GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs

Ahmed Shamsul Arefin, Carlos Riveros, Regina Berretta, Pablo Moscato
Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
PLoS ONE 7(8): e44000, 2012


   title={GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs},

   author={Arefin, A.S. and Riveros, C. and Berretta, R. and Moscato, P.},

   journal={PLoS ONE},





   publisher={Public Library of Science}


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BACKGROUND: The analysis of biological networks has become a major challenge due to the recent development of high-throughput techniques that are rapidly producing very large data sets. The exploding volumes of biological data are craving for extreme computational power and special computing facilities (i.e. super-computers). An inexpensive solution, such as General Purpose computation based on Graphics Processing Units (GPGPU), can be adapted to tackle this challenge, but the limitation of the device internal memory can pose a new problem of scalability. An efficient data and computational parallelism with partitioning is required to provide a fast and scalable solution to this problem. RESULTS: We propose an efficient parallel formulation of the k-Nearest Neighbour (kNN) search problem, which is a popular method for classifying objects in several fields of research, such as pattern recognition, machine learning and bioinformatics. Being very simple and straightforward, the performance of the kNN search degrades dramatically for large data sets, since the task is computationally intensive. The proposed approach is not only fast but also scalable to large-scale instances. Based on our approach, we implemented a software tool GPU-FS-kNN (GPU-based Fast and Scalable k-Nearest Neighbour) for CUDA enabled GPUs. The basic approach is simple and adaptable to other available GPU architectures. We observed speed-ups of 50-60 times compared with CPU implementation on a well-known breast microarray study and its associated data sets. CONCLUSION: Our GPU-based Fast and Scalable k-Nearest Neighbour search technique (GPU-FS-kNN) provides a significant performance improvement for nearest neighbour computation in large-scale networks. Source code and the software tool is available under GNU Public License (GPL) at https://sourceforge.net/p/gpufsknn/.
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