GPU-accelerated connectome discovery at scale.

Diffusion magnetic resonance imaging and tractography enable the estimation of anatomical connectivity in the human brain, in vivo. Yet, without ground-truth validation, different tractography algorithms can yield widely varying connectivity estimates. Although streamline pruning techniques mitigate this challenge, slow compute times preclude their use in big-data applications. We present 'Regularized, Accelerated, Linear Fascicle Evaluation' (ReAl-LiFE), a GPU-based implementation of a state-of-the-art streamline pruning algorithm (LiFE), which achieves >100× speedups over previous CPU-based implementations. Leveraging these speedups, we overcome key limitations with LiFE's algorithm to generate sparser and more accurate connectomes. We showcase ReAl-LiFE's ability to estimate connections with superlative test-retest reliability, while outperforming competing approaches. Moreover, we predicted inter-individual variations in multiple cognitive scores with ReAl-LiFE connectome features. We propose ReAl-LiFE as a timely tool, surpassing the state of the art, for accurate discovery of individualized brain connectomes at scale. Finally, our GPU-accelerated implementation of a popular non-negative least-squares optimization algorithm is widely applicable to many real-world problems.

Subcortical connectivity correlates selectively with attention's effects on spatial choice bias.

Neural mechanisms of attention are extensively studied in the neocortex; comparatively little is known about how subcortical regions contribute to attention. The superior colliculus (SC) is an evolutionarily conserved, subcortical (midbrain) structure that has been implicated in controlling visuospatial attention. Yet how the SC contributes mechanistically to attention remains unknown. We investigated the role of the SC in attention, combining model-based psychophysics, diffusion imaging, and tractography in human participants. Specifically, we asked whether the SC contributes to enhancing sensitivity (d') to attended information, or whether it contributes to biasing choices (criteria) in favor of attended information. We tested human participants on a multialternative change detection task, with endogenous spatial cueing, and quantified sensitivity and bias with a recently developed multidimensional signal detection model (m-ADC model). At baseline, sensitivity and bias exhibited complementary patterns of asymmetries across the visual hemifields: While sensitivity was consistently higher for detecting changes in the left hemifield, bias was higher for reporting changes in the right hemifield. Remarkably, white matter connectivity of the SC with the neocortex mirrored this pattern of asymmetries. Specifically, the asymmetry in SC-cortex connectivity correlated with the asymmetry in choice bias, but not in sensitivity. In addition, SC-cortex connectivity strength could predict cueing-induced modulation of bias, but not of sensitivity, across individuals. In summary, the SC may be a key node in an evolutionarily conserved network for controlling choice bias during visuospatial attention.

ReAl-LiFE: Accelerating the Discovery of Individualized Brain Connectomes on GPUs.

Diffusion imaging and tractography enable mapping structural connections in the human brain, in-vivo. Linear Fascicle Evaluation (LiFE) is a state-of-the-art approach for pruning spurious connections in the estimated structural connectome, by optimizing its fit to the measured diffusion data. Yet, LiFE imposes heavy demands on computing time, precluding its use in analyses of large connectome databases. Here, we introduce a GPU-based implementation of LiFE that achieves 50-100x speedups over conventional CPU-based implementations for connectome sizes of up to several million fibers. Briefly, the algorithm accelerates generalized matrix multiplications on a compressed tensor through efficient GPU kernels, while ensuring favorable memory access patterns. Leveraging these speedups, we advance LiFE's algorithm by imposing a regularization constraint on estimated fiber weights during connectome pruning. Our regularized, accelerated, LiFE algorithm ("ReAl-LiFE") estimates sparser connectomes that also provide more accurate fits to the underlying diffusion signal. We demonstrate the utility of our approach by classifying pathological signatures of structural connectivity in patients with Alzheimer's Disease (AD). We estimated million fiber whole-brain connectomes, followed by pruning with ReAl-LiFE, for 90 individuals (45 AD patients and 45 healthy controls). Linear classifiers, based on support vector machines, achieved over 80% accuracy in classifying AD patients from healthy controls based on their ReAl-LiFE pruned structural connectomes alone. Moreover, classification based on the ReAl-LiFE pruned connectome outperformed both the unpruned connectome, as well as the LiFE pruned connectome, in terms of accuracy. We propose our GPU-accelerated approach as a widely relevant tool for non-negative least squares optimization, across many domains.

Emergence of coupling-induced oscillations and broken symmetries in heterogeneously driven nonlinear reaction networks.

Many natural systems including the brain comprise coupled elements that are stimulated non-uniformly. In this paper we show that heterogeneously driven networks of excitatory-inhibitory units exhibit a diverse range of collective phenomena, including the appearance of spontaneous oscillations upon coupling quiescent elements. On varying the coupling strength a previously unreported transition is seen wherein the symmetries of the synchronization patterns in the stimulated and unstimulated groups undergo mutual exchange. The system also exhibits coexisting chaotic and non-chaotic attractors - a result that may be of interest in connection to earlier reports of varying degrees of chaoticity in the brain.