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At least 415 records · Page 23

Towards Autonomous Experiments by Connecting High Performance Microscopy with High Performance Computing

The digitization of controls, data, and analysis in microscopy is bringing the idea of autonomous microscopes closer to reality than ever before. Automated transmission electron microscopy (TEM) is already fairly routine for some experiments the only require simple repetitive tasks such as imaging biological macromolecules for single particle cryoEM [1], tilt series for electron tomography [2], and movies for crystallography [3]. The vast majority of TEM experiments are conducted completely by human operators who choose the regions of interest, optimize experimental parameters, and make decisions about data quality visually during an experiment. The field is still a long way from having completely autonomous TEMs that can adapt to sample difficulties and tune experimental parameters based on data quality and desired experimental outcomes. Part of the issue is the lack of capability for feeding information learned from on-line, live data analysis back into the on-going experiment [4]. Furthermore, this presentation will discuss current capabilities for large scale data reduction and analysis using high performance computing (i.e. supercomputing) and progress towards developing a true feed-back loop that places data analysis and theory in the experimental loop.

97 MATHEMATICS AND COMPUTING↗

Towards Interactive, Reproducible Analytics at Scale on HPC Systems

The growth in scientific data volumes has resulted in a need to scale up processing and analysis pipelines using High Performance Computing (HPC) systems. These workflows need interactive, reproducible analytics at scale. The Jupyter platform provides core capabilities for interactivity but was not designed for HPC systems. In this paper, we outline our efforts that bring together core technologies based on the Jupyter Platform to create interactive, reproducible analytics at scale on HPC systems. Our work is grounded in a real world science use case-applying geophysical simulations and inversions for imaging the subsurface. Our core platform addresses three key areas of the scientific analysis workflow-reproducibility, scalability, and interactivity. We describe our implemention of a system, using Binder, Science Capsule, and Dask software. We demonstrate the use of this software to run our use case and interactively visualize real-Time streams of HDF5 data.

containers↗

Anomaly detection in Hyper Suprime-Cam galaxy images with generative adversarial networks

ABSTRACT The problem of anomaly detection in astronomical surveys is becoming increasingly important as data sets grow in size. We present the results of an unsupervised anomaly detection method using a Wasserstein generative adversarial network (WGAN) on nearly one million optical galaxy images in the Hyper Suprime-Cam (HSC) survey. The WGAN learns to generate realistic HSC-like galaxies that follow the distribution of the data set; anomalous images are defined based on a poor reconstruction by the generator and outlying features learned by the discriminator. We find that the discriminator is more attuned to potentially interesting anomalies compared to the generator, and compared to a simpler autoencoder-based anomaly detection approach, so we use the discriminator-selected images to construct a high-anomaly sample of ∼13 000 objects. We propose a new approach to further characterize these anomalous images: we use a convolutional autoencoder to reduce the dimensionality of the residual differences between the real and WGAN-reconstructed images and perform UMAP clustering on these. We report detected anomalies of interest including galaxy mergers, tidal features, and extreme star-forming galaxies. A follow-up spectroscopic analysis of one of these anomalies is detailed in the Appendix; we find that it is an unusual system most likely to be a metal-poor dwarf galaxy with an extremely blue, higher-metallicity H ii region. We have released a catalogue with the WGAN anomaly scores; the code and catalogue are available at https://github.com/kstoreyf/anomalies-GAN-HSC; and our interactive visualization tool for exploring the clustered data is at https://weirdgalaxi.es.

