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GPU acceleration for statistical gene classification

Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino
Department of Control and Computer Engineering, Politecnico di Torino, I-10129, Torino, Italy
IEEE International Conference on Automation Quality and Testing Robotics (AQTR), 2010

@conference{benso2010gpu,

   title={GPU acceleration for statistical gene classification},

   author={Benso, A. and Di Carlo, S. and Politano, G. and Savino, A.},

   booktitle={2010 IEEE International Conference on Automation, Quality and Testing, Robotics},

   pages={1–6},

   year={2010},

   organization={IEEE}

}

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The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practice.
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