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hgpu.org » Applications » Biology

Exercising high-level parallel programming on streams: a systems biology use case

Marco Aldinucci, Maurizio Drocco, Guilherme Peretti Pezzi, Claudia Misale, Fabio Tordini, Massimo Torquati

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Tags: Bioinformatics, Biology, Cloud, CUDA, Monte Carlo simulation, nVidia, Tesla K40

April 30, 2014 by hgpu

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Kai Xu, Yiwen Wang, Fang Wang, Yuxi Liao, Qiaosheng Zhang, Hongbao Li, Xiaoxiang Zheng

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Tags: Algorithms, Biology, CUDA, nVidia, nVidia GeForce GT 730 M

April 25, 2014 by hgpu

Local Alignment Tool Based on Hadoop Framework and GPU Architecture

Che-Lun Hun, Guan-Jie Hua

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Tags: Biology, Cloud, CUDA, Hadoop, MapReduce, nVidia, nVidia GeForce GTS 480, Sequence alignment

April 19, 2014 by hgpu

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle

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Source codes

Tags: Bayesian, Biology, CUDA, Machine learning, Neural networks, nVidia, Package, Python

April 17, 2014 by hgpu

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M

April 16, 2014 by hgpu

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M, Sorting

April 16, 2014 by hgpu

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Neri Mickael, Denis Mestivier

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, Optimization, Stochastic simulation, Tesla K10, Tesla K20, Tesla M2075, Tesla M2090

April 4, 2014 by hgpu

Multicore and GPU Algorithms for Nussinov RNA Folding

J. Li, S. Ranka, S. Sahni

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Tags: Biology, CUDA, nVidia, nVidia Tesla C2050, RNA

April 3, 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

Competing computational approaches to reaction-diffusion equations in clusters of cells

S. Stella, R. Chignola, E. Milotti

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Tags: Biology, CUDA, Diffusion equation, Medicine, nVidia, nVidia Quadro 4000, Partial differential equations, PDEs

March 19, 2014 by hgpu

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Usman Roshan

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Tags: Bioinformatics, Biology, CUDA, nVidia, Short read mapping, Smith-Waterman algorithm, Tesla M2050

March 12, 2014 by hgpu

Parallelization of DNA alignment algorithms using GPUs

Gustavo Encarnacao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Sequence matching, Suffix trees

March 7, 2014 by hgpu

Vortex: Overcoming Memory Capacity Limitations in GPU-Accelerated Large-Scale Data Analytics

HexGen: Generative Inference of Large Language Model over Heterogeneous Environment

Demystifying Cost-Efficiency in LLM Serving over Heterogeneous GPUs

Ilargi: a GPU Compatible Factorized ML Model Training Framework

MPI-CorrBench 2.0.0

Modernization and Optimization of MPI Codes

VFLog: vertical + gpu + free join + datalog

Column-Oriented Datalog on the GPU

ViVid Project

Exploring data flow design and vectorization with oneAPI for streaming applications on CPU+GPU

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Multicore and GPU Algorithms for Nussinov RNA Folding

Pairwise Sequence Alignment for Very Long Sequences on GPUs

Competing computational approaches to reaction-diffusion equations in clusters of cells

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Parallelization of DNA alignment algorithms using GPUs

Recent source codes

cuSZp: Fast GPU error-bounded lossy compressor for floating-point data

Kokkos C++ Performance Portability Programming EcoSystem

Training-free Post-training Efficient Sub-quadratic Complexity Attention

Vortex: Overcoming Memory Capacity Limitations in GPU-Accelerated Large-Scale Data Analytics

HexGen: Generative Inference of Large Language Model over Heterogeneous Environment

Ilargi: a GPU Compatible Factorized ML Model Training Framework

MPI-CorrBench 2.0.0

VFLog: vertical + gpu + free join + datalog

ViVid Project

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

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