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DOE OSTI2024

Detection of Isotopes in Urban Source Search Gamma Spectra Using Hopfield Neural Network

Source search campaigns involve the measurement of consecutive background gamma-ray spectra obtained with a mobile detector-spectrometer, such as tellurium-doped sodium iodide NaI(Tl) scintillator detector-spectrometer. Counts are measured with NaI(Tl) detector in short acquisition intervals, such as one second. Detection of isotopes in search data is challenging because of the low signal-to-noise ratio (S/N) of the spectral lines and highly varying background due to naturally occurring radioactive material (NORM). In this work, we investigate the performance of the detection of orphan Cs-137, Am-241, and I-131 isotopes in a gamma ray data set obtained in a search survey. Isotopic detection is performed with a Hopfield Neural Network (HNN), which implements an auto-associative memory by matching incoming measurements to the closest one of its memory-stored signature patterns. HNN is trained on examples of spectra of calibrated isotopic sources with well-resolved spectral lines. During testing, HNN processes spectra with partially complete or distorted isotopic lines. The performance of the HNN detection algorithm is benchmarked with Precision, Recall, and F1 scores. Test results demonstrate the potential of HNN to detect the isotope of interest with high accuracy (F1 > 90%) for all isotopes in this study.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Prediction of the Cu oxidation state from EELS and XAS spectra using supervised machine learning

Abstract Electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS) provide detailed information about bonding, distributions and locations of atoms, and their coordination numbers and oxidation states. However, analysis of XAS/EELS data often relies on matching an unknown experimental sample to a series of simulated or experimental standard samples. This limits analysis throughput and the ability to extract quantitative information from a sample. In this work, we have trained a random forest model capable of predicting the oxidation state of copper based on its L-edge spectrum. Our model attains an R 2 score of 0.85 and a root mean square error of 0.24 on simulated data. It has also successfully predicted experimental L-edge EELS spectra taken in this work and XAS spectra extracted from the literature. We further demonstrate the utility of this model by predicting simulated and experimental spectra of mixed valence samples generated by this work. This model can be integrated into a real-time EELS/XAS analysis pipeline on mixtures of copper-containing materials of unknown composition and oxidation state. By expanding the training data, this methodology can be extended to data-driven spectral analysis of a broad range of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Detection of Isotopes in Urban Source Search Low-Count Gamma Spectra Using Hopfield Neural Networks

Source search campaigns involve measurements of background gamma-ray spectra with a mobile detector-spectrometer traveling along arbitrarily chosen trajectories over a wide screening area. Radiation counts are typically measured with a tellurium-doped sodium iodide [NaI(Tl)] scintillator detector-spectrometer in short acquisition intervals, usually 1 s. The objective is to detect orphan isotopes with half-lives shorter than those of the isotopes in the natural background. In principle, radioisotopes can be identified by their unique gamma emission spectrum. However, detecting orphan isotopes in search data is challenging because low counts measured in short acquisition intervals result in incomplete spectral lines. In this study, we investigate the performance of a Hopfield neural network (HNN) that implements an auto-associative memory for the detection of isotopes of interest in an urban search campaign. The HNN is trained on one example of gamma spectra with well-resolved spectral lines of each isotope of interest. During testing, the auto-associative memory implementation of the HNN processes low-count gamma spectra with partially complete isotopic lines by matching incoming measurements to the closest one of its memory-stored patterns. The testing database consisted of almost 10 000 1-s gamma spectra, including measurements of orphan isotopes 137 Cs, 241 Am, and 131 I, obtained during two urban search surveys with a NaI(Tl) detector. The performance of the HNN detection algorithm was evaluated using precision, recall, and F1 scores, and benchmarked with a multiple linear regression (MLR) identification algorithm. In conclusion, the test results demonstrate that HNN outperforms MLR in the detection of all the isotopes of interest.

Auto associative memory↗

DOE OSTI2024

An evaluation of GPT models for phenotype concept recognition

Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Using Artificial Neural Networks to Predict Physical Properties of Membrane Polymers

Membrane polymers are a promising technology for use in many challenging gas separation applications. Here, the techniques of computer-aided molecular design can be used to search through the massive molecular space of heteropolymers and develop a set of likely candidate repeat units matching specific physical property targets. However, reasonably accurate property prediction algorithms are needed, but these algorithms must be very fast in order to be combined with an optimization framework. Artificial neural networks (ANNs), a branch of machine learning, are applied in this work to predict the physical properties of polymers. All of the physical properties investigated were found to be predicted by ANNs with R 2 scores exceeding 0.82.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

