Effective Connectivity Analysis in Brain Networks: a GPU-Accelerated Implementation of the Cox Method

Vafa Andalibi, Francois Christophe, Teemu Laukkarinen, Tommi Mikkonen

    Research output: Contribution to journalArticleScientificpeer-review

    2 Citations (Scopus)


    The observation of interactions between neurons of a network can reveal important information about how information is processed within that network. Such observation can be established with the analysis of causality between the activities of the different neurons in the network. This analysis is called effective connectivity analysis. However, methods for such analysis are either computationally heavy for daily use or too inaccurate for making reliable analyses. Cox method produces reliable analysis, but the computation takes hours on CPUs, making it slow to use on research. In this paper, two algorithms are presented that speed up analysis of Cox method by parallelizing the computation on a Graphical Processing Unit (GPU) with the help of Compute Unified Device Architecture (CUDA) platform. Both algorithms are evaluated according to network size and recording duration. The interest of proposing GPU implementations is in gaining computation time but another important interest is that such implementation requires rethinking the algorithm in different ways as the sequential implementation. This rethinking itself brings new optimization possibilities, e.g. by employing OpenCL. Utilizing this accelerated implementation, the Cox method is then applied on an experimental dataset from CRCNS in a personal computer. This should facilitate observations of biological neural network organizations that can provide new insights to improve understanding of memory, learning and intelligence.
    Original languageEnglish
    Pages (from-to)1226-1237
    Number of pages12
    JournalIEEE Journal of Selected Topics in Signal Processing
    Issue number7
    Publication statusPublished - 24 Aug 2016
    Publication typeA1 Journal article-refereed

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