high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Accelerated protein structure comparison using TM-score-GPU

Ling-Hong Hung, Ram Samudrala

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, Clustering, OpenCL, Package

October 5, 2012 by hgpu

Compute Distance Matrices with GPU

Seongho Kim, Ming Ouyang

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Tesla C2050

October 1, 2012 by hgpu

ARVO-CL: The OpenCL version of the ARVO package – An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Jan Busa Jr., Shura Hayryan, Ming-Chya Wu, Jan Busa, Chin-Kun Hu

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Tags: Algorithms, Biology, Computer science, nVidia, nVidia GeForce GTX 480, OpenCL

September 30, 2012 by hgpu

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

You Li, Xiaowen Chu

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 280, Spectrometry

September 25, 2012 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

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Qianghua Zhu, Fei Xia, Guoqing Jin

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 470, Sequence alignment, Sequence matching, Smith-Waterman algorithm

September 16, 2012 by hgpu

High-Throughput parallel blind Virtual Screening using BINDSURF

Irene Sanchez-Linares, Horacio Perez-Sanchez, Jose M Cecilia, Jose M Garcia

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Tesla C2050

September 15, 2012 by hgpu

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

Fahian Ahmed, Saddam Quirem, Gak Min, Byeong Kil Lee

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Tesla C1060

September 12, 2012 by hgpu

GPU accelerated QTL detection

G. Chapuis, O. Filangi, J.M. Elsen, D. Lavenier, P. Le Roy

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Tesla C2050

September 11, 2012 by hgpu

CUDA-Accelerated Data-Mining for Putative Heteromeric Transcription Factors and Target Genes Using Microarray Gene Expression Profiles

Edward A. Salinas, Amitava Karmaker

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Tags: Algorithms, Biology, Computer science, CUDA, Data mining, nVidia, nVidia GeForce GTX 590

August 31, 2012 by hgpu

High performance transcription factor-DNA docking with GPU computing

Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo

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Tags: Algorithms, Benchmarking, Bioinformatics, Biology, CUDA, Genetics, GPU cluster, nVidia, Tesla M2070

August 20, 2012 by hgpu

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Search, Sequence alignment

August 17, 2012 by hgpu

True 4-Bit Quantized CNN Training on CPU

True 4-Bit Quantized Convolutional Neural Network Training on CPU: Achieving Full-Precision Parity

cuFuzz: A GPU-oriented coverage-guided fuzzer for userland CUDA application

Hunting CUDA Bugs at Scale with cuFuzz

KernelSkill: A Multi-Agent Framework for GPU Kernel Optimization

MSKernelBench & CUDAMaster

Making LLMs Optimize Multi-Scenario CUDA Kernels Like Experts

EvoScientist: Harness Vibe Research with Self-evolving AI Scientists

EvoScientist: Towards Multi-Agent Evolving AI Scientists for End-to-End Scientific Discovery

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build & Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build & Test Pipeline of Code Repositories on ANY Language and ANY Platform

CONCUR: a benchmark designed to evaluate multithreaded Java code generated by LLMs

CONCUR: Benchmarking LLMs for Concurrent Code Generation

HIPRT: Ray Tracing using HIP

Ray Tracing using HIP

MXFP4 Training Support Codebase

Practical FP4 Training for Large-Scale MoE Models on Hopper GPUs

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Accelerated protein structure comparison using TM-score-GPU

Compute Distance Matrices with GPU

ARVO-CL: The OpenCL version of the ARVO package – An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

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

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

High-Throughput parallel blind Virtual Screening using BINDSURF

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

GPU accelerated QTL detection

CUDA-Accelerated Data-Mining for Putative Heteromeric Transcription Factors and Target Genes Using Microarray Gene Expression Profiles

High performance transcription factor-DNA docking with GPU computing

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Recent source codes

True 4-Bit Quantized CNN Training on CPU

cuFuzz: A GPU-oriented coverage-guided fuzzer for userland CUDA application

KernelSkill: A Multi-Agent Framework for GPU Kernel Optimization

MSKernelBench & CUDAMaster

EvoScientist: Harness Vibe Research with Self-evolving AI Scientists

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

CONCUR: a benchmark designed to evaluate multithreaded Java code generated by LLMs

HIPRT: Ray Tracing using HIP

MXFP4 Training Support Codebase

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