79 ASTRONOMY AND ASTROPHYSICS↗

Utah FORGE 2439: Well 16B(78)-32 Field-Test Data from Mini-Frac Tests

This submittal includes the field-test data collected during stress tests conducted in the Utah FORGE 16B(78)-32 wellbore to measure/characterize the stresses in the geothermal reservoir. The type of stress test performed is referred to as a mini-frac test or a micro-frac test. The test is a hydraulic fracture test that involves injecting a small volume of water into a short interval of the reservoir that is isolated by a straddle packer to create a fracture. The test provides information about the minimum and maximum horizontal stress at the test depths. A total of seven mini-frac tests were performed within the upper (vertical or nearly vertical) section of the 9-5/8-inch diameter uncased wellbore, between depths of 5,202 ft MD [5,202 ft TVD] and 5,980 ft MD [5966.18 ft TVD]. Two types of data were generated as part of the mini-frac tests. The first type of data is time-series data for each mini-frac test (e.g., injection-rate, test-interval pressure), and are contained in the "Mini-Frac Test Data.zip" file below. The second type is geophysical log data, attached below in the "Geophysical Logs.zip" file. Here, two types of image logs and acoustic logs were obtained before and after the mini-frac tests to examine each test depth for visual evidence of induced fracture(s) and to measure the azimuth (orientation) of any observed fractures. The attached Readme file includes the test depth information and contents of each data file included here. Analysis of the field-test data was conducted and is documented in the attached report below.

15 GEOTHERMAL ENERGY↗

Volumetric Rendering on Wavelet-Based Adaptive Grid

Numerical modeling of physical phenomena frequently involves processes across a wide range of spatial and temporal scales. In the last two decades, the advancements in wavelet-based numerical methodologies to solve partial differential equations, combined with the unique properties of wavelet analysis to resolve localized structures of the solution on dynamically adaptive computational meshes, make it feasible to perform large-scale numerical simulations of a variety of physical systems on a dynamically adaptive computational mesh that changes both in space and time. Volumetric visualization of the solution is an essential part of scientific computing, yet the existing volumetric visualization techniques do not take full advantage of multi-resolution wavelet analysis and are not fully tailored for visualization of a compressed solution on the wavelet-based adaptive computational mesh. Our objective is to explore the alternatives for the visualization of time-dependent data on space-time varying adaptive mesh using volume rendering while capitalizing on the available sparse data representation. Two alternative formulations are explored. The first one is based on volumetric ray casting of multi-scale datasets in wavelet space. Rather than working with the wavelets at the finest possible resolution, a partial inverse wavelet transform is performed as a preprocessing step to obtain scaling functions on a uniform grid at a user-prescribed resolution. As a result, a solution in physical space is represented by a superposition of scaling functions on a coarse regular grid and wavelets on an adaptive mesh. An efficient and accurate ray casting algorithm is based just on these coarse scaling functions. Additional details are added during the ray tracing by taking an appropriate number of wavelets into account based on support overlap with the interpolation point, wavelet coefficient magnitude, and other characteristics, such as opacity accumulation (front to back ordering) and deviation from frontal viewing direction. The second approach is based on complementing of wavelet-based adaptive mesh to the traditional Adaptive Mesh Refinement (AMR) mesh. Both algorithms are illustrated and compared to the existing volume visualization software for Rayleigh-Benard thermal convection and electron density data sets in terms of rendering time and visual quality for different data compression of both wavelet-based and AMR adaptive meshes.

Vezolainen, Alexei V.↗

Factorized visual representations in the primate visual system and deep neural networks

Object classification has been proposed as a principal objective of the primate ventral visual stream and has been used as an optimization target for deep neural network models (DNNs) of the visual system. However, visual brain areas represent many different types of information, and optimizing for classification of object identity alone does not constrain how other information may be encoded in visual representations. Information about different scene parameters may be discarded altogether (‘invariance’), represented in non-interfering subspaces of population activity (‘factorization’) or encoded in an entangled fashion. In this work, we provide evidence that factorization is a normative principle of biological visual representations. In the monkey ventral visual hierarchy, we found that factorization of object pose and background information from object identity increased in higher-level regions and strongly contributed to improving object identity decoding performance. We then conducted a large-scale analysis of factorization of individual scene parameters – lighting, background, camera viewpoint, and object pose – in a diverse library of DNN models of the visual system. Models which best matched neural, fMRI, and behavioral data from both monkeys and humans across 12 datasets tended to be those which factorized scene parameters most strongly. Notably, invariance to these parameters was not as consistently associated with matches to neural and behavioral data, suggesting that maintaining non-class information in factorized activity subspaces is often preferred to dropping it altogether. Thus, we propose that factorization of visual scene information is a widely used strategy in brains and DNN models thereof.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient Clustering of Software Vulnerabilities using Self Organizing Map (SOM)

