Objective. During deep brain stimulation (DBS), it is well understood that extracellular cathodic stimulation can cause activation of passing axons. Activation can be predicted from the second derivative of the electric potential along an axon, which depends on axonal orientation with respect to the stimulation source. We hypothesize that fiber orientation influences activation thresholds and that fiber orientations can be selectively targeted with DBS waveforms. Approach. We used bioelectric field and multicompartment NEURON models to explore preferential activation based on fiber orientation during monopolar or bipolar stimulation. Preferential fiber orientation was extracted from the principal eigenvectors and eigenvalues of the Hessian matrix of the electric potential. We tested cathodic, anodic, and charge-balanced pulses to target neurons based on fiber orientation in general and clinical scenarios. Main results. Axons passing the DBS lead have positive second derivatives around a cathode, whereas orthogonal axons have positive second derivatives around an anode, as indicated by the Hessian. Multicompartment NEURON models confirm that passing fibers are activated by cathodic stimulation, and orthogonal fibers are activated by anodic stimulation. Additionally, orthogonal axons have lower thresholds compared to passing axons. In a clinical scenario, fiber pathways associated with therapeutic benefit can be targeted with anodic stimulation at 50% lower stimulation amplitudes. Significance. Fiber orientations can be selectively targeted with simple changes to the stimulus waveform. Anodic stimulation preferentially activates orthogonal fibers, approaching or leaving the electrode, at lower thresholds for similar therapeutic benefit in DBS with decreased power consumption.
C.J. Anderson, D.N. Anderson, S.M. Pulst, C.R. Butson, A.D. Dorval.
Neural Selectivity, Efficiency, and Dose Equivalence in Deep Brain Stimulation through Pulse Width Tuning and Segmented Electrodes, In bioRxiv, Cold Spring Harbor Laboratory, April, 2019.
Achieving deep brain stimulation (DBS) dose equivalence is challenging, especially with pulse width tuning and directional contacts. Further, the precise effects of pulse width tuning are unknown.
We created multicompartment neuron models for two axon diameters and used finite element modeling to determine extracellular influence from standard and segmented electrodes. We analyzed axon activation profiles and calculated volumes of tissue activated.
Long pulse widths focus the stimulation effect on small, nearby fibers, suppressing white matter tract activation (responsible for some DBS side effects) and improving battery utilization. Directional leads enable similar benefits to a greater degree. We derive equations for equivalent activation with pulse width tuning and segmented contacts.
We find agreement with classic studies and reinterpret recent articles concluding that short pulse widths focus the stimulation effect on small, nearby fibers, decrease side effects, and improve power consumption. Our field should reconsider shortened pulse widths.
We present a framework for the analysis of uncertainty in isocontour extraction. The marching squares (MS) algorithm for isocontour reconstruction generates a linear topology that is consistent with hyperbolic curves of a piecewise bilinear interpolation. The saddle points of the bilinear interpolant cause topological ambiguity in isocontour extraction. The midpoint decider and the asymptotic decider are well-known mathematical techniques for resolving topological ambiguities. The latter technique investigates the data values at the cell saddle points for ambiguity resolution. The uncertainty in data, however, leads to uncertainty in underlying bilinear interpolation functions for the MS algorithm, and hence, their saddle points. In our work, we study the behavior of the asymptotic decider when data at grid vertices is uncertain. First, we derive closed-form distributions characterizing variations in the saddle point values for uncertain bilinear interpolants. The derivation assumes uniform and nonparametric noise models, and it exploits the concept of ratio distribution for analytic formulations. Next, the probabilistic asymptotic decider is devised for ambiguity resolution in uncertain data using distributions of the saddle point values derived in the first step. Finally, the confidence in probabilistic topological decisions is visualized using a colormapping technique. We demonstrate the higher accuracy and stability of the probabilistic asymptotic decider in uncertain data with regard to existing decision frameworks, such as deciders in the mean field and the probabilistic midpoint decider, through the isocontour visualization of synthetic and real datasets.
A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes, In Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, Vol. 7, No. 4, Taylor & Francis, pp. 438-449. 2019.
