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Interactive GPU active contours for segmenting inhomogeneous objects

Chris G. Willcocks, Philip T. G. Jackson, Carl J. Nelson, Amar V. Nasrulloh, Boguslaw Obara

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Tags: Biology, Image processing, Medicine, nVidia, nVidia GeForce GTX Titan X, OpenCL, Package

February 9, 2018 by hgpu

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J. Andrew McCammon, Ross C. Walker

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 1080 Ti, nVidia GeForce GTX Titan X

January 20, 2018 by hgpu

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana L. Varbanescu, Jan-Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 1070, OpenCL, Package, Python, Sequence alignment, Smith-Waterman algorithm

January 13, 2018 by hgpu

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

Nilay Khare, Alind Khare and Farhan Khan

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Tags: Algorithms, Bioinformatics, Biology, BLAST, CUDA, Hadoop, nVidia, nVidia Quadro 2000, nVidia Quadro 600, Tesla C2075

December 3, 2017 by hgpu

A Hybrid-parallel Architecture for Applications in Bioinformatics

Jan Christian Kassens

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, FPGA, nVidia, nVidia GeForce GTX 780 Ti, Thesis

December 3, 2017 by hgpu

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Ernst Joachim Houtgast, Vlad-Mihai Sima, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, FPGA, OpenCL, Smith-Waterman algorithm

November 26, 2017 by hgpu

Accelerating Genomics Research with OpenCL and FPGAs

Chris Rauer, George S. Powley, Mir Ahsan, Nicholas Finamore

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Tags: Algorithms, Biology, Computer science, FPGA, Genomics, OpenCL

October 15, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider

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Tags: Biology, Computer science, Java, Next-Generation sequencing, nVidia, OpenCL, Package, R, Tesla K20

August 26, 2017 by hgpu

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Zelimkhan Gerikhanov

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Tags: AMD Radeon HD 8970 M, ATI, Biology, Biomechanics, FEM, Finite element method, Medicine, MRI, OpenCL, Thesis

August 17, 2017 by hgpu

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Adrian Przybylski, Bjorn Thiel, Jan Keller-Findeisen, Bernd Stock, Mark Bates

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Tags: Biology, Computer science, CUDA, Microscopy, nVidia, nVidia GeForce GTX 1080, Package, Python

August 17, 2017 by hgpu

TVM: Open deep learning compiler stack for cpu, gpu and specialized accelerators

TVM: An Automated End-to-End Optimizing Compiler for Deep Learning

MyCaffe: A complete deep learning platform written almost entirely in C# for Windows developers

MyCaffe: A Complete C# Re-Write of Caffe with Reinforcement Learning

Characterising Across-Stack Optimisations for Deep Convolutional Neural Networks

Using the Tsetlin Machine to Learn Human-Interpretable Rules for High-Accuracy Text Categorization with Medical Applications

ZUCL: A ZYNQ UltraScale+ Framework for OpenCL HLS Applications

CL-kmeans: Efficient k-Means in OpenCL

Efficient and Scalable k-Means on GPUs

Doctor AI: Interpretable Deep Learning for Modeling Electronic Health Records

pyJac: a Python package that generates source code used to analytically calculate chemical kinetics Jacobian matrices

Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms

CUTLASS: CUDA Templates for Linear Algebra Subroutines

Implementing Strassen’s Algorithm with CUTLASS on NVIDIA Volta GPUs

Integer sorting on multicore

A study of integer sorting on multicores

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high performance computing on graphics processing units: hgpu.org

Interactive GPU active contours for segmenting inhomogeneous objects

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Molecular dynamics recipes for genome research

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

A Hybrid-parallel Architecture for Applications in Bioinformatics

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Accelerating Genomics Research with OpenCL and FPGAs

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Recent source codes

TVM: Open deep learning compiler stack for cpu, gpu and specialized accelerators

MyCaffe: A complete deep learning platform written almost entirely in C# for Windows developers

Characterising Across-Stack Optimisations for Deep Convolutional Neural Networks

Using the Tsetlin Machine to Learn Human-Interpretable Rules for High-Accuracy Text Categorization with Medical Applications

ZUCL: A ZYNQ UltraScale+ Framework for OpenCL HLS Applications

CL-kmeans: Efficient k-Means in OpenCL

Doctor AI: Interpretable Deep Learning for Modeling Electronic Health Records

pyJac: a Python package that generates source code used to analytically calculate chemical kinetics Jacobian matrices

CUTLASS: CUDA Templates for Linear Algebra Subroutines

Integer sorting on multicore

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International Conference on Image, Video and Signal Processing (IVSP), 2019

International Joint Conference on Signals, Systems and Computers (CSSC), 2018

International Joint Conference on Robotics, Automation and Mechatronics (JCRAM), 2018

International Joint Conference on Robotics and Artificial Intelligence (JCRAI), 2018

International Joint Conference on Computer Vision and Pattern Recognition (CCVPR), 2018