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Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs

Zheming Jin, Jeffrey S. Vetter

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Tags: AMD Radeon Instinct MI100, AMD Radeon Instinct MI60, AMD Radeon VII, ATI, ATI Radeon HD 7870, Bioinformatics, Biology, OpenCL, performance portability, RNA, SYCL

October 1, 2023 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

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

Rahul Shirude, Valmik B. Nikam, B.B. Meshram

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX Titan, RNA, Sequence alignment, String matching, Tesla K20

July 26, 2014 by hgpu

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Kedhar M, DR. M. Rajasekhara Babu, Mayank G, Abhinivesh M

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Tags: Bioinformatics, Biology, CUDA, nVidia, Programming techniques, RNA, Sequence alignment, Tesla C2070

July 12, 2014 by hgpu

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Shuang Wang, Jihoon Kim, Xiaoqian Jiang, Stefan F Brunner, Lucila Ohno-Machado

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Smith-Waterman algorithm, Tesla M2090

May 10, 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

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

DynaProg for Scala: A Scala DSL for Dynamic Programming on CPU and GPU

Thierry Coppey

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Tags: Computer science, CUDA, Heterogeneous systems, High-level Languages, nVidia, nVidia GeForce GT 650 M, Package, RNA, Smith-Waterman algorithm

November 4, 2013 by hgpu

High-performance Dynamic Programming on FPGAs with OpenCL

Sean O. Settle

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Tags: Bioinformatics, Computer science, FPGA, Heterogeneous systems, OpenCL, RNA, Smith-Waterman algorithm

October 29, 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

Faster Algorithms for RNA-folding using the Four-Russians method

Balaji Venkatachalam, Yelena Frid, Dan Gusfield

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 550 Ti, RNA, Tesla C2070

January 30, 2013 by hgpu

CFAL-bench

Comparing Parallel Functional Array Languages: Programming and Performance

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

Data-efficient LLM Fine-tuning for Code Generation

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

DeepCompile: A Compiler-Driven Approach to Optimizing Distributed Deep Learning Training

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

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high performance computing on graphics processing units: hgpu.org

Experience Migrating OpenCL to SYCL: A Case Study on Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases on AMD GPUs

A Massively Parallel Algorithm for Cell Classification Using CUDA

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Multicore and GPU Algorithms for Nussinov RNA Folding

Accelerating calculations of RNA secondary structure partition functions using GPUs

DynaProg for Scala: A Scala DSL for Dynamic Programming on CPU and GPU

High-performance Dynamic Programming on FPGAs with OpenCL

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

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Faster Algorithms for RNA-folding using the Four-Russians method

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CFAL-bench

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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