Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2021


T. McDonald, R. Shrestha, X. Yi, H. Bhatia, D. Chen, D. Goswami, V. Pascucci, T. Turbyville, P‐T Bremer. “Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion,” In Computer Graphics Forum, Vol. 40, No. 3, pp. 251-262. 2021.

ABSTRACT

Single particle tracking (SPT) of fluorescent molecules provides significant insights into the diffusion and relative motion of tagged proteins and other structures of interest in biology. However, despite the latest advances in high-resolution microscopy, individual particles are typically not distinguished from clusters of particles. This lack of resolution obscures potential evidence for how merging and splitting of particles affect their diffusion and any implications on the biological environment. The particle tracks are typically decomposed into individual segments at observed merge and split events, and analysis is performed without knowing the true count of particles in the resulting segments. Here, we address the challenges in analyzing particle tracks in the context of cancer biology. In particular, we study the tracks of KRAS protein, which is implicated in nearly 20% of all human cancers, and whose clustering and aggregation have been linked to the signaling pathway leading to uncontrolled cell growth. We present a new analysis approach for particle tracks by representing them as tracking graphs and using topological events – merging and splitting, to disambiguate the tracks. Using this analysis, we infer a lower bound on the count of particles as they cluster and create conditional distributions of diffusion speeds before and after merge and split events. Using thousands of time-steps of simulated and in-vitro SPT data, we demonstrate the efficacy of our method, as it offers the biologists a new, detailed look into the relationship between KRAS clustering and diffusion speeds.



R. A. Moore, A. Narayan. “Adaptive Density Tracking by Quadrature for Stochastic Differential Equations,” Subtitled “arXiv preprint arXiv:2105.08148,” 2021.

ABSTRACT

Density tracking by quadrature (DTQ) is a numerical procedure for computing solutions to Fokker-Planck equations that describe probability densities for stochastic differential equations (SDEs). In this paper, we extend upon existing tensorized DTQ procedures by utilizing a flexible quadrature rule that allows for unstructured, adaptive meshes. We propose and describe the procedure for -dimensions, and demonstrate that the resulting adaptive procedure is significantly more efficient than a tensorized approach. Although we consider two-dimensional examples, all our computational procedures are extendable to higher dimensional problems.



N. Morrical, J. Tremblay, Y. Lin, S. Tyree, S. Birchfield, V. Pascucci, I. Wald. “NViSII: A Scriptable Tool for Photorealistic Image Generation,” Subtitled “arXiv preprint arXiv:2105.13962,” 2021.

ABSTRACT

We present a Python-based renderer built on NVIDIA's OptiX ray tracing engine and the OptiX AI denoiser, designed to generate high-quality synthetic images for research in computer vision and deep learning. Our tool enables the description and manipulation of complex dynamic 3D scenes containing object meshes, materials, textures, lighting, volumetric data (e.g., smoke), and backgrounds. Metadata, such as 2D/3D bounding boxes, segmentation masks, depth maps, normal maps, material properties, and optical flow vectors, can also be generated. In this work, we discuss design goals, architecture, and performance. We demonstrate the use of data generated by path tracing for training an object detector and pose estimator, showing improved performance in sim-to-real transfer in situations that are difficult for traditional raster-based renderers. We offer this tool as an easy-to-use, performant, high-quality renderer for advancing research in synthetic data generation and deep learning.



A. Narayan, L. Yan, T. Zhou. “Optimal design for kernel interpolation: Applications to uncertainty quantification,” In Journal of Computational Physics, Vol. 430, Academic Press, pp. 110094. 2021.

ABSTRACT

The paper is concerned with classic kernel interpolation methods, in addition to approximation methods that are augmented by gradient measurements. To apply kernel interpolation using radial basis functions (RBFs) in a stable way, we propose a type of quasi-optimal interpolation points, searching from a large set of candidate points, using a procedure similar to designing Fekete points or power function maximizing points that use pivot from a Cholesky decomposition. The proposed quasi-optimal points results in smaller condition number, and thus mitigates the instability of the interpolation procedure when the number of points becomes large. Applications to parametric uncertainty quantification are presented, and it is shown that the proposed interpolation method can outperform sparse grid methods in many interesting cases. We also demonstrate the new procedure can be applied to constructing gradient-enhanced Gaussian process emulators.



