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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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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Comparison of point cloud and image-based models for calorimeter fast simulation

Score based generative models are a new class of generative models that have been shown to accurately generate high dimensional calorimeter datasets. Recent advances in generative models have used images with 3D voxels to represent and model complex calorimeter showers. Point clouds, however, are likely a more natural representation of calorimeter showers, particularly in calorimeters with high granularity. Furthermore, point clouds preserve all of the information of the original simulation, more naturally deal with sparse datasets, and can be implemented with more compact models and data files. In this work, two state-of-the-art score based models are trained on the same set of calorimeter simulation and directly compared.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Plan evaluation for heat resilience: complementary methods to comprehensively assess heat planning in Tempe and Tucson, Arizona

Abstract Escalating impacts from climate change and urban heat are increasing the urgency for communities to equitably plan for heat resilience. Cities in the desert Southwest are among the hottest and fastest warming in the U.S., placing them on the front lines of heat planning. Urban heat resilience requires an integrated planning approach that coordinates strategies across the network of plans that shape the built environment and risk patterns. To date, few studies have assessed cities’ progress on heat planning. This research is the first to combine two emerging plan evaluation approaches to examine how networks of plans shape urban heat resilience through case studies of Tempe and Tucson, Arizona. The first methodology, Plan Quality Evaluation for Heat Resilience, adapts existing plan quality assessment approaches to heat. We assess whether plans meet 56 criteria across seven principles of high-quality planning and the types of heat strategies included in the plans. The second methodology, the Plan Integration for Resilience Scorecard™ (PIRS™) for Heat, focuses on plan policies that could influence urban heat hazards. We categorize policies by policy tool and heat mitigation strategy and score them based on their heat impact. Scored policies are then mapped to evaluate their spatial distribution and the net effect of the plan network. The resulting PIRS™ for Heat scorecard is compared with heat vulnerability indicators to assess policy alignment with risks. We find that both cities are proactively planning for heat resilience using similar plan and strategy types, however, there are clear and consistent opportunities for improvement. Combining these complementary plan evaluation methods provides a more comprehensive understanding of how plans address heat and a generalizable approach that communities everywhere could use to identify opportunities for improved heat resilience planning.

Environmental Sciences & Ecology↗
DOE OSTI2023

The drivers and predictability of wildfire re-burns in the western United States (US)

Evidence is mounting that the effectiveness of using prescribed burns as a management tactic may be diminishing due to the higher incidence of wildfire re-burns. The development of predictive models of re-burns is thus essential to better understand their primary drivers so that forest management practices can be updated to account for these events. First, we assess the potential for human activity as a driver of re-burns by evaluating re-burn trends both within and outside of the wildland–urban interface (WUI) of the western US. Next, we investigate the predictability of re-burns through the application of both random forest and the explanatory machine learning non-negative matrix factorization using k-means clustering (NMFk) algorithms to predict re-burn occurrence over California based on a number of climate factors. Our findings indicate that while most states showed increasing trends within the WUI when trends were conducted over longer moving windows (e.g. 20 years), California was the only state where the rate of increase was consistently higher in the WUI, indicating a stronger potential for human activity as a driver in that location. Furthermore, we find model performance was found to be robust over most of California (Testing F1 scores = 0.688), although results were highly variable based on EPA level III Ecoregion (F1 scores = 0.0–0.778). Insights provided from this study will lead to a better understanding of climate and human activity drivers of re-burns and how these vary at broad spatial scales so that improvements in forest management practices can be tuned according to the level of change that is expected for a given region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Heat exposure and maternal stress: evidence from the GRAPHS pregnancy cohort in Ghana

