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Graphics Processing Unit-Accelerated Code for Computing Second-Order Wiener Kernels and Spike-Triggered Covariance

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  • Omer Mano
  • Damon A Clark

Abstract

Sensory neuroscience seeks to understand and predict how sensory neurons respond to stimuli. Nonlinear components of neural responses are frequently characterized by the second-order Wiener kernel and the closely-related spike-triggered covariance (STC). Recent advances in data acquisition have made it increasingly common and computationally intensive to compute second-order Wiener kernels/STC matrices. In order to speed up this sort of analysis, we developed a graphics processing unit (GPU)-accelerated module that computes the second-order Wiener kernel of a system’s response to a stimulus. The generated kernel can be easily transformed for use in standard STC analyses. Our code speeds up such analyses by factors of over 100 relative to current methods that utilize central processing units (CPUs). It works on any modern GPU and may be integrated into many data analysis workflows. This module accelerates data analysis so that more time can be spent exploring parameter space and interpreting data.

Suggested Citation

  • Omer Mano & Damon A Clark, 2017. "Graphics Processing Unit-Accelerated Code for Computing Second-Order Wiener Kernels and Spike-Triggered Covariance," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-11, January.
    • Handle: RePEc:plo:pone00:0169842
    DOI: 10.1371/journal.pone.0169842
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    References listed on IDEAS

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    1. Jian K Liu & Tim Gollisch, 2015. "Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-30, July.
    2. Miguel Maravall & Rasmus S Petersen & Adrienne L Fairhall & Ehsan Arabzadeh & Mathew E Diamond, 2007. "Shifts in Coding Properties and Maintenance of Information Transmission during Adaptation in Barrel Cortex," PLOS Biology, Public Library of Science, vol. 5(2), pages 1-12, January.
    3. Xiaonan R. Sun & Aleksandra Badura & Diego A. Pacheco & Laura A. Lynch & Eve R. Schneider & Matthew P. Taylor & Ian B. Hogue & Lynn W. Enquist & Mala Murthy & Samuel S. -H. Wang, 2013. "Fast GCaMPs for improved tracking of neuronal activity," Nature Communications, Nature, vol. 4(1), pages 1-10, October.
    4. Timm Lochmann & Timothy J Blanche & Daniel A Butts, 2013. "Construction of Direction Selectivity through Local Energy Computations in Primary Visual Cortex," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-13, March.
    5. Donald R Cantrell & Jianhua Cang & John B Troy & Xiaorong Liu, 2010. "Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells," PLOS Computational Biology, Public Library of Science, vol. 6(10), pages 1-16, October.
    6. Tsai-Wen Chen & Trevor J. Wardill & Yi Sun & Stefan R. Pulver & Sabine L. Renninger & Amy Baohan & Eric R. Schreiter & Rex A. Kerr & Michael B. Orger & Vivek Jayaraman & Loren L. Looger & Karel Svobod, 2013. "Ultrasensitive fluorescent proteins for imaging neuronal activity," Nature, Nature, vol. 499(7458), pages 295-300, July.
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