Q. C Nguyen, J. M. Keralis, P. Dwivedi, A. E. Ng, M. Javanmardi, S. Khanna, Y. Huang, K. D. Brunisholz, A. Kumar, T. Tasdizen. “Leveraging 31 Million Google Street View Images to Characterize Built Environments and Examine County Health Outcomes ,” In Public Health Reports, Vol. 136, No. 2, SAGE Publications, pp. 201-211. 2021.
DOI: doi.org/10.1177/0033354920968799

ABSTRACT

Objectives
Built environments can affect health, but data in many geographic areas are limited. We used a big data source to create national indicators of neighborhood quality and assess their associations with health.

Methods
We leveraged computer vision and Google Street View images accessed from December 15, 2017, through July 17, 2018, to detect features of the built environment (presence of a crosswalk, non–single-family home, single-lane roads, and visible utility wires) for 2916 US counties. We used multivariate linear regression models to determine associations between features of the built environment and county-level health outcomes (prevalence of adult obesity, prevalence of diabetes, physical inactivity, frequent physical and mental distress, poor or fair self-rated health, and premature death [in years of potential life lost]).
Results
Compared with counties with the least number of crosswalks, counties with the most crosswalks were associated with decreases of 1.3%, 2.7%, and 1.3% of adult obesity, physical inactivity, and fair or poor self-rated health, respectively, and 477 fewer years of potential life lost before age 75 (per 100 000 population). The presence of non–single-family homes was associated with lower levels of all health outcomes except for premature death. The presence of single-lane roads was associated with an increase in physical inactivity, frequent physical distress, and fair or poor self-rated health. Visible utility wires were associated with increases in adult obesity, diabetes, physical and mental distress, and fair or poor self-rated health.
Conclusions
The use of computer vision and big data image sources makes possible national studies of the built environm



C. A. Nizinski, C. Ly, L. W. McDonald IV, T. Tasdizen. “Computational Image Techniques for Analyzing Lanthanide and Actinide Morphology,” In Rare Earth Elements and Actinides: Progress in Computational Science Applications, Ch. 6, pp. 133-155. 2021.
DOI: 10.1021/bk-2021-1388.ch006

ABSTRACT

This chapter introduces computational image analysis techniques and how they may be used for material characterization as it pertains to lanthanide and actinide chemistry. Specifically, the underlying theory behind particle segmentation, texture analysis, and convolutional neural networks for material characterization are briefly summarized. The variety of particle segmentation techniques that have been used to effectively measure the size and shape of morphological features from scanning electron microscope images will be discussed. In addition, the extraction of image texture features via gray-level co-occurrence matrices and angle measurement techniques are described and demonstrated. To conclude, the application of convolutional neural networks to lanthanide and actinide materials science challenges are described with applications for image classification, feature extraction, and predicting a materials morphology discussed.



C. Nobre, D. Wootton, Z. T. Cutler, L. Harrison, H. Pfister, A. Lex. “reVISit: Looking Under the Hood of Interactive Visualization Studies,” In SIGCHI Conference on Human Factors in Computing Systems (CHI), ACM, pp. 1--12. 2021.
DOI: 10.31219/osf.io/cbw36

ABSTRACT

Quantifying user performance with metrics such as time and accuracy does not show the whole picture when researchers evaluate complex, interactive visualization tools. In such systems, performance is often influenced by different analysis strategies that statistical analysis methods cannot account for. To remedy this lack of nuance, we propose a novel analysis methodology for evaluating complex interactive visualizations at scale. We implement our analysis methods in reVISit, which enables analysts to explore participant interaction performance metrics and responses in the context of users' analysis strategies. Replays of participant sessions can aid in identifying usability problems during pilot studies and make individual analysis processes salient. To demonstrate the applicability of reVISit to visualization studies, we analyze participant data from two published crowdsourced studies. Our findings show that reVISit can be used to reveal and describe novel interaction patterns, to analyze performance differences between different analysis strategies, and to validate or challenge design decisions.