Heat exposure has been linked to psychosocial stress, an established antecedent of perinatal depression; however, evidence on heat-related stress during pregnancy in sub-Saharan Africa remains limited. We analyzed psychosocial stress scores and covariate data from the Ghana Randomized Air Pollution and Health Study, linking daily maximum and minimum shaded wet bulb globe temperature (WBGT) metrics to participants’ stress scores derived from the Crisis in Family Systems-Revised Life Events Questionnaire. We evaluated associations using ordinal logistic regression of pregnancy-average and trimester-average exposures and distributed lag non-linear models (DLNMs) to assess time-varying associations across gestation. Higher average maximum WBGT exposure across pregnancy was associated with increased odds of higher psychosocial stress; each 1 °C increase in maximum WBGT was associated with 64% higher odds of belonging to a higher stress category (OR = 1.64; 95% CI = 1.17–2.31; p = 0.0040). In trimester-average models, higher first-trimester maximum WBGT was also associated with higher stress (OR = 1.44; 95% CI = 1.15–1.81; p = 0.0014). DLNMs suggested that relatively cooler daily maximum WBGT values (25th percentile) were associated with decreased odds of stress in early pregnancy, whereas extreme daily maximum WBGT values (99th percentile) showed a pattern consistent with increased odds of stress in mid-to-late gestation. These findings highlight gestational windows in which heat exposure may influence stress, emphasizing the need for further research into underlying mechanisms and effective interventions to protect maternal mental health in heat-vulnerable settings.

White, Lewis [Columbia University] (ORCID:00090005↗
DOE OSTI2023

MS1Connect: a mass spectrometry run similarity measure

Abstract Motivation Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. Results We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though these data are not used by MS1Connect. Availability and implementation The MS1Connect software is available at https://github.com/bmx8177/MS1Connect. Supplementary information Supplementary data are available at Bioinformatics online.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

SeqMask: Behavior Extraction Over Cyber Threat Intelligence Via Multi-Instance Learning

Abstract Identification and extraction of Tactics, Techniques and Procedures (TTPs) for Cyber Threat Intelligence (CTI) restore the full picture of cyber attacks and guide the analysts to assess the system risk. Existing frameworks can hardly provide uniform and complete processing mechanisms for TTPs information extraction without adequate knowledge background. A multi-instance learning approach named SeqMask is proposed in this paper as a solution. SeqMask extracts behavior keywords from CTI evaluated by the semantic impact, and predicts TTPs labels by conditional probabilities. Still, the framework has two mechanisms to determine the validity of keywords. One using expert experience verification. The other verifies the distortion of the classification effect by blocking existing keywords. In the experiments, SeqMask reached 86.07% and 73.99% in F1 scores for TTPs classifications. For the top 20% of keywords, the expert approval rating is 92.20%, where the average repetition of keywords whose scores between 100% and 90% is 60.02%. Particularly, when the top 65% of the keywords were blocked, the F1 decreased to about 50%; when removing the top 50%, the F1 was under 31%. Further, we also validate the possibility of extracting TTPs from full-size CTI and malware whose F1 are improved by 2.16% and 0.81%.

Ge, Wenhan↗
DOE OSTI2021

Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Abstract Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Generating Older Adult Multimorbidity Trajectories Using Various Comorbidity Indices and Calculation Methods

Older adult multimorbidity trajectories are helpful for understanding the current and future health patterns of aging populations. The construction of multimorbidity trajectories from comorbidity index scores will help inform public health and clinical interventions targeting those individuals that are on unhealthy trajectories. Investigators have used many different techniques when creating multimorbidity trajectories in prior literature, and no standard way has emerged. This study compares and contrasts multimorbidity trajectories constructed from various methods. We describe the difference between aging trajectories constructed with the Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI). We also explore the differences between acute (single year) and chronic (cumulative) derivations of CCI and ECI scores. Social determinants of health can affect disease burden over time; thus, our models include income, race/ethnicity, and sex differences. We use group-based trajectory modeling (GBTM) to estimate multimorbidity trajectories for 86,909 individuals aged 66–75 in 1992 using Medicare claims data collected over the following 21 years. We identify low-chronic disease and high-chronic disease trajectories in all 8 generated trajectory models. Additionally, all 8 models satisfied prior established statistical diagnostic criteria for well-performing GBTM models. Clinicians may use these trajectories to identify patients on an unhealthy path and prompt a possible intervention that may shift the patient to a healthier trajectory.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Comparison of Different Variants of the U.S. Army Occupational Physical Assessment Test