Deep brain stimulation (DBS) is an established therapy for treating patients with movement disorders such as Parkinson’s disease. Patient-specific computational modelling and visualisation have been shown to play a key role in surgical and therapeutic decisions for DBS. The computational models use brain imaging, such as magnetic resonance (MR) and computed tomography (CT), to determine the DBS electrode positions within the patient’s head. The finite resolution of brain imaging, however, introduces uncertainty in electrode positions. The DBS stimulation settings for optimal patient response are sensitive to the relative positioning of DBS electrodes to a specific neural substrate (white/grey matter). In our contribution, we study positional uncertainty in the DBS electrodes for imaging with finite resolution. In a three-step approach, we first derive a closed-form mathematical model characterising the geometry of the DBS electrodes. Second, we devise a statistical framework for quantifying the uncertainty in the positional attributes of the DBS electrodes, namely the direction of longitudinal axis and the contact-centre positions at subvoxel levels. The statistical framework leverages the analytical model derived in step one and a Bayesian probabilistic model for uncertainty quantification. Finally, the uncertainty in contact-centre positions is interactively visualised through volume rendering and isosurfacing techniques. We demonstrate the efficacy of our contribution through experiments on synthetic and real datasets. We show that the spatial variations in true electrode positions are significant for finite resolution imaging, and interactive visualisation can be instrumental in exploring probabilistic positional variations in the DBS lead.
Computational models are a popular tool for predicting the effects of deep brain stimulation (DBS) on neural tissue. One commonly used model, the volume of tissue activated (VTA), is computed using multiple methodologies. We quantified differences in the VTAs generated by five methodologies: the traditional axon model method, the electric field norm, and three activating function based approaches - the activating function at each grid point in the tangential direction (AF-Tan) or in the maximally activating direction (AF-3D), and the maximum activating function along the entire length of a tangential fiber (AF-Max).
Approach: We computed the VTA using each method across multiple stimulation settings. The resulting volumes were compared for similarity, and the methodologies were analyzed for their differences in behavior.
Main Results: Activation threshold values for both the electric field norm and the activating function vary with regards to electrode configuration, pulse width, and frequency. All methods produced highly similar volumes for monopolar stimulation. For bipolar electrode configurations, only the maximum activating function along the tangential axon method, AF-Max, produced similar volumes to those produced by the axon model method. Further analysis revealed that both of these methods are biased by their exclusive use of tangential fiber orientations. In contrast, the activating function in the maximally activating direction method, AF-3D, produces a VTA that is free of axon orientation and projection bias.
Significance: Simulating tangentially oriented axons, the standard approach of computing the VTA, is too computationally expensive for widespread implementation and yields results biased by the assumption of tangential fiber orientation. In this work, we show that a computationally efficient method based on the activating function, AF-Max, reliably reproduces the VTAs generated by direct axon modeling. Further, we propose another method, AF-3D as a potentially superior model for representing generic neural tissue activation.
Topological techniques have proven to be a powerful tool in the analysis and visualization of large-scale scientific data. In particular, the Morse-Smale complex and its various components provide a rich framework for robust feature definition and computation. Consequently, there now exist a number of approaches to compute Morse-Smale complexes for large-scale data in parallel. However, existing techniques are based on discrete concepts which produce the correct topological structure but are known to introduce grid artifacts in the resulting geometry. Here, we present a new approach that combines parallel streamline computation with combinatorial methods to construct a high-quality discrete Morse-Smale complex. In addition to being invariant to the orientation of the underlying grid, this algorithm allows users to selectively build a subset of features using high-quality geometry. In particular, a user may specifically select which ascending/descending manifolds are reconstructed with improved accuracy, focusing computational effort where it matters for subsequent analysis. This approach computes Morse-Smale complexes for larger data than previously feasible with significant speedups. We demonstrate and validate our approach using several examples from a variety of different scientific domains, and evaluate the performance of our method.
M. Han, I. Wald, W. Usher, Q. Wu, F. Wang, V. Pascicci, C. D. Hansen, C. R. Johnson. Ray Tracing Generalized Tube Primitives: Method and Applications, In Computer Graphics Forum, Vol. 38, No. 3, John Wiley & Sons Ltd., 2019.
We present a general high-performance technique for ray tracing generalized tube primitives. Our technique efficiently supports tube primitives with fixed and varying radii, general acyclic graph structures with bifurcations, and correct transparency with interior surface removal. Such tube primitives are widely used in scientific visualization to represent diffusion tensor imaging tractographies, neuron morphologies, and scalar or vector fields of 3D flow. We implement our approach within the OSPRay ray tracing framework, and evaluate it on a range of interactive visualization use cases of fixed- and varying-radius streamlines, pathlines, complex neuron morphologies, and brain tractographies. Our proposed approach provides interactive, high-quality rendering, with low memory overhead.
