J. Edwards, S. Kumar, V. Pascucci. Big data from scientific simulations, In Big Data and High Performance Computing, Vol. 26, IOS Press, pp. 32. 2015.
Scientic simulations often generate massive amounts of data used for debugging, restarts, and scientic analysis and discovery. Challenges that practitioners face using these types of big data are unique. Of primary importance is speed of writing data during a simulation, but this need for fast I/O is at odds with other priorities, such as data access time for visualization and analysis, ecient storage, and portability across a variety of supercomputer topologies, congurations, le systems, and storage devices. The computational power of high-performance computing systems continues to increase according to Moore's law, but the same is not true for I/O subsystems, creating a performance gap between computation and I/O. This chapter explores these issues, as well as possible optimization strategies, the use of in situ analytics, and a case study using the PIDX I/O library in a typical simulation.
J. Edwards, E. Daniel, V. Pascucci, C. Bajaj.
Approximating the Generalized Voronoi Diagram of Closely Spaced Objects, In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 299-309. May, 2015.
Generalized Voronoi Diagrams (GVDs) have far-reaching applications in robotics, visualization, graphics, and simulation. However, while the ordinary Voronoi Diagram has mature and efficient algorithms for its computation, the GVD is difficult to compute in general, and in fact, has only approximation algorithms for anything but the simplest of datasets. Our work is focused on developing algorithms to compute the GVD efficiently and with bounded error on the most difficult of datasets -- those with objects that are extremely close to each other.
Shape priors have been successfully used in challenging biomedical imaging problems. However when the shape distribution involves multiple shape classes, leading to a multimodal shape density, effective use of shape priors in segmentation becomes more challenging. In such scenarios, knowing the class of the shape can aid the segmentation process, which is of course unknown a priori. In this paper, we propose a joint classification and segmentation approach for dendritic spine segmentation which infers the class of the spine during segmentation and adapts the remaining segmentation process accordingly. We evaluate our proposed approach on 2-photon microscopy images containing dendritic spines and compare its performance quantitatively to an existing approach based on nonparametric shape priors. Both visual and quantitative results demonstrate the effectiveness of our approach in dendritic spine segmentation.
T. Etiene, R.M. Kirby, C. Silva. An Introduction to Verification of Visualization Techniques, Morgan & Claypool Publishers, 2015.
SCI Institute. Note: FluoRender: An interactive rendering tool for confocal microscopy data visualization. Scientific Computing and Imaging Institute (SCI) Download from: http://www.fluorender.org, 2015.
Note: FusionView: Problem Solving Environment for MHD Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org, 2015.
Y. Gao, L. Zhu, J. Cates, R. S. MacLeod, S. Bouix,, A. Tannenbaum.
A Kalman Filtering Perspective for Multiatlas Segmentation, In SIAM J. Imaging Sciences, Vol. 8, No. 2, pp. 1007-1029. 2015.
Functional properties of a neuron are coupled with its morphology, particularly the morphology of dendritic spines. Spine volume has been used as the primary morphological parameter in order the characterize the structure and function coupling. However, this reductionist approach neglects the rich shape repertoire of dendritic spines. First step to incorporate spine shape information into functional coupling is classifying main spine shapes that were proposed in the literature. Due to the lack of reliable and fully automatic tools to analyze the morphology of the spines, such analysis is often performed manually, which is a laborious and time intensive task and prone to subjectivity. In this paper we present an automated approach to extract features using basic image processing techniques, and classify spines into mushroom or stubby by applying machine learning algorithms. Out of 50 manually segmented mushroom and stubby spines, Support Vector Machine was able to classify 98% of the spines correctly.
K. Gillette, J.D. Tate, B. Kindall, P. Van Dam, E. Kholmovski, R.S. MacLeod. Generation of Combined-Modality Tetrahedral Meshes, In Computing in Cardiology, 2015.
Registering and combining anatomical components from different image modalities, like MRI and CT that have different tissue contrast, could result in patient-specific models that more closely represent underlying anatomical structures.
In this study, we combined a pair of CT and MRI scans of a pig thorax to make a tetrahedral mesh and compared different registration techniques including rigid, affine, thin plate spline morphing (TPSM), and iterative closest point (ICP), to superimpose the segmented bones from the CT scan on the soft tissues segmented from the MRI. The TPSM and affine-registered bones remained close to, but not overlapping, important soft tissue.
Simulation models, including an ECG forward model and a defibrillation model, were computed on generated multi-modality meshes after TPSM and affine registration and compared to those based on the original torso mesh.
B. D. Goodwin, C. R. Butson.
Subject-Specific Multiscale Modeling to Investigate Effects of Transcranial Magnetic Stimulation, In Neuromodulation: Technology at the Neural Interface, Vol. 18, No. 8, Wiley-Blackwell, pp. 694--704. May, 2015.
Transcranial magnetic stimulation (TMS) is an effective intervention in noninvasive neuromodulation used to treat a number of neurophysiological disorders. Predicting the spatial extent to which neural tissue is affected by TMS remains a challenge. The goal of this study was to develop a computational model to predict specific locations of neural tissue that are activated during TMS. Using this approach, we assessed the effects of changing TMS coil orientation and waveform.