A. Nouri, P.E. Davis, P. Subedi, M. Parashar. “Scalable Graph Embedding LearningOn A Single GPU,” Subtitled “arXiv preprint arXiv:2110.06991,” 2021.

ABSTRACT

Graph embedding techniques have attracted growing interest since they convert the graph data into continuous and low-dimensional space. Effective graph analytic provides users a deeper understanding of what is behind the data and thus can benefit a variety of machine learning tasks. With the current scale of real-world applications, most graph analytic methods suffer high computation and space costs. These methods and systems can process a network with thousands to a few million nodes. However, scaling to large-scale networks remains a challenge. The complexity of training graph embedding system requires the use of existing accelerators such as GPU. In this paper, we introduce a hybrid CPU-GPU framework that addresses the challenges of learning embedding of large-scale graphs. The performance of our method is compared qualitatively and quantitatively with the existing embedding systems on common benchmarks. We also show that our system can scale training to datasets with an order of magnitude greater than a single machine's total memory capacity. The effectiveness of the learned embedding is evaluated within multiple downstream applications. The experimental results indicate the effectiveness of the learned embedding in terms of performance and accuracy.



A. Nouri, P.E. Davis, P. Subedi, M. Parashar. “Exploring the Role of Machine Learning in Scientific Workflows: Opportunities and Challenges,” Subtitled “arXiv preprint arXiv:2110.13999,” 2021.

ABSTRACT

In this survey, we discuss the challenges of executing scientific workflows as well as existing Machine Learning (ML) techniques to alleviate those challenges. We provide the context and motivation for applying ML to each step of the execution of these workflows. Furthermore, we provide recommendations on how to extend ML techniques to unresolved challenges in the execution of scientific workflows. Moreover, we discuss the possibility of using ML techniques for in-situ operations. We explore the challenges of in-situ workflows and provide suggestions for improving the performance of their execution using ML techniques.



M. Penwarden, S. Zhe, A. Narayan, R. M. Kirby. “Multifidelity Modeling for Physics-Informed Neural Networks (PINNs),” Subtitled “arXiv preprint arXiv:2106.13361,” 2021.

ABSTRACT

Multifidelity simulation methodologies are often used in an attempt to judiciously combine low-fidelity and high-fidelity simulation results in an accuracy-increasing, cost-saving way. Candidates for this approach are simulation methodologies for which there are fidelity differences connected with significant computational cost differences. Physics-informed Neural Networks (PINNs) are candidates for these types of approaches due to the significant difference in training times required when different fidelities (expressed in terms of architecture width and depth as well as optimization criteria) are employed. In this paper, we propose a particular multifidelity approach applied to PINNs that exploits low-rank structure. We demonstrate that width, depth, and optimization criteria can be used as parameters related to model fidelity, and show numerical justification of cost differences in training due to fidelity parameter choices. We test our multifidelity scheme on various canonical forward PDE models that have been presented in the emerging PINNs literature.



M. Penwarden, S. Zhe, A. Narayan, R. M. Kirby. “Physics-Informed Neural Networks (PINNs) for Parameterized PDEs: A Metalearning Approach,” Subtitled “arXiv preprint arXiv:2110.13361,” 2021.

ABSTRACT

Physics-informed neural networks (PINNs) as a means of discretizing partial differential equations (PDEs) are garnering much attention in the Computational Science and Engineering (CS&E) world. At least two challenges exist for PINNs at present: an understanding of accuracy and convergence characteristics with respect to tunable parameters and identification of optimization strategies that make PINNs as efficient as other computational science tools. The cost of PINNs training remains a major challenge of Physics-informed Machine Learning (PiML) – and, in fact, machine learning (ML) in general. This paper is meant to move towards addressing the latter through the study of PINNs for parameterized PDEs. Following the ML world, we introduce metalearning of PINNs for parameterized PDEs. By introducing metalearning and transfer learning concepts, we can greatly accelerate the PINNs optimization process. We present a survey of model-agnostic metalearning, and then discuss our model-aware metalearning applied to PINNs. We provide theoretically motivated and empirically backed assumptions that make our metalearning approach possible. We then test our approach on various canonical forward parameterized PDEs that have been presented in the emerging PINNs literature.