Quantifying Impurity Effects on the Surface Morphology of α-U3O8, In Analytical Chemistry, 2019.
The morphological effect of impurities on α-U3O8 has been investigated. This study provides the first evidence that the presence of impurities can alter nuclear material morphology, and these changes can be quantified to aid in revealing processing history. Four elements: Ca, Mg, V, and Zr were implemented in the uranyl peroxide synthesis route and studied individually within the α-U3O8. Six total replicates were synthesized, and replicates 1–3 were filtered and washed with Millipore water (18.2 MΩ) to remove any residual nitrates. Replicates 4–6 were filtered but not washed to determine the amount of impurities removed during washing. Inductively coupled plasma mass spectrometry (ICP-MS) was employed at key points during the synthesis to quantify incorporation of the impurity. Each sample was characterized using powder X-ray diffraction (p-XRD), high-resolution scanning electron microscopy (HRSEM), and SEM with energy dispersive X-ray spectroscopy (SEM-EDS). p-XRD was utilized to evaluate any crystallographic changes due to the impurities; HRSEM imagery was analyzed with Morphological Analysis for MAterials (MAMA) software and machine learning classification for quantification of the morphology; and SEM-EDS was utilized to locate the impurity within the α-U3O8. All samples were found to be quantifiably distinguishable, further demonstrating the utility of quantitative morphology as a signature for the processing history of nuclear material.
In the present study, surface morphological differences of mixtures of triuranium octoxide (U3O8), synthesized from uranyl peroxide (UO4) and ammonium diuranate (ADU), were investigated. The purity of each sample was verified using powder X-ray diffractometry (p-XRD), and scanning electron microscopy (SEM) images were collected to identify unique morphological features. The U3O8 from ADU and UO4 was found to be unique. Qualitatively, both particles have similar features being primarily circular in shape. Using the morphological analysis of materials (MAMA) software, particle shape and size were quantified. UO4 was found to produce U3O8 particles three times the area of those produced from ADU. With the starting morphologies quantified, U3O8 samples from ADU and UO4 were physically mixed in known quantities. SEM images were collected of the mixed samples, and the MAMA software was used to quantify particle attributes. As U3O8 particles from ADU were unique from UO4, the composition of the mixtures could be quantified using SEM imaging coupled with particle analysis. This provides a novel means of quantifying processing histories of mixtures of uranium oxides. Machine learning was also used to help further quantify characteristics in the image database through direct classification and particle segmentation using deep learning techniques based on Convolutional Neural Networks (CNN). It demonstrates that these techniques can distinguish the mixtures with high accuracy as well as showing significant differences in morphology between the mixtures. Results from this study demonstrate the power of quantitative morphological analysis for determining the processing history of nuclear materials.
There currently exist two dominant strategies to reduce data sizes in analysis and visualization: reducing the precision of the data, e.g., through quantization, or reducing its resolution, e.g., by subsampling. Both have advantages and disadvantages and both face fundamental limits at which the reduced information ceases to be useful. The paper explores the additional gains that could be achieved by combining both strategies. In particular, we present a common framework that allows us to study the trade-off in reducing precision and/or resolution in a principled manner. We represent data reduction schemes as progressive streams of bits and study how various bit orderings such as by resolution, by precision, etc., impact the resulting approximation error across a variety of data sets as well as analysis tasks. Furthermore, we compute streams that are optimized for different tasks to serve as lower bounds on the achievable error. Scientific data management systems can use the results presented in this paper as guidance on how to store and stream data to make efficient use of the limited storage and bandwidth in practice.
J. K. Holmen, B. Peterson, A. Humphrey, D. Sunderland, O. H. Diaz-Ibarra, J. N. Thornock, M. Berzins. Portably Improving Uintah's Readiness for Exascale Systems Through the Use of Kokkos, SCI Institute, 2019.