The common vulnerabilities and exposures (CVE) database was created with a mission to ``identify, define, and catalog publicly disclosed cybersecurity vulnerabilities''. This rich body of information can be used to enable rapid and efficient response to secure and defend cyber operations and protect critical cyber infrastructure. The main goal of this paper is to develop a visual analytics tool to enable deep analysis of CVEs using unsupervised clustering techniques. We enhance our analysis by first mapping CVEs to hierarchical-classes in Common Weakness Enumeration (CWE) using information in the National Vulnerability Database (NVD). Both the mapping and the numerical representation of CVEs are enabled by V2W-BERT, which uses natural language processing of the extensive information in NVD to generate a large tabular database of 137,226 CVE entries from 1999 to 2020, where each CVE is represented by a vector of 768 numerical features. The vectorized data is processed by Self-Organizing Maps (SOM), which is an unsupervised machine learning technique for dimensionality reduction, visual representation and clustering. Using a Torus map of 6417 units, we achieve ~10-fold data compression of ~140k CVEs using SOM. The trained map is further clustered using standard K-means clustering into 138 clusters of CVEs. We conducted a brief investigation of the rich mapping of CVEs to best-matching-units to K-means clusters, as well as CVEs to CWEs. For example, this novel mapping provided insight into the role of CWE-59 and CWE-264 in several CVEs that is otherwise hard to explore in the original data. We conclude that our this novel approach will not only enable deep analysis of the complex relationships between CVEs and CWEs, but also a mechanism to quickly respond to and design mitigation actions for rapidly evolving vulnerabilities that have not been mapped to existing CWEs.

Panchal, Khyati↗

Predicting U 3 O 8 powder processing conditions: An AI/ML approach analyzing deep learning embeddings of SEM micrographs

High-resolution SEM images of uranium-oxide powders encode micro- and nanoscale clues to their synthesis route and calcination temperature. We trained a ResNet-50 model on 11 commercial-scale U₃O₈ classes, ammonium diuranate (ADU) or uranyl peroxide (H₂O₂) precursors calcined at temperatures ranging from 400 to 750 °C and added a 256-D projection head before the classifier to analyze the learned representation. The best of eight seeds reached 92.4 % accuracy on reserved testing data, but our focus is the structure of the embedding space rather than the accuracy and labels. We quantify class relatedness in the original 256-D space using centroid similarity and distributional distances, and we use Uniform Manifold Approximation Projection (UMAP) for visualization. ‘Unknown’ images from different preparation methods, SEM operators, and from the literature localized near the expected classes under a nearest-centroid analysis without retraining, as well as clustered in similar UMAP space. In conclusion, this embedding-centered workflow complements black-box classification by providing quantitative, similarity-based comparisons of U₃O₈ morphologies and reduces storage space by up to 98 % for image data used in millisecond vector search comparisons.

36 MATERIALS SCIENCE↗

Memory-Aware External Facelist Calculation: A Data-Parallel Atomic Hash Counting Approach

Unstructured volumetric meshes serve as fundamental data representations in various scientific simulations and analyses. They play a crucial role in representing complex computational domains and are essential for important numerical techniques, such as finite element analysis. Whenever such a mesh is read from a file, streamed in-situ, or generated by algorithms, scientific visualization libraries rely on calculating the external surface of a geometry, named “external facelist”, to produce a polygonal mesh for rendering. Consequently, external facelist calculation has become one of the most widely used algorithms in the scientific visualization domain, necessitating optimal performance. In this paper, we explore relevant work on external facelist calculation algorithms in two common visualization libraries, VTK and Viskores, assess their performance and memory constraints, and introduce a novel memory-aware external facelist calculation algorithm employing an atomic hash counting approach. This algorithm fully leverages Viskores' data-parallel primitive operations, facilitating its execution across diverse many-core architectures. Our algorithm features the lowest memory footprint on the GPU and the second-lowest on the CPU among all evaluated methods, and it also delivers the fastest performance on both CPU and GPU. It has been made available under an open-source license in the VTK and Viskores visualization systems.