MATERIALS AND METHODS:
We integrated novel techniques to develop a subject-specific computational model, which contains three main components: 1) a figure-8 coil (Magstim, Magstim Company Limited, Carmarthenshire, UK); 2) an electromagnetic, time-dependent, nonhomogeneous, finite element model of the whole head; and 3) an adaptation of a previously published pyramidal cell neuron model. We then used our modeling approach to quantify the spatial extent of affected neural tissue for changes in TMS coil rotation and waveform.
We found that our model shows more detailed predictions than previously published models, which underestimate the spatial extent of neural activation. Our results suggest that fortuitous sites of neural activation occur for all tested coil orientations. Additionally, our model predictions show that excitability of individual neural elements changes with a coil rotation of ±15°.
Our results indicate that the extent of neuromodulation is more widespread than previous published models suggest. Additionally, both specific locations in cortex and the extent of stimulation in cortex depend on coil orientation to within ±15° at a minimum. Lastly, through computational means, we are able to provide insight into the effects of TMS at a cellular level, which is currently unachievable by imaging modalities.
Proceedings of the IV International Conference on Particle-Based Methods - Fundamentals and Applications, Barcelona, Spain, Edited by E. Onate and M. Bischoff and D.R.J. Owen and P. Wriggers and T. Zohdi, CIMNE, pp. 202-213. September, 2015.
While particle-in-cell type methods, such as MPM, have been very successful in providing solutions to many challenging problems there are some important issues that remain to be resolved with regard to their analysis. One such challenge relates to the difference in dimensionality between the particles and the grid points to which they are mapped. There exists a non-trivial null space of the linear operator that maps particles values onto nodal values. In other words, there are non-zero particle values values that when mapped to the nodes are zero there. Given positive mapping weights such null space values are oscillatory in nature. The null space may be viewed as a more general form of the ringing instability identified by Brackbill for PIC methods. It will be shown that it is possible to remove these null-space values from the solution and so to improve the accuracy of PIC methods, using a matrix SVD approach. The expense of doing this is prohibitive for real problems and so a local method is developed for doing this.
A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen. TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism, In Eurographics Symposium on Parallel Graphics and Visualization (2015), Edited by C. Dachsbacher, P. Navrátil, 2015.
The proceedings of the 2nd Annual Deep Brain Stimulation Think Tank summarize the most contemporary clinical, electrophysiological, and computational work on DBS for the treatment of neurological and neuropsychiatric disease and represent the insights of a unique multidisciplinary ensemble of expert neurologists, neurosurgeons, neuropsychologists, psychiatrists, scientists, engineers and members of industry. Presentations and discussions covered a broad range of topics, including advocacy for DBS, improving clinical outcomes, innovations in computational models of DBS, understanding of the neurophysiology of Parkinson's disease (PD) and Tourette syndrome (TS) and evolving sensor and device technologies.
Morse-Smale Analysis of Ion Diffusion for DFT Battery Materials Simulations, In Topology-Based Methods in Visualization (TopoInVis), 2015.A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, P. T. Bremer, M. E. Papka, L. A. Curtiss, V. Pascucci.
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrodinger's equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.
A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, PT. Bremer, M.l E. Papka, L. A. Curtiss, V. Pascucci. Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials, In Proceedings IEEE Visualization Conference, 2015.
In this chapter, we illustrate benefits of thinking in terms of thread management techniques when using a centralized scheduler model along with interoperability of MPI and PThreads. This is facilitated through an exploration of thread placement strategies for an algorithm modeling radiative heat transfer with special attention to the 61st core. This algorithm plays a key role within the Uintah Computational Framework (UCF) and current efforts taking place at the University of Utah to model next-generation, large-scale clean coal boilers. In such simulations, this algorithm models the dominant form of heat transfer and consumes a large portion of compute time. Exemplified by a real-world example, this chapter presents our early efforts in porting a key portion of a scalability-centric codebase to the Intel ® Xeon PhiTM coprocessor. Specifically, this chapter presents results from our experiments profiling the native execution of a reverse Monte-Carlo ray tracing-based radiation model on a single coprocessor. These results demonstrate that our fastest run confiurations utilized the 61st core and that performance was not profoundly impacted when explicitly over-subscribing the coprocessor operating system thread. Additionally, this chapter presents a portion of radiation model source code, a MIC-centric UCF cross-compilation example, and less conventional thread management techniques for developers utilizing the PThreads threading model.
A Scalable Algorithm for Radiative Heat Transfer Using Reverse Monte Carlo Ray Tracing, In High Performance Computing, Lecture Notes in Computer Science, Vol. 9137, Edited by Kunkel, Julian M. and Ludwig, Thomas, Springer International Publishing, pp. 212-230. 2015.
Keywords: Uintah; Radiation modeling; Parallel; Scalability; Adaptive mesh refinement; Simulation science; Titan
CIBC. Note: ImageVis3D: An interactive visualization software system for large-scale volume data. Scientific Computing and Imaging Institute (SCI), Download from: http://www.imagevis3d.org, 2015.
Data Science: What Is It and How Is It Taught?, In SIAM News, SIAM, July, 2015.H. De Sterck, C.R. Johnson.