$\mathrm{IH}$-$\mathrm{GAN}$: A conditional generative model for implicit surface-based inverse design of cellular structures

Variable-density cellular structures can overcome connectivity and manufacturability issues of topologically optimized structures, particularly those represented as discrete density maps. However, the optimization of such cellular structures is challenging due to the multiscale design problem. Past work addressing this problem generally either only optimizes the volume fraction of single-type unit cells but ignoring the effects of unit cell geometry on properties, or considers the geometry–property relation but builds this relation via heuristics. In contrast, we propose a simple yet more principled way to accurately model the property to geometry mapping using a conditional deep generative model, named Inverse Homogenization Generative Adversarial Network (IH-GAN). It learns the conditional distribution of unit cell geometries given properties and can realize the one-to-many mapping from properties to geometries. Here we further reduce the complexity of IH-GAN by using the implicit function parameterization to represent unit cell geometries. Results show that our method can 1) generate various unit cells that satisfy given material properties with high accuracy (R 2 -scores between target properties and properties of generated unit cells >98%) and 2) improve the optimized structural performance over the conventional variable-density single-type structure. In the minimum compliance example, our IH-GAN generated structure achieves a 79.7% reduction in concentrated stress and an extra 3.03% reduction in displacement. In the target deformation examples, our IH-GAN generated structure reduces the target matching error by 86.4% and 79.6% for two test cases, respectively. We also demonstrated that the connectivity issue for multi-type unit cells can be solved by transition layer blending.

42 ENGINEERING↗

DOE OSTI2021

Neuronally-derived tau is increased in experienced breachers and is associated with neurobehavioral symptoms

Military and law enforcement breachers are exposed to many low-level blasts during their training and occupational experiences in which they detonate explosives to force entry into secured structures. There is a concern that exposure to these repetitive blast events in career breachers could result in cumulative neurological effects. This study aimed to determine concentrations of neurofilament light (NF-L), tau, and amyloid-beta 42 (Aβ42) in serum and in neuronal-derived extracellular vesicles (EVs) in an experienced breacher population, and to examine biomarker associations with neurobehavioral symptoms. Thirty-four participants enrolled in the study: 20 experienced breachers and 14 matched military or civilian law enforcement controls. EV tau concentrations were significantly elevated in experienced breachers (0.3301 ± 0.5225) compared to controls (–0.4279 ± 0.7557; F = 10.43, p = 0.003). No statistically significant changes were observed in EV levels of NF-L or Aβ42 or in serum levels of NF-L, tau, or Aβ42 (p’s > 0.05). Elevated EV tau concentrations correlated with increased Neurobehavioral Symptom Inventory (NSI) score in experienced breachers (r = 0.596, p = 0.015) and predicted higher NSI score (F(1,14) = 7.702, p = 0.015, R 2 = 0.355). These findings show that neuronal-derived EV concentrations of tau are significantly elevated and associated with neurobehavioral symptoms in this sample of experienced breachers who have a history of many low-level blast exposures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2007

Feasibility of Turing-Style Tests for Autonomous Aerial Vehicle "Intelligence"

A new approach is suggested to define and evaluate key metrics as to autonomous aerial vehicle performance. This approach entails the conceptual definition of a "Turing Test" for UAVs. Such a "UAV Turing test" would be conducted by means of mission simulations and/or tailored flight demonstrations of vehicles under the guidance of their autonomous system software. These autonomous vehicle mission simulations and flight demonstrations would also have to be benchmarked against missions "flown" with pilots/human-operators in the loop. In turn, scoring criteria for such testing could be based upon both quantitative mission success metrics (unique to each mission) and by turning to analog "handling quality" metrics similar to the well-known Cooper-Harper pilot ratings used for manned aircraft. Autonomous aerial vehicles would be considered to have successfully passed this "UAV Turing Test" if the aggregate mission success metrics and handling qualities for the autonomous aerial vehicle matched or exceeded the equivalent metrics for missions conducted with pilots/human-operators in the loop. Alternatively, an independent, knowledgeable observer could provide the "UAV Turing Test" ratings of whether a vehicle is autonomous or "piloted." This observer ideally would, in the more sophisticated mission simulations, also have the enhanced capability of being able to override the scripted mission scenario and instigate failure modes and change of flight profile/plans. If a majority of mission tasks are rated as "piloted" by the observer, when in reality the vehicle/simulation is fully- or semi- autonomously controlled, then the vehicle/simulation "passes" the "UAV Turing Test." In this regards, this second "UAV Turing Test" approach is more consistent with Turing s original "imitation game" proposal. The overall feasibility, and important considerations and limitations, of such an approach for judging/evaluating autonomous aerial vehicle "intelligence" will be discussed from a theoretical perspective.

