In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. Colza relies on the widely used ParaView Catalyst in situ visualization framework and enables elasticity by replacing MPI with a custom collective communication library based on the Mochi suite of libraries. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.
S. Fang, A. Narayan, R.M. Kirby, S. Zhe. Bayesian Continuous-Time Tucker Decomposition, In Proceedings of the 39 th International Conference on Machine Learning, 2022.
Tensor decomposition is a dominant framework for multiway data analysis and prediction. Although practical data often contains timestamps for the observed entries, existing tensor decomposition approaches overlook or under-use this valuable time information. They either drop the timestamps or bin them into crude steps and hence ignore the temporal dynamics within each step or use simple parametric time coefficients. To overcome these limitations, we propose Bayesian Continuous-Time Tucker Decomposition (BCTT). We model the tensor-core of the classical Tucker decomposition as a time-varying function, and place a Gaussian process prior to flexibly estimate all kinds of temporal dynamics. In this way, our model maintains the interpretability while is flexible enough to capture various complex temporal relationships between the tensor nodes. For efficient and high-quality posterior inference, we use the stochastic differential equation (SDE) representation of temporal GPs to build an equivalent state-space prior, which avoids huge kernel matrix computation and sparse/low-rank approximations. We then use Kalman filtering, RTS smoothing, and conditional moment matching to develop a scalable message-passing inference algorithm. We show the advantage of our method in simulation and several real-world applications.
R. Faust, C. Scheidegger, K. Isaacs, W.Z. Bernstein, M. Sharp, C. North. Interactive Visualization for Data Science Scripts, In 2022 IEEE Visualization in Data Science (VDS), IEEE, pp. 37-45. 2022.
As the field of data science continues to grow, so does the need for adequate tools to understand and debug data science scripts. Current debugging practices fall short when applied to a data science setting, due to the exploratory and iterative nature of analysis scripts. Additionally, computational notebooks, the preferred scripting environment of many data scientists, present additional challenges to understanding and debugging workflows, including the non-linear execution of code snippets. This paper presents Anteater, a trace-based visual debugging method for data science scripts. Anteater automatically traces and visualizes execution data with minimal analyst input. The visualizations illustrate execution and value behaviors that aid in understanding the results of analysis scripts. To maximize the number of workflows supported, we present prototype implementations in both Python and Jupyter. Last, to demonstrate Anteater’s support for analysis understanding tasks, we provide two usage scenarios on real world analysis scripts.
A Pathologist-Informed Workflow for Classification of Prostate Glands in Histopathology, In Medical Optical Imaging and Virtual Microscopy Image Analysis, Springer Nature Switzerland, pp. 53--62. 2022.
Pathologists diagnose and grade prostate cancer by examining tissue from needle biopsies on glass slides. The cancer's severity and risk of metastasis are determined by the Gleason grade, a score based on the organization and morphology of prostate cancer glands. For diagnostic work-up, pathologists first locate glands in the whole biopsy core, and---if they detect cancer---they assign a Gleason grade. This time-consuming process is subject to errors and significant inter-observer variability, despite strict diagnostic criteria. This paper proposes an automated workflow that follows pathologists' modus operandi, isolating and classifying multi-scale patches of individual glands in whole slide images (WSI) of biopsy tissues using distinct steps: (1) two fully convolutional networks segment epithelium versus stroma and gland boundaries, respectively; (2) a classifier network separates benign from cancer glands at high magnification; and (3) an additional classifier predicts the grade of each cancer gland at low magnification. Altogether, this process provides a gland-specific approach for prostate cancer grading that we compare against other machine-learning-based grading methods.
M. Grant, M. R. Kunz, K. Iyer, L. I. Held, T. Tasdizen, J. A. Aguiar, P. P. Dholabhai. Integrating atomistic simulations and machine learning to design multi-principal element alloys with superior elastic modulus, In Journal of Materials Research, Springer International Publishing, pp. 1--16. 2022.