Uncertainty and diversity in future HPC systems, including those for exascale, makes portable codebases desirable. To ease future ports, the Uintah Computational Framework has adopted the Kokkos C++ Performance Portability Library. This paper describes infrastructure advancements and performance improvements using partitioning functionality recently added to Kokkos within Uintah's MPI+Kokkos hybrid parallelism approach. Results are presented for two challenging calculations that have been refactored to support Kokkos::OpenMP and Kokkos::Cuda back-ends. These results demonstrate performance improvements up to (i) 2.66x when refactoring for portability, (ii) 81.59x when adding loop-level parallelism via Kokkos back-ends, and (iii) 2.63x when more eciently using a node. Good strong-scaling characteristics to 442,368 threads across 1728 Knights Landing processors are also shown. These improvements have been achieved with little added overhead (sub-millisecond, consuming up to 0.18% of per-timestep time). Kokkos adoption and refactoring lessons are also discussed.
Alan Humphrey. Scalable Asynchronous Many-Task Runtime Solutions to Globally Coupled Problems, School of Computing, University of Utah, 2019.
Thermal radiation is an important physical process and a key mechanism in a class of challenging engineering and research problems. The principal exascale-candidate application motivating this research is a large eddy simulation (LES) aimed at predicting the performance of a commercial, 1200 MWe ultra-super critical (USC) coal boiler, with radiation as the dominant mode of heat transfer. Scalable modeling of radiation is currently one of the most challenging problems in large-scale simulations, due to the global, all-to-all physical and resulting computational connectivity. Fundamentally, radiation models impose global data dependencies, requiring each compute node in a distributed memory system to send data to, and receive data from, potentially every other node. This process can be prohibitively expensive on large distributed memory systems due to pervasive all-to-all message passing interface (MPI) communication. Correctness is also difficult to achieve when coordinating global communication of this kind. Asynchronous many-task (AMT) runtime systems are a possible leading alternative to mitigate programming challenges at the runtime system-level, sheltering the application developer from the complexities introduced by future architectures. However, large-scale parallel applications with complex global data dependencies, such as in radiation modeling, pose significant scalability challenges themselves, even for a highly tuned AMT runtime. The principal aims of this research are to demonstrate how the Uintah AMT runtime can be adapted, making it possible for complex multiphysics applications with radiation to scale on current petascale and emerging exascale architectures. For Uintah, which uses a directed acyclic graph to represent the computation and associated data dependencies, these aims are achieved through: 1) the use of an AMT runtime; 2) adapting and leveraging Uintah’s adaptive mesh refinement support to dramatically reduce computation, communication volume, and nodal memory footprint for radiation calculations; and 3) automating the all-to-all communication at the runtime level through a task graph dependency analysis phase designed to efficiently manage data dependencies inherent in globally coupled problems.
A. Humphreys, M. Berzins.
An Evaluation of An Asynchronous Task Based Dataflow Approach For Uintah, In 2019 IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC), Vol. 2, pp. 652-657. July, 2019.
The challenge of running complex physics code on the largest computers available has led to dataflow paradigms being explored. While such approaches are often applied at smaller scales, the challenge of extreme-scale data flow computing remains. The Uintah dataflow framework has consistently used dataflow computing at the largest scales on complex physics applications. At present Uintah contains two main dataflow models. Both are based upon asynchronous communication. One uses a static graph-based approach with asynchronous communication and the other uses a more dynamic approach that was introduced almost a decade ago. Subsequent changes within the Uintah runtime system combined with many more large scale experiments, has necessitated a reevaluation of these two approaches, comparing them in the context of large scale problems. While the static approach has worked well for some large-scale simulations, the dynamic approach is seen to offer performance improvements over the static case for a challenging fluid-structure interaction problem at large scale that involves fluid flow and a moving solid represented using particle method on an adaptive mesh.
Deep brain stimulation (DBS) can be an effective therapy for tics and comorbidities in select cases of severe, treatment-refractory Tourette syndrome (TS). Clinical responses remain variable across patients, which may be attributed to differences in the location of the neuroanatomical regions being stimulated. We evaluated active contact locations and regions of stimulation across a large cohort of patients with TS in an effort to guide future targeting.
D. Sahasrabudhe, M. Berzins, J. Schmidt.
Node failure resiliency for Uintah without checkpointing, In Concurrency and Computation: Practice and Experience, pp. e5340. 2019.