Tsalikis, Spiros [Kitware] (ORCID:0000000151137195↗

EPIsembleVis: A geo-visual analysis and comparison of the prediction ensembles of multiple COVID-19 models

In this work, we present EPIsembleVis, a web-based comparative visual analysis tool for evaluating the consistency of multiple COVID-19 prediction models. Our approach analyzes a collection of COVID-19 predictions from different epidemiological models as an ensemble and utilizes two metrics to quantify model performance. These metrics include (a) prediction uncertainty (represented as the dispersion of predictions in each ensemble) and (b) prediction error (calculated by comparing individual model predictions with the recorded data). Through an interactive visual interface, our approach provides a data-driven workflow for (a) selecting and constructing the COVID-19 model prediction ensemble based on the spatiotemporal overlap of available predictions of multiple epidemiological models, (b) quantifying the model performance using both the uncertainty of each model prediction ensemble, and the error of each ensemble member that represents individual model predictions, and (c) visualizing the spatiotemporal variability in the projection performance of individual models using a suite of novel ensemble visualization techniques, such as the data availability map, a spatiotemporal textured-tile calendar, multivariate rose chart, and time-series leaflet glyph. We demonstrate the capability of our ensemble visual interface through a case study that investigates the performance of weekly COVID-19 predictions, which are provided through the COVID-19 Forecast Hub UMass-Amherst Influenza Forecasting Center of Excellence [47] for the United States and United States Territories. The EPIsembleVis tool is implemented using open-source web technologies and adaptive system design, rendering it interoperable with Elasticsearch and Kibana for automatically ingesting COVID-19 predictions from online repositories, and it is generalizable for analyzing worldwide projections from more epidemiological models.

60 APPLIED LIFE SCIENCES↗

Exploiting correlations in multi-coincidence Coulomb explosion patterns for differentiating molecular structures using machine learning

Coulomb explosion imaging (CEI) is a powerful technique for capturing the real-time motion of individual atoms during ultrafast photochemical reactions. CEI generates high-dimensional data with naturally embedded correlations that allow mapping the coordinated motion of nuclei in molecules. This enables reliable separation of competing reaction pathways and makes this approach uniquely suited for characterizing weak reaction channels. However, rich information contained in experimental CEI patterns remains largely underexploited due to challenges in visualizing correlations between multiple observables in multi-dimensional parameter space. Here we present a new approach to CEI of intermediate-sized polyatomic molecules, detecting up to eight ionic fragments in coincidence and leveraging machine-learning-based analysis to identify patterns and correlations in the resulting high-dimensional momentum-space data, enabling robust molecular structure identification and differentiation. Our approach provides high-dimensional background-free data encoding exceptionally rich structural information and establishes an automated, scalable framework for extracting insightful information from the data. As a demonstration, we apply this method to image and distinguish dichloroethylene isomers, showcasing its potential for broader applications in molecular imaging. Our results pave the way for channel-specific analysis of ultrafast structural dynamics in chemically relevant systems, particularly for disentangling mixed reaction pathways and detecting contributions from weak channels and minority species.

Chemical Physics (physics.chem-ph)↗

Laboratory-Based Micro-X-ray Computed Tomography of Energy Materials at Idaho National Laboratory

Abstract The Idaho National Laboratory (INL) has implemented laboratory-based micro-X-ray computed tomography in a laboratory equipped for the examination of highly radioactive samples. This capability provides nondestructive three-dimensional volumetric information on samples to inform subsequent traditional destructive examinations as well as real-world inputs for high-fidelity scientific modeling. Samples can be imaged with spatial resolutions ranging from several hundred nm/voxel up to ~ 100 µm/voxel. The best usable spatial resolution achieved to date is 384 nm/voxel with this instrument, while the highest radiological dose rate of a sample imaged is ~ 60 R/h β/γ on contact. Advanced data analysis, including custom tomographic reconstruction and segmentation methods, have also been developed to support this capability. In addition to traditional digital X-ray radiography and tomography, this instrument is also able to visualize in situ tensile and compression testing as well as perform diffraction contrast tomography. This work describes the X-ray computed tomography post-irradiation examination capabilities at INL, as well as detailing a variety of applications this instrument has examined.

