of Gene Expressions

Exploiting parallel features of modern computer architectures in bioinformatics

CFMDS: CUDA-based fast multidimensional scaling for genome-scale data

GPU based Eulerian Assembly of Genomes

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Recent source codes

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

HPX: a C++ Standard Library for Concurrency and Parallelism

TorchQC: Quantum Dynamics and Machine Learning

Matrix multiplication using Tensor Cores in CUDA

CPP Joules: Energy Measurement tool for CPP/CUDA programs

HPC-Coder-v2

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