R. Pulch, A. Narayan, T. Stykel. “Sensitivity analysis of random linear differential–algebraic equations using system norms,” In Journal of Computational and Applied Mathematics, North-Holland, pp. 113666. 2021.

ABSTRACT

We consider linear dynamical systems composed of differential–algebraic equations (DAEs), where a quantity of interest (QoI) is assigned as output. Physical parameters of a system are modelled as random variables to quantify uncertainty, and we investigate a variance-based sensitivity analysis of the random QoI. Based on expansions via generalised polynomial chaos, the stochastic Galerkin method yields a new deterministic system of DAEs of high dimension. We define sensitivity measures by system norms, ie, the H∞-norm of the transfer function associated with the Galerkin system for different combinations of outputs. To ameliorate the enormous computational effort required to compute norms of high-dimensional systems, we apply balanced truncation, a particular method of model order reduction (MOR), to obtain a low-dimensional linear dynamical system that produces approximations of system norms …



E. Qian, J.M. Tabeart, C. Beattie, S. Gugercin, J. Jiang, P. Kramer, A. Narayan. “Model Reduction of Linear Dynamical Systems via Balancing for Bayesian Inference,” Subtitled “arXiv preprint arXiv:2111.13246,” 2021.

ABSTRACT

We consider the Bayesian approach to the linear Gaussian inference problem of inferring the initial condition of a linear dynamical system from noisy output measurements taken after the initial time. In practical applications, the large dimension of the dynamical system state poses a computational obstacle to computing the exact posterior distribution. Model reduction offers a variety of computational tools that seek to reduce this computational burden. In particular, balanced truncation is a system-theoretic approach to model reduction which obtains an efficient reduced-dimension dynamical system by projecting the system operators onto state directions which trade off the reachability and observability of state directions as expressed through the associated Gramians. We introduce Gramian definitions relevant to the inference setting and propose a balanced truncation approach based on these inference Gramians that yield a reduced dynamical system that can be used to cheaply approximate the posterior mean and covariance. Our definitions exploit natural connections between (i) the reachability Gramian and the prior covariance and (ii) the observability Gramian and the Fisher information. The resulting reduced model then inherits stability properties and error bounds from system theoretic considerations, and in some settings yields an optimal posterior covariance approximation. Numerical demonstrations on two benchmark problems in model reduction show that our method can yield near-optimal posterior covariance approximations with order-of-magnitude state dimension reduction.



Y. Qin, A. Narayan, K. Cheng, P. Wang. “An efficient method of calculating composition-dependent inter-diffusion coefficients based on compressed sensing method,” In Computational Materials Science, Vol. 188, Elsevier, pp. 110145. 2021.

ABSTRACT

Composition-dependent inter-diffusion coefficients are key parameters in many physical processes. Due to the under-determinedness of the governing diffusion equations, numerical methods either impose strict physical conditions on the samples or require a computationally onerous amount of data. To address such problems, we propose a novel inverse framework to recover the diffusion coefficients using a compressed sensing method, which in principle can be extended to alloy systems with arbitrary number of species. Comparing to conventional methods, the new approach does not impose any priori assumptions on the functional relationship between diffusion coefficients and concentrations, nor any preference on the locations of the samples, as long as it is in the diffused zone. It also requires much less data compared to least-squares approaches. Through a few numerical examples of ternary and quandary systems, we demonstrate the accuracy and robustness of the new method.