36 MATERIALS SCIENCE↗

Comparing Mapper Graphs of Artificial Neuron Activations

The mapper graph is a popular tool from topological data analysis that provides a graphical summary of point cloud data. It has been used to study data from cancer research, sports analytics, neurosciences, and machine learning. In particular, mapper graphs have been used recently to visualize the topology of high-dimensional artificial neural activations from convolutional neural networks and large language models. However, a key question that arises from using mapper graphs across applications is how to compare mapper graphs to study their structural differences. In this paper, we introduce a distance between mapper graphs using tools from optimal transport. We demonstrate the utility of such a distance by studying the topological changes of neural activations across convolutional layers in deep learning, as well as by capturing the loss of structural information for multiscale mapper.

mapper graphs, computational topology, machine lea↗

Background-Oriented Schlieren Velocimetry of Helium Coolant Flow in Additively Manufactured Channels

High-pressure helium gas cooling is an attractive solution for thermal management of the fusion blanket first wall, as this coolant is chemically and neutronically inert and separable from hydrogenic species. However, due to the low thermal mass of helium, geometric optimization of these channels is required to provide sufficient cooling at manageable flow rates and pumping burdens. Increasingly, analysis and optimization of these coolant channels rely on computational fluid dynamics (CFD) simulations, and these require relevant experimental data for turbulence model validation. Toward this end, a high-pressure helium gas flow visualization system has been employed to image the flow of helium in flow channels with one-sided heating, mimicking the blanket first wall environment. Flow of helium at 4 MPa pressure and flow rates up to 68 g/s (Reynolds number 57 000) is supplied to rectangular channel test sections, with uniform heating applied to the bottom wall of the channel at heat fluxes varied between roughly 50 and 130 kW/m2. A high-speed camera is used to image index of refraction (IOR) gradients in the fluid via background-oriented schlieren (BOS), and temperature and pressure instrumentation are used to characterize thermal-hydraulic performance of each channel. Cross correlation of time-resolved BOS images is then used to calculate time-averaged 2-D helium velocity fields. Flow in additively manufactured (AM) channels is examined in this manner, including both featureless channels and those containing baffling as a heat transfer enhancement. The flow distribution seen in the featureless case differs significantly from that seen in prior simulations, whereas the flow in the baffled case shows the predicted behavior of flow forced along the heated wall. This augmented flow distribution is seen to increase the heat transfer coefficient in the baffled test section. Here, strategies are discussed for ongoing and future validation of these simulations, with the aim of model deployment for blanket cooling design and optimization.

Additive manufacturing↗

GRid Analysis and Visualization Interface (GRAVI) [SWR-24-16]

GRAVI (GRid Analysis and Visualization Interface) is a web application for viewing and analyzing nodal Production Cost Model (PCM) and Capacity Expansion Model (CEM) simulations. The web application provides the ability to animate geospatially coupled timeseries data in an agnostic way regardless of the underlying simulation tool used to generate the data. GRAVI also provides capabilities to animate non-geospatial data relevant to a PCM or CEM model. Furthermore, this web application can be tailored as an real-time operational tool to better understand a live grid.

Webb, Micah↗

3013 Inner Container Closure Weld Region (ICCWR) Characterization by Wide Area 3D Measurement System (WAMS) Analysis (FY21 Progress Report)