Multi-principal element, high entropy alloys (HEAs) are an emerging class of materials that have found applications across the board. Owing to the multitude of possible candidate alloys, exploration and compositional design of HEAs for targeted applications is challenging since it necessitates a rational approach to identify compositions exhibiting enriched performance. Here, we report an innovative framework that integrates molecular dynamics and machine learning to explore a large chemical-configurational space for evaluating elastic modulus of equiatomic and non-equiatomic HEAs along primary crystallographic directions. Vital thermodynamic properties and machine learning features have been incorporated to establish fundamental relationships correlating Young’s modulus with Gibbs free energy, valence electron concentration, and atomic size difference. In HEAs, as the number of elements increases …
J. Gu, P. Davis, G. Eisenhauer, W. Godoy, A. Huebl, S. Klasky, M. Parashar, N. Podhorszki, F. Poeschel, J. Vay, L. Wan, R. Wang, K. Wu. Organizing Large Data Sets for Efficient Analyses on HPC Systems, In Journal of Physics: Conference Series, Vol. 2224, No. 1, IOP Publishing, pp. 012042. 2022.
Upcoming exascale applications could introduce significant data management challenges due to their large sizes, dynamic work distribution, and involvement of accelerators such as graphical processing units, GPUs. In this work, we explore the performance of reading and writing operations involving one such scientific application on two different supercomputers. Our tests showed that the Adaptable Input and Output System, ADIOS, was able to achieve speeds over 1TB/s, a significant fraction of the peak I/O performance on Summit. We also demonstrated the querying functionality in ADIOS could effectively support common selective data analysis operations, such as conditional histograms. In tests, this query mechanism was able to reduce the execution time by a factor of five. More importantly, ADIOS data management framework allows us to achieve these performance improvements with only a minimal amount …
Time-varying vector fields produced by computational fluid dynamics simulations are often prohibitively large and pose challenges for accurate interactive analysis and exploration. To address these challenges, reduced Lagrangian representations have been increasingly researched as a means to improve scientific time-varying vector field exploration capabilities. This paper presents a novel deep neural network-based particle tracing method to explore time-varying vector fields represented by Lagrangian flow maps. In our workflow, in situ processing is first utilized to extract Lagrangian flow maps, and deep neural networks then use the extracted data to learn flow field behavior. Using a trained model to predict new particle trajectories offers a fixed small memory footprint and fast inference. To demonstrate and evaluate the proposed method, we perform an in-depth study of performance using a well-known analytical data set, the Double Gyre. Our study considers two flow map extraction strategies, the impact of the number of training samples and integration durations on efficacy, evaluates multiple sampling options for training and testing, and informs hyperparameter settings. Overall, we find our method requires a fixed memory footprint of 10.5 MB to encode a Lagrangian representation of a time-varying vector field while maintaining accuracy. For post hoc analysis, loading the trained model costs only two seconds, significantly reducing the burden of I/O when reading data for visualization. Moreover, our parallel implementation can infer one hundred locations for each of two thousand new pathlines in 1.3 seconds using one NVIDIA Titan RTX GPU.
Visualizing the uncertainty of ensemble simulations is challenging due to the large size and multivariate and temporal features of en-semble data sets. One popular approach to studying the uncertainty of ensembles is analyzing the positional uncertainty of the level sets. Probabilistic marching cubes is a technique that performs Monte Carlo sampling of multivariate Gaussian noise distributions for positional uncertainty visualization of level sets. However, the technique suffers from high computational time, making interactive visualization and analysis impossible to achieve. This paper introduces a deep-learning-based approach to learning the level-set uncertainty for two-dimensional ensemble data with a multivariate Gaussian noise assumption. We train the model using the first few time steps from time-varying ensemble data in our workflow. We demonstrate that our trained model accurately infers uncertainty in level sets for new time steps and is up to 170X faster than that of the original probabilistic model with serial computation and 10X faster than that of the original parallel computation.
J.D. Hogue, R.M. Kirby, A. Narayan. Dimensionality Reduction in Deep Learning via Kronecker Multi-layer Architectures, Subtitled arXiv:2204.04273, 2022.