Young, Larry A.↗

DOE OSTI2024

Score-based denoising for atomic structure identification

We propose an effective method for removing thermal vibrations that complicate the task of analyzing complex dynamics in atomistic simulation of condensed matter. Our method iteratively subtracts thermal noises or perturbations in atomic positions using a denoising score function trained on synthetically noised but otherwise perfect crystal lattices. The resulting denoised structures clearly reveal underlying crystal order while retaining disorder associated with crystal defects. Purely geometric, agnostic to interatomic potentials, and trained without inputs from explicit simulations, our denoiser can be applied to simulation data generated from vastly different interatomic interactions. The denoiser is shown to improve existing classification methods, such as common neighbor analysis and polyhedral template matching, reaching perfect classification accuracy on a recent benchmark dataset of thermally perturbed structures up to the melting point. Demonstrated here in a wide variety of atomistic simulation contexts, the denoiser is general, robust, and readily extendable to delineate order from disorder in structurally and chemically complex materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Synthetic method of analogues for emerging infectious disease forecasting

The Method of Analogues (MOA) has gained popularity in the past decade for infectious disease forecasting due to its non-parametric nature. In MOA, the local behavior observed in a time series is matched to the local behaviors of several historical time series. The known values that directly follow the historical time series that best match the observed time series are used to calculate a forecast. This non-parametric approach leverages historical trends to produce forecasts without extensive parameterization, making it highly adaptable. However, MOA is limited in scenarios where historical data is sparse. This limitation was particularly evident during the early stages of the COVID-19 pandemic, where the emerging global epidemic had little-to-no historical data. In this work, we propose a new method inspired by MOA, called the Synthetic Method of Analogues (sMOA). sMOA replaces historical disease data with a library of synthetic data that describe a broad range of possible disease trends. This model circumvents the need to estimate explicit parameter values by instead matching segments of ongoing time series data to a comprehensive library of synthetically generated segments of time series data. We demonstrate that sMOA has competitive performance with state-of-the-art infectious disease forecasting models, out-performing 78% of models from the COVID-19 Forecasting Hub in terms of averaged Mean Absolute Error and 76% of models from the COVID-19 Forecasting Hub in terms of averaged Weighted Interval Score. Additionally, we introduce a novel uncertainty quantification methodology designed for the onset of emerging epidemics. Developing versatile approaches that do not rely on historical data and can maintain high accuracy in the face of novel pandemics is critical for enhancing public health decision-making and strengthening preparedness for future outbreaks.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

Neurobehavioral Effects Of Five-Ion GCRSim Exposure In Male And Female Mice

Exposure to space galactic cosmic radiation is a principal consideration of spaceflight missions, and with upcoming missions to the Moon and Mars, it is increasingly imperative to elucidate the detrimental effects of space travel beyond the lower Earth orbit. Additionally, with the first female astronaut to soon travel to the Moon and beyond lower Earth orbit, there is a strong need to understand the biological sex differences to adaptation to the deep space environment. While the effects of spaceflight on the nervous system are not fully known, studies in animal models have shown that exposure to ionizing radiation can cause neuronal damage and lead to downstream cognitive and behavioral deficits. Therefore, we investigated the neurobehavioral responses to space environment-like radiation exposure. Male and female 23–24-week-old mice (age-matched to average astronaut age) were exposed to 5, 15 and 50 cGy via Five-Ion Galactic Cosmic Ray Simulation at the NASA National Space Radiation Laboratory at Brookhaven National Laboratory. Both early (72hrs post exposure) and late (1-4 months post exposure) cognitive and behavioral deficits were investigated. In-cage behavior was analyzed as frequency/duration of digging, rearing, and grooming and nestlet building using a 5-stage Deacon score. Additionally, at NASA Ames, behavior tests included Catwalk (gait), Zero Maze (anxiety), Adhesive Removal (sensory motor), Novel Object Recognition and Barnes Maze (working memory). There were pronounced sex differences in both early and late time points. Females typically performed the tests better than males, specifically in nestlet building, gait and working memory, though males performed better at the sensory motor (adhesive removal) test. Dose effects were primarily observed at 50 cGy for both sexes, particularly with the Barnes Maze (working memory), where both males and females exposed to 50 cGy showed little to no improvement in test performance, though females again performed better than males. Currently, we are investigating the correlations between the observed behavior and cytokine levels in the plasma and brain. Future studies will continue to investigate cognitive consequences of galactic cosmic radiation in combination with other space-like environment stressors, including antigravity and social versus single housing.

