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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2025

SHF: Symmetrical Hierarchical Forest with Pretrained Vision Transformer Encoder for High-Resolution Medical Segmentation

This paper presents a novel approach to addressing the long-sequence problem in high-resolution medical images for Vision Transformers (ViTs). Using smaller patches as tokens can enhance ViT performance, but quadratically increases computation and memory requirements. Therefore, the common practice for applying ViTs to high-resolution images is either to: (a) employ complex sub-quadratic attention schemes or (b) use large to medium-sized patches and rely on additional mechanisms within the model to capture the spatial hierarchy of details. We propose Symmetrical Hierarchical Forest (SHF), a lightweight approach that adaptively patches the input image to increase token information density and encode hierarchical spatial structures into the input embedding. We then apply a reverse depatching scheme to the output embeddings of the transformer encoder, eliminating the need for convolution-based decoders. Unlike previous methods that modify attention mechanisms or use a complex hierarchy of interacting models, SHF can be retrofitted to any ViT model to allow it to learn the hierarchical structure of details in high-resolution images without requiring architectural changes. Experimental results demonstrate significant gains in computational efficiency and performance: on the PAIP WSI dataset, we achieved a 3∼32×speedup or a 2.95%∼7.03% increase in accuracy (measured by Dice score) at a 64K2 resolution with the same computational budget, compared to state-of-the-art production models. On the 3D medical datasets BTCV and KiTS, training was 6×faster, with accuracy gains of 6.93% and 5.9%, respectively, compared to models without SHF.

Zhang, Enzhi [Hokkaido University, Japan]↗
DOE OSTI2024

Assessing the reliability of medical resource demand models in the context of COVID-19

Abstract Background Numerous medical resource demand models have been created as tools for governments or hospitals, aiming to predict the need for crucial resources like ventilators, hospital beds, personal protective equipment (PPE), and diagnostic kits during crises such as the COVID-19 pandemic. However, the reliability of these demand models remains uncertain. Methods Demand models typically consist of two main components: hospital use epidemiological models that predict hospitalizations or daily admissions, and a demand calculator that translates the outputs of the epidemiological model into predictions for resource usage. We conducted separate analyses to evaluate each of these components. In the first analysis, we validated various hospital use epidemiological models using a recent validation framework designed for epidemiological models. This allowed us to quantify the accuracy of the models in predicting critical aspects such as the date and magnitude of local COVID-19 peaks, among other factors. In the second analysis, we evaluated a range of demand calculators for ventilators, medical gowns, and COVID-19 test kits. To achieve this, we decoupled these demand calculators from the underlying epidemiological models and provided ground truth data for their inputs. This approach enabled a direct comparison of the demand calculators, comparing them against each other and actual usage data when available. The code is available athttps://doi.org/10.5281/zenodo.13712387. Results Performance varied greatly across the epidemiological models, with greater variability in COVID-19 hospital use predictions than for COVID-19 deaths as analyzed previously. Some models did not have any peaks. Among those that did, the models under-estimated date of peak approximately as often as they over-estimated, but were more likely to under-estimate magnitude of peak, with typical relative errors around 50%. Regarding demand calculator predictions, there was significant variability, including five-fold differences in predictions for gown models. Validation against actual or surrogate usage data illustrated the potential value of demand models while demonstrating their limitations. Conclusions The emerging field of demand modeling holds promise in averting medical resource shortages during future public health emergencies. However, achieving this potential necessitates focused efforts on standardization, transparency, and rigorous model validation before placing reliance on demand models in critical public health decision-making.

Medical Informatics↗
DOE OSTI2021

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗
DOE OSTI2022

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