Deep learning using neural networks is an effective technique for generating models of complex data. However, training such models can be expensive when networks have large model capacity resulting from a large number of layers and nodes. For training in such a computationally prohibitive regime, dimensionality reduction techniques ease the computational burden, and allow implementations of more robust networks. We propose a novel type of such dimensionality reduction via a new deep learning architecture based on fast matrix multiplication of a Kronecker product decomposition; in particular our network construction can be viewed as a Kronecker product-induced sparsification of an "extended" fully connected network. Analysis and practical examples show that this architecture allows a neural network to be trained and implemented with a significant reduction in computational time and resources, while achieving a similar error level compared to a traditional feedforward neural network.
John Holmen. Portable, Scalable Approaches For Improving Asynchronous Many-Task Runtime Node Use, School of Computing, University of Utah, 2022.
This research addresses node-level scalability, portability, and heterogeneous computing challenges facing asynchronous many-task (AMT) runtime systems. These challenges have arisen due to increasing socket/core/thread counts and diversity among supported architectures on current and emerging high-performance computing (HPC) systems. This places greater emphasis on thread scalability and simultaneous use of diverse architectures to maximize node use and is complicated by architecture-specific programming models.
Porting Uintah to Heterogeneous Systems, In Proceedings of the Platform for Advanced Scientific Computing Conference (PASC22) Best Paper Award, ACM, 2022.J.K. Holmen, D. Sahasrabudhe, M. Berzins.
The Uintah Computational Framework is being prepared to make portable use of forthcoming exascale systems, initially the DOE Aurora system through the Aurora Early Science Program. This paper describes the evolution of Uintah to be ready for such architectures. A key part of this preparation has been the adoption of the Kokkos performance portability layer in Uintah. The sheer size of the Uintah codebase has made it imperative to have a representative benchmark. The design of this benchmark and the use of Kokkos within it is discussed. This paper complements recent work with additional details and new scaling studies run 24x further than earlier studies. Results are shown for two benchmarks executing workloads representative of typical Uintah applications. These results demonstrate single-source portability across the DOE Summit and NSF Frontera systems with good strong-scaling characteristics. The challenge of extending this approach to anticipated exascale systems is also considered.
Short-Term Natural Course of Esophageal Thermal Injury After Ablation for Atrial Fibrillation, In Journal of Cardiovascular Electrophysiology, Wiley, 2022.
To provide insight into the short-term natural history of esophageal thermal injury (ETI) after radiofrequency catheter ablation (RFCA) for atrial fibrillation (AF) by esophagogastroduodenoscopy (EGD).
Shorter Distance Between The Esophagus And The Left Atrium Is Associated With Higher Rates Of Esophageal Thermal Injury After Radiofrequency Ablation, In Journal of Cardiovascular Electrophysiology, Wiley, 2022.
Esophageal thermal injury (ETI) is a known and potentially serious complication of catheter ablation for atrial fibrillation. We intended to evaluate the distance between the esophagus and the left atrium posterior wall (LAPW) and its association with esophageal thermal injury.
K. Iyer, A. Morris, B. Zenger, K. Karnath, B.A. Orkild, O. Korshak, S. Elhabian. Statistical Shape Modeling of Biventricular Anatomy with Shared Boundaries, Subtitled arXiv:2209.02706v1, 2022.
Statistical shape modeling (SSM) is a valuable and powerful tool to generate a detailed representation of complex anatomy that enables quantitative analysis and the comparison of shapes and their variations. SSM applies mathematics, statistics, and computing to parse the shape into a quantitative representation (such as correspondence points or landmarks) that will help answer various questions about the anatomical variations across the population. Complex anatomical structures have many diverse parts with varying interactions or intricate architecture. For example, the heart is a four-chambered anatomy with several shared boundaries between chambers. Coordinated and efficient contraction of the chambers of the heart is necessary to adequately perfuse end organs throughout the body. Subtle shape changes within these shared boundaries of the heart can indicate potential pathological changes that lead to uncoordinated contraction and poor end-organ perfusion. Early detection and robust quantification could provide insight into ideal treatment techniques and intervention timing. However, existing SSM approaches fall short of explicitly modeling the statistics of shared boundaries. In this paper, we present a general and flexible data-driven approach for building statistical shape models of multi-organ anatomies with shared boundaries that captures morphological and alignment changes of individual anatomies and their shared boundary surfaces throughout the population. We demonstrate the effectiveness of the proposed methods using a biventricular heart dataset by developing shape models that consistently parameterize the cardiac biventricular structure and the interventricular septum (shared boundary surface) across the population data.