The U.S. Army Occupational Physical Assessment Test (OPAT) is a pre-enlistment physical employment screening assessment developed to place recruits and soldiers into Military Occupational Specialties (MOSs) based on their physical capabilities in order to optimize performance and limit injury. The OPAT consists of the seated power throw (SPT), strength deadlift (SDL), standing long jump, and interval aerobic run. During the scientific validation of the OPAT, two variants of the SPT and two variants of the SDL were used. Although the OPAT was validated using both variants for each test, U.S. Army scientists and policymakers have received queries regarding how these variants compare to each other. Therefore, the purpose of this study was to compare different variants of the SPT and SDL. Thirty-two participants (14 male and 18 female) between the ages of 18 and 42 years visited the laboratory on one occasion and performed two variants of the SPT (seated on the ground [the current OPAT standard] versus seated in a chair with a 35 cm seat height) and two variants of the SDL (using a hex-bar [the current OPAT standard] versus using paired dumbbells). Testing order for the different variants was randomized. The protocol was approved by the U.S. Army Medical Research and Development Command Institutional Review Board. Performing the SPT from a chair significantly (P < .05) increased performance when compared to performing the SPT from the ground (5.4 ± 1.3 m versus 5.0 ± 1.4 m, respectively). Values for the two SPT variants were correlated (tau = 0.90). Performing the SDL using the hex-bar significantly increased the maximal weight lifted when compared to performing the SDL using paired dumbbells (86.9 ± 18.4 kg versus 83.1 ± 18.0 kg, respectively). Values for the two SDL variants were correlated (tau = 0.83). Performing different variants of the SPT and SDL influenced the resulting score. Although these findings do not alter the administration or scoring of the OPAT, they do provide a valuable reference in the event of future inquiries regarding the development of the OPAT.

General & Internal Medicine↗
DOE OSTI2021

Optimizing a magnitude-limited spectroscopic training sample for photometric classification of supernovae

ABSTRACT In preparation for photometric classification of transients from the Legacy Survey of Space and Time (LSST) we run tests with different training data sets. Using estimates of the depth to which the 4-m Multi-Object Spectroscopic Telescope (4MOST) Time Domain Extragalactic Survey (TiDES) can classify transients, we simulate a magnitude-limited sample reaching rAB ≈ 22.5 mag. We run our simulations with the software snmachine, a photometric classification pipeline using machine learning. The machine-learning algorithms struggle to classify supernovae when the training sample is magnitude limited, in contrast to representative training samples. Classification performance noticeably improves when we combine the magnitude-limited training sample with a simulated realistic sample of faint high-redshift supernovae observed from larger spectroscopic facilities; the algorithms’ range of average area under receiver operator characteristic curve (AUC) scores over 10 runs increases from 0.547–0.628 to 0.946–0.969 and purity of the classified sample reaches 95 per cent in all runs for two of the four algorithms. By creating new, artificial light curves using the augmentation software avocado, we achieve a purity in our classified sample of 95 per cent in all 10 runs performed for all machine-learning algorithms considered. We also reach a highest average AUC score of 0.986 with the artificial neural network algorithm. Having ‘true’ faint supernovae to complement our magnitude-limited sample is a crucial requirement in optimization of a 4MOST spectroscopic sample. However, our results are a proof of concept that augmentation is also necessary to achieve the best classification results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Survey of gravitationally lensed objects in HSC imaging (SuGOHI) – X. Strong lens finding in the HSC-SSP using convolutional neural networks