Y. Qin, I. Rodero, A. Simonet, C. Meertens, D. Reiner, J. Riley, M. Parashar. “Leveraging user access patterns and advanced cyberinfrastructure to accelerate data delivery from shared-use scientific observatories,” In Future Generation Computer Systems, North-Holland, pp. 14-27. 2021.
DOI: https://doi.org/10.1016/j.future.2021.03.004

ABSTRACT

With the growing number and increasing availability of shared-use instruments and observatories, observational data is becoming an essential part of application workflows and contributor to scientific discoveries in a range of disciplines. However, the corresponding growth in the number of users accessing these facilities coupled with the expansion in the scale and variety of the data, is making it challenging for these facilities to ensure their data can be accessed, integrated, and analyzed in a timely manner, and is resulting significant demands on their cyberinfrastructure (CI). In this paper, we present the design of a push-based data delivery framework that leverages emerging in-network capabilities, along with data pre-fetching techniques based on a hybrid data management model. Specifically, we analyze data access traces for two large-scale observatories, Ocean Observatories Initiative (OOI) and Geodetic Facility for the Advancement of Geoscience (GAGE), to identify typical user access patterns and to develop a model that can be used for data pre-fetching. Furthermore, we evaluate our data pre-fetching model and the proposed framework using a simulation of the Virtual Data Collaboratory (VDC) platform that provides in-network data staging and processing capabilities. The results demonstrate that the ability of the framework to significantly improve data delivery performance and reduce network traffic at the observatories’ facilities.



Y. Qin, I. Rodero, M. Parashar. “Facilitating Data Discovery for Large-scale Science Facilities using Knowledge Networks,” In 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS), IEEE, pp. 651-660. 2021.
DOI: 10.1109/IPDPS49936.2021.00073

ABSTRACT

Large-scale multiuser scientific facilities, such as geographically distributed observatories, remote instruments, and experimental platforms, represent some of the largest national investments and can enable dramatic advances across many areas of science. Recent examples of such advances include the detection of gravitational waves and the imaging of a black hole’s event horizon. However, as the number of such facilities and their users grow, along with the complexity, diversity, and volumes of their data products, finding and accessing relevant data is becoming increasingly challenging, limiting the potential impact of facilities. These challenges are further amplified as scientists and application workflows increasingly try to integrate facilities’ data from diverse domains. In this paper, we leverage concepts underlying recommender systems, which are extremely effective in e-commerce, to address these data-discovery and data-access challenges for large-scale distributed scientific facilities. We first analyze data from facilities and identify and model user-query patterns in terms of facility location and spatial localities, domain-specific data models, and user associations. We then use this analysis to generate a knowledge graph and develop the collaborative knowledge-aware graph attention network (CKAT) recommendation model, which leverages graph neural networks (GNNs) to explicitly encode the collaborative signals through propagation and combine them with knowledge associations. Moreover, we integrate a knowledge-aware neural attention mechanism to enable the CKAT to pay more attention to key information while reducing irrelevant noise, thereby increasing the accuracy of the recommendations. We apply the proposed model on two real-world facility datasets and empirically demonstrate that the CKAT can effectively facilitate data discovery, significantly outperforming several compelling state-of-the-art baseline models.



Y. Qin, I. Rodero, M. Parashar. “Toward Democratizing Access to Facilities Data: A Framework for Intelligent Data Discovery and Delivery,” Subtitled “arXiv:2112.06479,” 2021.

ABSTRACT

Data collected by large-scale instruments, observatories, and sensor networks are key enablers of scientific discoveries in many disciplines. However, ensuring that these data can be accessed, integrated, and analyzed in a democratized and timely manner remains a challenge. In this article, we explore how state-of-the-art techniques for data discovery and access can be adapted to facility data and develop a conceptual framework for intelligent data access and discovery.



A.S. Rababah, L.R. Bear, Y.S. Dogrusoz, W. Good, J. Bergquist, J. Stoks, R. MacLeod, K. Rjoob, M. Jennings, J. Mclaughlin, D. D. Finlay. “Reducing Line-of-block Artifacts in Cardiac Activation Maps Estimated Using ECG Imaging: A Comparison of Source Models and Estimation Methods,” In Computers in Biology and Medicine, Vol. 136, pp. 104666. 2021.

