mpdcm: A toolbox for massively parallel dynamic causal modeling

作者：Aponte Eduardo A^*; Raman Sudhir; Sengupta Biswa; Penny Will D; Stephan Klaas E; Heinzle Jakob

来源：Journal of Neuroscience Methods, 2016, 257: 7-16.

DOI：10.1016/j.jneumeth.2015.09.009

• Dynamic causal modeling
• GPU
• Markov chain Monte Carlo
• Thermodynamic integration
• Parallel tempering
• Model inversion
• Model evidence
• Bayesian model comparison

Background: Dynamic causal modeling (DCM) for fMRI is an established method for Bayesian system identification and inference on effective brain connectivity. DCM relies on a biophysical model that links hidden neuronal activity to measurable BOLD signals. Currently, biophysical simulations from DCM constitute a serious computational hindrance. Here, we present Massively Parallel Dynamic Causal Modeling (mpdcm), a toolbox designed to address this bottleneck.
New method: mpdcm delegates the generation of simulations from DCM's biophysical model to graphical processing units (GPUs). Simulations are generated in parallel by implementing a low storage explicit Runge Kutta's scheme on a GPU architecture. mpdcm is publicly available under the GPLv3 license.
Results: We found that mpdcm efficiently generates large number of simulations without compromising their accuracy. As applications of mpdcm, we suggest two computationally expensive sampling algorithms: thermodynamic integration and parallel tempering.
Comparison with existing method(s): mpdcm is up to two orders of magnitude more efficient than the standard implementation in the software package SPM. Parallel tempering increases the mixing properties of the traditional Metropolis Hastings algorithm at low computational cost given efficient, parallel simulations of a model.
Conclusions: Future applications of DCM will likely require increasingly large computational resources, for example, when the likelihood landscape of a model is multimodal, or when implementing sampling methods for multi-subject analysis. Due to the wide availability of GPUs, algorithmic advances can be readily available in the absence of access to large computer grids, or when there is a lack of expertise to implement algorithms in such grids.

• 出版日期2016-1-15