ABSTRACT We apply a novel model based on convolutional neural networks (CNN) to identify gravitationally lensed galaxies in multiband imaging of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) Survey. The trained model is applied to a parent sample of 2350 061 galaxies selected from the $\sim$ 800 deg$^2$ Wide area of the HSC-SSP Public Data Release 2. The galaxies in HSC Wide are selected based on stringent pre-selection criteria, such as multiband magnitudes, stellar mass, star formation rate, extendedness limit, photometric redshift range, etc. The trained CNN assigns a score from 0 to 1, with 1 representing lenses and 0 representing non-lenses. Initially, the CNN selects a total of 20 241 cutouts with a score greater than 0.9, but this number is subsequently reduced to 1522 cutouts after removing definite non-lenses for further visual inspection. We discover 43 grade A (definite) and 269 grade B (probable) strong lens candidates, of which 97 are completely new. In addition, we also discover 880 grade C (possible) lens candidates, 289 of which are known systems in the literature. We identify 143 candidates from the known systems of grade C that had higher confidence in previous searches. Our model can also recover 285 candidate galaxy-scale lenses from the Survey of Gravitationally lensed Objects in HSC Imaging (SuGOHI), where a single foreground galaxy acts as the deflector. Even though group-scale and cluster-scale lens systems are not included in the training, a sample of 32 SuGOHI-c (i.e. group/cluster-scale systems) lens candidates is retrieved. Our discoveries will be useful for ongoing and planned spectroscopic surveys, such as the Subaru Prime Focus Spectrograph project, to measure lens and source redshifts in order to enable detailed lens modelling.

Jaelani, Anton T. (ORCID:0000000162825778)↗
DOE OSTI2020

Photometric classification of Hyper Suprime-Cam transients using machine learning

Abstract The advancement of technology has resulted in a rapid increase in supernova (SN) discoveries. The Subaru/Hyper Suprime-Cam (HSC) transient survey, conducted from fall 2016 through spring 2017, yielded 1824 SN candidates. This gave rise to the need for fast type classification for spectroscopic follow-up and prompted us to develop a machine learning algorithm using a deep neural network with highway layers. This algorithm is trained by actual observed cadence and filter combinations such that we can directly input the observed data array without any interpretation. We tested our model with a dataset from the LSST classification challenge (Deep Drilling Field). Our classifier scores an area under the curve (AUC) of 0.996 for binary classification (SN Ia or non-SN Ia) and 95.3% accuracy for three-class classification (SN Ia, SN Ibc, or SN II). Application of our binary classification to HSC transient data yields an AUC score of 0.925. With two weeks of HSC data since the first detection, this classifier achieves 78.1% accuracy for binary classification, and the accuracy increases to 84.2% with the full dataset. This paper discusses the potential use of machine learning for SN type classification purposes.

Takahashi, Ichiro↗
DOE OSTI2019

Quality of life trajectories during the first three years after diagnosis of breast cancer: the NEON-BC study

Abstract Background We aimed to identify and characterize quality of life trajectories up to 3 years after breast cancer diagnosis. Methods A total of 460 patients were evaluated at baseline (before treatments), and after 1- and 3-years. Patient-reported outcomes, including quality of life (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30, QLQ-C30), anxiety, depression and sleep quality, were assessed in all evaluations. Model-based clustering was used to identify quality of life trajectories. Results We identified four trajectories without intersection during 3 years. The two trajectories characterized by better quality of life depicted relatively stable scores; in the other trajectories, quality of life worsened until 1 year, though in one of them the score at 3 years improved. Sociodemographic and clinical characteristics at baseline did not differ between trajectories, except for mastectomy, which was higher in the worst trajectory. Anxiety, depression and poor sleep quality increased from the best to the worst trajectory. Conclusions The type of surgery and the variation of other patient-reported outcomes were associated with the course of quality of life over 3 years. More research to understand the heterogeneity of individual trajectories within these major patterns of variation is needed.