M.H. Jensen, S. Joshi, S. Sommer.
Discrete-Time Observations of Brownian Motion on Lie Groups and Homogeneous Spaces: Sampling and Metric Estimation, In Algorithms, Vol. 15, No. 8, 2022.
We present schemes for simulating Brownian bridges on complete and connected Lie groups and homogeneous spaces. We use this to construct an estimation scheme for recovering an unknown left- or right-invariant Riemannian metric on the Lie group from samples. We subsequently show how pushing forward the distributions generated by Brownian motions on the group results in distributions on homogeneous spaces that exhibit a non-trivial covariance structure. The pushforward measure gives rise to new non-parametric families of distributions on commonly occurring spaces such as spheres and symmetric positive tensors. We extend the estimation scheme to fit these distributions to homogeneous space-valued data. We demonstrate both the simulation schemes and estimation procedures on Lie groups and homogenous spaces, including SPD(3)=GL+(3)/SO(3) and S2=SO(3)/SO(2).
Few-Shot Generation of Personalized Neural Surrogates for Cardiac Simulation via Bayesian Meta-learning, In Medical Image Computing and Computer Assisted Intervention -- MICCAI 2022, Springer Nature Switzerland, pp. 46--56. 2022.
Clinical adoption of personalized virtual heart simulations faces challenges in model personalization and expensive computation. While an ideal solution is an efficient neural surrogate that at the same time is personalized to an individual subject, the state-of-the-art is either concerned with personalizing an expensive simulation model, or learning an efficient yet generic surrogate. This paper presents a completely new concept to achieve personalized neural surrogates in a single coherent framework of meta-learning (metaPNS). Instead of learning a single neural surrogate, we pursue the process of learning a personalized neural surrogate using a small amount of context data from a subject, in a novel formulation of few-shot generative modeling underpinned by: 1) a set-conditioned neural surrogate for cardiac simulation that, conditioned on subject-specific context data, learns to generate query simulations not included in the context set, and 2) a meta-model of amortized variational inference that learns to condition the neural surrogate via simple feed-forward embedding of context data. As test time, metaPNS delivers a personalized neural surrogate by fast feed-forward embedding of a small and flexible number of data available from an individual, achieving -- for the first time -- personalization and surrogate construction for expensive simulations in one end-to-end learning framework. Synthetic and real-data experiments demonstrated that metaPNS was able to improve personalization and predictive accuracy in comparison to conventionally-optimized cardiac simulation models, at a fraction of computation.
Deep neural networks have shown promise in image reconstruction tasks, although often on the premise of large amounts of training data. In this paper, we present a new approach to exploit the geometry and physics underlying electrocardiographic imaging (ECGI) to learn efficiently with a relatively small dataset. We first introduce a non-Euclidean encoding-decoding network that allows us to describe the unknown and measurement variables over their respective geometrical domains. We then explicitly model the geometry-dependent physics in between the two domains via a bipartite graph over their graphical embeddings. We applied the resulting network to reconstruct electrical activity on the heart surface from body-surface potentials. In a series of generalization tasks with increasing difficulty, we demonstrated the improved ability of the network to generalize across geometrical changes underlying the data using less than 10% of training data and fewer variations of training geometry in comparison to its Euclidean alternatives. In both simulation and real-data experiments, we further demonstrated its ability to be quickly fine-tuned to new geometry using a modest amount of data.