The frequency of failures in upcoming exascale supercomputers may well be greater than at present due to many-core architectures if component failure rates remain unchanged. This potential increase in failure frequency coupled with I/O challenges at exascale may prove problematic for current resiliency approaches such as checkpoint restarting, although the use of fast intermediate memory may help. Algorithm-Based Fault Tolerance (ABFT) using Adaptive Mesh Refinement (AMR) is one resiliency approach used to address these challenges. For adaptive mesh codes, a coarse mesh version of the solution may be used to restore the fine mesh solution. This paper addresses the implementation of the ABFT approach within the Uintah software framework: both at a software level within Uintah and in the data reconstruction method used for the recovery of lost data. This method has two problems: inaccuracies introduced during the reconstruction propagate forward in time, and the physical consistency of variables such as positivity or boundedness may be violated during interpolation. These challenges can be addressed by the combination of two techniques: 1. a fault-tolerant MPI implementation to recover from runtime node failures, and 2. high-order interpolation schemes to preserve the physical solution and reconstruct lost data. The approach considered here uses a "Limited Essentially Non-Oscillatory" (LENO) scheme along with AMR to rebuild the lost data without checkpointing using Uintah. Experiments were carried out using a fault-tolerant MPI - ULFM to recover from runtime failure, and LENO to recover data on patches belonging to failed ranks, while the simulation was continued to the end. Results show that this ABFT approach is up to 10x faster than the traditional checkpointing method. The new interpolation approach is more accurate than linear interpolation and not subject to the overshoots found in other interpolation methods.
G. S. Smith, K. A. Mills, G. M. Pontone, W. S. Anderson, K. M. Perepezko, J. Brasic, Y. Zhou, J. Brandt, C. R. Butson, D. P. Holt, W. B. Mathews, R. F. Dannals, D. F. Wong, Z. Mari. Effect of STN DBS on vesicular monoamine transporter 2 and glucose metabolism in Parkinson's disease, In Parkinsonism and Related Disorders, Elsevier, 2019.
Deep brain stimulation (DBS) is an established treatment Parkinson's Disease (PD). Despite the improvement of motor symptoms in most patients by sub-thalamic nucleus (STN) DBS and its widespread use, the neurobiological mechanisms are not completely understood. The objective of the present study was to elucidate the effects of STN DBS in PD on the dopamine system and neural circuitry employing high-resolution positron emission tomography (PET) imaging. The hypotheses tested were that STN DBS would decrease striatal VMAT2, secondary to an increase in dopamine concentrations, and would decrease striatal cerebral metabolism and increase cortical metabolism.
Q. Tran, M. Berzins, W. Solowski. An improved moving least squares method for the Material Point Method, In Proceedings of the 2nd International Conference on the Material Point Method for Modelling Soil-Water-Structure Interaction (MPM 2019), 2019.
The paper presents an improved moving least squares reconstruction technique for the Material Point Method. The moving least squares reconstruction(MLS)can improve spatial accuracy in simulations involving large deformations. However, the MLS algorithm relies on computing the inverse of the moment matrix.This is both expensive and potentially unstable when there are not enough material points to reconstruct the high-order least squares function, which leads to a singular or an ill-conditioned matrix. The shown formulation can overcome this limitation while retain the same order of accuracy compared with the conventional moving least squares reconstruction.Numerical experiments demonstrate the improvements in the accuracy and comparison with the original Material Point Method and the Convected Particles Domain Interpolation method.
W. Usher, I. Wald, J. Amstutz, J. Gunther, C. Brownlee, V. Pascucci. Scalable Ray Tracing Using the Distributed FrameBuffer, In Eurographics Conference on Visualization (EuroVis) 2019, Vol. 38, No. 3, 2019.
Image- and data-parallel rendering across multiple nodes on high-performance computing systems is widely used in visualization to provide higher frame rates, support large data sets, and render data in situ. Specifically for in situ visualization, reducing bottlenecks incurred by the visualization and compositing is of key concern to reduce the overall simulation runtime. Moreover, prior algorithms have been designed to support either image- or data-parallel rendering and impose restrictions on the data distribution, requiring different implementations for each configuration. In this paper, we introduce the Distributed FrameBuffer, an asynchronous image-processing framework for multi-node rendering. We demonstrate that our approach achieves performance superior to the state of the art for common use cases, while providing the flexibility to support a wide range of parallel rendering algorithms and data distributions. By building on this framework, we extend the open-source ray tracing library OSPRay with a data-distributed API, enabling its use in data-distributed and in situ visualization applications.
A Retrospective Evaluation of Automated Optimization of Deep Brain Stimulation Settings, In Brain Stimulation, Vol. 12, No. 2, Elsevier, pp. e54--e55. March, 2019.