Lopes-Conceição, Luisa↗
DOE OSTI2022

AbBERT: Learning Antibody Humanness via Masked Language Modeling

Understanding the degree of humanness of antibody sequences is critical to the therapeutic antibody development process to reduce the risk of failure modes like immunogenicity or poor manufacturability. We introduce AbBERT, a transformer-based language model trained on up to 20 million unpaired heavy/light chain sequences from the Observed Antibody Space database. We first validate AbBERT using a novel “multi-mask” scoring procedure to demonstrate high accuracy in predicting complementary determining regions—including the challenging hypervariable H3 region. We then demonstrate several uses of AbBERT at various points along the antibody design process. AbBERT enhances in silico antibody optimization via deep reinforcement learning by utilizing its learned embeddings as additional observations during optimization. Within a larger computational antibody design platform, AbBERT has been successfully applied as an additional design objective, where it displays strong correlations with computational tools predicting antibody structural stability. Finally, mutant antibody sequences that have been scored as unfavorable by AbBERT have shown corresponding low yields when expressed in cells. These use cases demonstrate the power of language modeling within computational antibody design.

Bioinformatics↗
DOE OSTI2025

Inferring the Isotropic-Nematic Phase Transition with Generative Machine Learning

Generative machine learning models are capable of learning the phase behavior in condensed matter systems such as the Ising model. We utilize a score-based modeling procedure called thermodynamic maps to describe the isotropic-nematic phase transition in a melt of Gay-Berne ellipsoids. When trained on samples from a single temperature on either side of the phase transition, this generative machine learning approach infers effectively the nematic order parameter at intermediate temperatures. Furthermore, these results demonstrate score-based models’ ability to learn the physics of a nontrivial liquid crystal phase transition.

Critical exponents↗
DOE OSTI2022

End-to-end jet classification of boosted top quarks with the CMS open data

Here we describe a novel application of the end-to-end deep learning technique to the task of discriminating top quark-initiated jets from those originating from the hadronization of a light quark or a gluon. The end-to-end deep learning technique uses low-level detector representation of high-energy collision event as inputs to deep learning algorithms. In this study, we use low-level detector information from the simulated Compact Muon Solenoid (CMS) open data samples to construct the top jet classifiers. To optimize classifier performance we progressively add low-level information from the CMS tracking detector, including pixel detector reconstructed hits and impact parameters, and demonstrate the value of additional tracking information even when no new spatial structures are added. Relying only on calorimeter energy deposits and reconstructed pixel detector hits, the end-to-end classifier achieves an area under the receiver operator curve (AUC) score of 0.975 ± 0.002 for the task of classifying boosted top quark jets. After adding derived track quantities, the classifier AUC score increases to 0.9824 ± 0.0013, serving as the first performance benchmark for these CMS open data samples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Spoofing Cross-Entropy Measure in Boson Sampling

Cross-entropy (XE) measure is a widely used benchmark to demonstrate quantum computational advantage from sampling problems, such as random circuit sampling using superconducting qubits and boson sampling (BS). We present a heuristic classical algorithm that attains a better XE than the current BS experiments in a verifiable regime and is likely to attain a better XE score than the near-future BS experiments in a reasonable running time. The key idea behind the algorithm is that there exist distributions that correlate with the ideal BS probability distribution and that can be efficiently computed. The correlation and the computability of the distribution enable us to postselect heavy outcomes of the ideal probability distribution without computing the ideal probability, which essentially leads to a large XE. Our method scores a better XE than the recent Gaussian BS experiments when implemented at intermediate, verifiable system sizes. Much like current state-of-the-art experiments, we cannot verify that our spoofer works for quantum-advantage-size systems. However, we demonstrate that our approach works for much larger system sizes in fermion sampling, where we can efficiently compute output probabilities. Finally, we provide analytic evidence that the classical algorithm is likely to spoof noisy BS efficiently.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