X. Jiang, J. Tate, J. Bergquist, A. Narayan, R. MacLeod, L. Wang. Uncertainty Quantification of Cardiac Position on Deep Graph Network ECGI, In Computing in Cardiology, Vol. 49, 2022.
Subject-specific geometry such as cardiac position and torso size plays an important role in electrocardiographic imaging (ECGI). Previously, we introduced a graph-based neural network (GNN) that is dependent on patient-specific geometry to improve reconstruction accuracy. However, geometric uncertainty, including changes in cardiac position and torso size, has not been addressed in network-based methods. In this study, we estimate geometrical uncertainty on GNN by applying uncertainty quantification with polynomial chaos emulators (PCE). To estimate the effect of geometric variation from common motions, we evaluated the model on samples generated by different heart torso geometries. The experiments shows that the GNN is less sensitive to heart position and torso shape and helps us direct development of similar models to account of possible variability.
Computational models have made it possible to study the effect of fibrosis and scar on atrial fibrillation (AF) and plan future personalized treatments. Here, we study the effect of area available for fibrillatory waves to sustain AF. Then we use it to plan for AF ablation to improve procedural outcomes. CARPentry was used to create patient-specific models to determine the association between the size of residual contiguous areas available for AF wavefronts to propagate and sustain AF [fibrillatory area (FA)] after ablation with procedural outcomes. The FA was quantified in a novel manner accounting for gaps in ablation lines. We selected 30 persistent AF patients with known ablation outcomes. We divided the atrial surface into five areas based on ablation scar pattern and anatomical landmarks and calculated the FAs. We validated the models based on clinical outcomes and suggested future ablation lines that minimize the FAs and terminate rotor activities in simulations. We also simulated the effects of three common antiarrhythmic drugs. In the patient-specific models, the predicted arrhythmias matched the clinical outcomes in 25 of 30 patients (accuracy 83.33%). The average largest FA (FAmax) in the recurrence group was 8517 ± 1444 vs. 6772 ± 1531 mm2 in the no recurrence group (p < 0.004). The final FAs after adding the suggested ablation lines in the AF recurrence group reduced the average FAmax from 8517 ± 1444 to 6168 ± 1358 mm2 (p < 0.001) and stopped the sustained rotor activity. Simulations also correctly anticipated the effect of antiarrhythmic drugs in 5 out of 6 patients who used drug therapy post unsuccessful ablation (accuracy 83.33%). Sizes of FAs available for AF wavefronts to propagate are important determinants for ablation outcomes. FA size in combination with computational simulations can be used to direct ablation in persistent AF to minimize the critical mass required to sustain recurrent AF.
V. Keshavarzzadeh, R.M. Kirby, A. Narayan. Variational Inference for Nonlinear Inverse Problems via Neural Net Kernels: Comparison to Bayesian Neural Networks, Application to Topology Optimization, Subtitled arXiv:2205.03681, 2022.
Inverse problems and, in particular, inferring unknown or latent parameters from data are ubiquitous in engineering simulations. A predominant viewpoint in identifying unknown parameters is Bayesian inference where both prior information about the parameters and the information from the observations via likelihood evaluations are incorporated into the inference process. In this paper, we adopt a similar viewpoint with a slightly different numerical procedure from standard inference approaches to provide insight about the localized behavior of unknown underlying parameters. We present a variational inference approach which mainly incorporates the observation data in a point-wise manner, i.e. we invert a limited number of observation data leveraging the gradient information of the forward map with respect to parameters, and find true individual samples of the latent parameters when the forward map is noise-free and one-to-one. For statistical calculations (as the ultimate goal in simulations), a large number of samples are generated from a trained neural network which serves as a transport map from the prior to posterior latent parameters. Our neural network machinery, developed as part of the inference framework and referred to as Neural Net Kernels (NNK), is based on hierarchical (deep) kernels which provide greater flexibility for training compared to standard neural networks. We showcase the effectiveness of our inference procedure in identifying bimodal and irregular distributions compared to a number of approaches including Markov Chain Monte Carlo sampling approaches and a Bayesian neural network approach.