As part of the 3013 Surveillance Program, through-wall penetration from stress corrosion cracking (SCC) of the 3013 inner containers has been identified as the most credible condition for failure withing the 50- years lifetime. Chlorides contained in Pu-bearing material, together with intra-canister humidity levels, metallurgical conditions, and internal stresses have been found to produce corrosion in the Inner Container Closure Weld Region (ICCWR) of the 3013 canister system. A Laser Confocal Microscope (LCM) is used as part of the 3013 Surveillance Program protocol to identify the prevalence of corrosion and corrosionrelated cracking in the ICCWR2. With the LCM, a close visual examination is made of the ICCWR surface along with measurements of corrosion-related features. LCM inspections produce immense amounts of image data that is time intensive to analyze. There is also a 9-year backlog of images, with approximately 49 canisters that must be evaluated. To expedite data analysis and reduce the amount of generated data, a Wide Area 3D Measurement System (WAMS) microscope has been added to the examination protocol. Although WAMS is a lower resolution microscope, small features of interest can be still identified. The advantage of collecting data for the full circumference using the WAMS is that it can take about 1/16 of the time needed with the LCM. Both systems offer capabilities that combined can be utilized to expedite the examination of the ICCWR. The WAMS is an efficient system for screening and identification of corrosion features while the LCM can be utilized to obtain higher resolution images areas identified by the WAMS. This report explains and justifies the data collection methods used with the WAMS. It includes a summary of the data generated by WAMS in FY21. The goals set for data collection in FY21 were met. A total of twenty-two DE’s were imaged, and analysis was carried out on eleven samples. The analyzed samples showed large numbers of potential cracks and pits distributed throughout the surfaces. Lastly, to explain the advantages of the WAMS, its capabilities were compared to those of a simpler microscope. Micrographs of the samples imaged in FY21 and those analyzed are included in the appendices.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Immersive Scientific Visualization of Molten-Salt Reactor Waste Characteristics Using Virtual Reality

Immersive visualization is changing how we explore, communicate, and understand complex scientific systems. In nuclear energy, an area in which data are often multidimensional, time-dependent, and difficult to interpret, virtual reality (VR) represents a powerful and intuitive informational medium. This work introduces a VR-based platform that visualizes the post-shutdown behavior and waste management lifecycle of molten-salt reactors (MSRs), a next-generation reactor type with unique operational and safety characteristics. The platform, built in Unity, is streamed on the Meta Quest 3 headset. It transforms high-fidelity simulation data into an interactive, immersive experience. Users can explore time-dependent reactor characteristics such as nuclide decay, which is a key factor for evaluating reactor waste strategies. The datasets were generated using the MOOSE (Multiphysics Object-Oriented Simulation Environment) framework and then processed through ParaView scripting for smooth integration into Unity. From a visualization standpoint, the platform emphasizes spatial storytelling, temporal exploration, and user-centered interaction. Users can navigate 3D reactor geometries, slice through volumetric data, and manipulate time to observe how physical phenomena evolve. Real-scale rendering and embodied interaction make the experience feel tangible. The interface is designed to be accessible, even to those without nuclear or simulation expertise. This lowers the barrier for stakeholders, policymakers, and the general public, while still supporting expert analysis and collaborative decision-making. This work shows how immersive visualization can function as both a scientific tool and a communication interface. By integrating simulation, processing, and visualization into a cohesive workflow, we offer a scalable framework for immersive scientific storytelling. The modular design supports future extensions to other reactor types and lifecycle stages, from shutdown to long-term storage, making the platform adaptable for both research and outreach.

99 - GENERAL AND MISCELLANEOUS↗

Using Visual Systems Mapping to Improve Transparency and Comparability of Life Cycle Assessment Baseline Scenarios

Visual systems mapping is a systems engineering approach used to represent complex processes and interactions. This study evaluates its application for documenting assumptions in life cycle assessment (LCA) baseline scenarios. In LCA, the baseline or reference case represents the business as usual system against which changes in impacts (e.g., emissions) are assessed. These baseline assumptions are particularly influential in biomass LCAs, yet they often vary across studies due to regional context, system boundaries, and simplifying assumptions that are not consistently or transparently documented. As a result, key feedbacks, omitted processes, and boundary choices may remain unclear, limiting comparability across studies and weakening their usefulness for decision-making. This study examines whether visual systems mapping can improve the transparency and comparability of biomass LCA baseline scenarios. A case study of five published biomass-related LCAs were reviewed, and their baseline scenarios were translated into visual system maps to identify included processes, omitted components, and underlying assumptions. The analysis demonstrates that visual systems mapping can make baseline assumptions more explicit, highlight excluded dynamics, and improve documentation of system boundaries. Based on these findings, the study recommends the use of visual systems mapping alongside open data repositories and reproducible workflows to support greater transparency, reproducibility, and comparability in LCAs. These improvements can strengthen the role of LCAs in informing decisions related to sustainable biomass systems.

Davis, Maggie [ORNL] (ORCID:0000000181319328)↗