Biology | Page 15

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Parallel birth and death process for cell nuclei extraction in histopathology images

Christophe Avenel, Pierre Fortin, Dominique Bereziat

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Tags: Biology, CUDA, Medicine, nVidia, Tesla C2070

July 25, 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

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman

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Tags: Algorithms, Biology, Biomolecules, Fast multipole method, Macromolecule, nVidia, nVidia GeForce GT 330 M, nVidia GeForce GTX 295, OpenCL, RNA

June 12, 2013 by hgpu

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Matthias Alexander Lee

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Tags: Bioinformatics, Biology, Computational Complexity, CUDA, nVidia, Package, Python, RNA, Sequence alignment, Signal processing

May 31, 2013 by hgpu

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

Dylan Jackson

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Tags: Biology, Biomolecules, CUDA, nVidia, nVidia GeForce GTX 680, Sensing, Thesis

May 31, 2013 by hgpu

Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

Ian C. Atkinson, Geng Liu, Nady Obeid, Keith R. Thulborn, Wen-mei Hwu

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Tags: Algorithms, Biology, CUDA, FFT, Image reconstruction, Magnetic resonance imaging, MRI, nVidia, Tesla C2050

May 27, 2013 by hgpu

GPU-accelerated protein family identification for metagenomics

Changjun Wu, Ananth Kalyanaraman

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Tags: Biology, Clustering, CUDA, Graph theory, nVidia, Tesla K20

May 25, 2013 by hgpu

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi

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Tags: Bioinformatics, Biology, Computational biology, CUDA, GPU cluster, Heterogeneous systems, MPI, nVidia, nVidia Quadro FX 2000, Sequence alignment, Tesla K20

May 11, 2013 by hgpu

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Dongliang Xu, Hongli Zhang, Yujian Fan

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Tags: Biology, Computer science, CUDA, Information Retrieval, nVidia, nVidia GeForce 9800 GTS, nVidia GeForce GTX 570, Security, String matching

May 11, 2013 by hgpu

Simulation of Biological Tissue using Mass-Spring-Damper Models

Emil Eriksson

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Tags: ATI, ATI Radeon HD 7970, Biology, OpenCL, Surgical simulation, Thesis, Visualization

May 6, 2013 by hgpu

GPU-based Steady-State Solution of the Chemical Master Equation

Marco Maggioni, Tanya Berger-Wolf, Jie Liang

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Tags: Biology, CUDA, Macromolecule, nVidia, nVidia GeForce GTX 580, Probability, Sparse matrix

May 1, 2013 by hgpu

SW# – GPU enabled exact alignments on genome scale

Matija Korpar, Mile Sikic

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 560, nVidia GeForce GTX 570, nVidia GeForce GTX 690, Package, Sequence alignment, Smith-Waterman algorithm

April 23, 2013 by hgpu

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Accelerating a Linear Programming Algorithm on AMD GPUs

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Towards Efficient and Practical GPU Multitasking in the Era of LLM

Bandicoot: C++ library for GPU accelerated linear algebra

Bandicoot: A Templated C++ Library for GPU Linear Algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

The Fused Kernel Library: A C++ API to Develop Highly-Efficient GPU Libraries

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

Block: Balancing Load in LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

SIGMo: High-Throughput Batched Subgraph Isomorphism on GPUs for Molecular Matching

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

DGEMM without FP64 Arithmetic – using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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high performance computing on graphics processing units: hgpu.org

Applications

Parallel birth and death process for cell nuclei extraction in histopathology images

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

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

GPU-accelerated protein family identification for metagenomics

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Simulation of Biological Tissue using Mass-Spring-Damper Models

GPU-based Steady-State Solution of the Chemical Master Equation

SW# – GPU enabled exact alignments on genome scale

Recent source codes

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Bandicoot: C++ library for GPU accelerated linear algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

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