ABSTRACT

Electrocardiographic imaging is an imaging modality that has been introduced recently to help in visualizing the electrical activity of the heart and consequently guide the ablation therapy for ventricular arrhythmias. One of the main challenges of this modality is that the electrocardiographic signals recorded at the torso surface are contaminated with noise from different sources. Low amplitude leads are more affected by noise due to their low peak-to-peak amplitude. In this paper, we have studied 6 datasets from two torso tank experiments (Bordeaux and Utah experiments) to investigate the impact of removing or interpolating these low amplitude leads on the inverse reconstruction of cardiac electrical activity. Body surface potential maps used were calculated by using the full set of recorded leads, removing 1, 6, 11, 16, or 21 low amplitude leads, or interpolating 1, 6, 11, 16, or 21 low amplitude leads using one of the three interpolation methods – Laplacian interpolation, hybrid interpolation, or the inverse-forward interpolation. The epicardial potential maps and activation time maps were computed from these body surface potential maps and compared with those recorded directly from the heart surface in the torso tank experiments. There was no significant change in the potential maps and activation time maps after the removal of up to 11 low amplitude leads. Laplacian interpolation and hybrid interpolation improved the inverse reconstruction in some datasets and worsened it in the rest. The inverse forward interpolation of low amplitude leads improved it in two out of 6 datasets and at least remained the same in the other datasets. It was noticed that after doing the inverse-forward interpolation, the selected lambda value was closer to the optimum lambda value that gives the inverse solution best correlated with the recorded one.



N. Ramesh, T. Tasdizen. “Detection and segmentation in microscopy images,” In Computer Vision for Microscopy Image Analysis, Academic Press, pp. 43-71. 2021.
DOI: 10.1016/B978-0-12-814972-0.00003-5

ABSTRACT

The plethora of heterogeneous data generated using modern microscopy imaging techniques eliminates the possibility of manual image analysis for biologists. Consequently, reliable and robust computerized techniques are critical to analyze microscopy data. Detection problems in microscopy images focuses on accurately identifying the objects of interest in an image that can be used to investigate hypotheses about developmental or pathological processes and can be indicative of prognosis in patients. Detection is also considered to be the preliminary step for solving subsequent problems, such as segmentation and tracking for various biological applications. Segmentation of the desired structures and regions in microscopy images require pixel-level labels to uniquely identify the individual structures and regions with contours for morphological and physiological analysis. Distributions of features extracted from the segmented regions can be used to compare normal versus disease or normal versus wild-type populations. Segmentation can be considered as a precursor for solving classification, reconstruction, and tracking problems in microscopy images. In this chapter, we discuss how the field of microscopic image analysis has progressed over the years, starting with traditional approaches and then followed by the study of learning algorithms. Because there is a lot of variability in microscopy data, it is essential to study learning algorithms that can adapt to these changes. We focus on deep learning approaches with convolutional neural networks (CNNs), as well as hierarchical methods for segmentation and detection in optical and electron microscopy images. Limitation of training data is one of the significant problems; hence, we explore solutions to learn better models with minimal user annotations.



M. Rasouli, R. M. Kirby, H. Sundar. “A Compressed, Divide and Conquer Algorithm for Scalable Distributed Matrix-Matrix Multiplication,” In The International Conference on High Performance Computing in Asia-Pacific Region, pp. 110-119. 2021.

ABSTRACT

Matrix-matrix multiplication (GEMM) is a widely used linear algebra primitive common in scientific computing and data sciences. While several highly-tuned libraries and implementations exist, these typically target either sparse or dense matrices. The performance of these tuned implementations on unsupported types can be poor, and this is critical in cases where the structure of the computations is associated with varying degrees of sparsity. One such example is Algebraic Multigrid (AMG), a popular solver and preconditioner for large sparse linear systems. In this work, we present a new divide and conquer sparse GEMM, that is also highly performant and scalable when the matrix becomes dense, as in the case of AMG matrix hierarchies. In addition, we implement a lossless data compression method to reduce the communication cost. We combine this with an efficient communication pattern during distributed-memory GEMM to provide 2.24 times (on average) better performance than the state-of-the-art library PETSc. Additionally, we show that the performance and scalability of our method surpass PETSc even more when the density of the matrix increases. We demonstrate the efficacy of our methods by comparing our GEMM with PETSc on a wide range of matrices.