Stephanie Puukila↗

NASA NTRSDate not supplied

Neurobehavioral Effects Of Five-Ion GCRSim Exposure In Male And Female Mice

S. Puukila↗

DOE OSTI2021

Measuring the electron temperature and identifying plasma detachment using machine learning and spectroscopy

A machine learning approach has been implemented to measure the electron temperature directly from the emission spectra of a tokamak plasma. This approach utilized a neural network (NN) trained on a dataset of 1865 time slices from operation of the DIII-D tokamak using extreme ultraviolet/vacuum ultraviolet emission spectroscopy matched with high-accuracy divertor Thomson scattering measurements of the electron temperature, T e . This NN is shown to be particularly good at predicting T e at low temperatures (T e < 10 eV) where the NN demonstrated a mean average error of less than 1 eV. Trained to detect plasma detachment in the tokamak divertor, a NN classifier was able to correctly identify detached states (T e < 5 eV) with a 99% accuracy (an F 1 score of 0.96) at an acquisition rate 10× faster than the Thomson scattering measurement. The performance of the model is understood by examining a set of 4800 theoretical spectra generated using collisional radiative modeling that was also used to predict the performance of a low-cost spectrometer viewing nitrogen emission in the visible wavelengths. Furthermore, these results provide a proof-of-principle that low-cost spectrometers leveraged with machine learning can be used to boost the performance of more expensive diagnostics on fusion devices and be used independently as a fast and accurate T e measurement and detachment classifier.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2018

Pre-Flight Training of Autonomic Responses for Mitigating the Effects of Spatial Disorientation During Spaceflight

The National Aeronautics and Space Administration (NASA) has identified a potential risk of spatial disorientation, motion sickness, and degraded performance to astronauts during re-entry and landing of the proposed Orion crew vehicle. The purpose of this study was to determine if a physiological training procedure, Autogenic-Feedback Training Exercise (AFTE), can mitigate these adverse effects. Fourteen men and six women were assigned to two groups (AFTE, no-treatment Control) matched for motion sickness susceptibility and gender. All subjects received a standard rotating chair test to determine motion sickness susceptibility; three training sessions on a manual performance task; and four exposures in the rotating chair (Orion tests) simulating angular accelerations of the crew vehicle during re-entry. AFTE subjects received 2 hours of training before Orion tests 2, 3, and 4. Motion sickness symptoms, task performance, and physiological measures were recorded on all subjects. Results showed that the AFTE group had significantly lower symptom scores when compared to Controls on test 2 (p=.05), test 3 (p=.03), and test 4 (p=.02). Although there were no significant group differences on task performance, trends showed that AFTE subjects were less impaired than Controls. Heart rate change scores (20 revolutions per minute minus baseline) of AFTE subjects indicated significantly less reactivity on Test 4 compared to Test 1 (10.09 versus 16.59, p=.02), while Controls did not change significantly across tests. Results of this study indicate that AFTE may be an effective countermeasure for mitigating spatial dis-orientation and motion sickness in astronauts.

Orion↗

DOE OSTI2026

EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties

Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a computational framework that integrates evolutionary algorithms with three-dimensional diffusion models for property-driven molecular generation. The method operates through adaptive evolutionary optimization, where population-based selection guides the generation process toward desired property landscapes. EvoDiffMol supports both unconstrained molecular design and scaffold-constrained generation that preserves fixed substructures while optimizing complementary regions. Comprehensive evaluation demonstrates exceptional performance, achieving the highest drug-likeness score (0.94) among all compared state-of-the-art methods while maintaining excellent validity, uniqueness, and novelty. Beyond single property optimization, the framework demonstrates flexible multi-property optimization capabilities, simultaneously controlling multiple molecular descriptors including synthetic accessibility, lipophilicity, topological polar surface area, and clinically relevant ADMET properties such as cardiotoxicity (hERG) and intestinal permeability (Caco-2). This adaptability spans from simple descriptors to practical pharmaceutical endpoints without requiring complete model retraining. The framework achieves precise control over target property values, generating molecules with properties closely matching specified targets for both single and multiple descriptors. Scaffold-constrained experiments preserve fixed molecular cores while maintaining effective property optimization. The three-dimensional representation offers advantages in maintaining structural validity during iterative optimization, with potential for geometry-aware applications in materials science and drug discovery.

3D molecular generation↗

DOE OSTI2021

An Integrated Paradigm for the Management of Delivery Risk in Electricity Markets: From Batteries to Insurance and Beyond [Slides]

In wholesale electricity markets today, flexibility from a limited number of distributed energy resources (DERs) is offered daily, and the value of flexibility is not yet recognized for economic hedging of delivery risk. Under a three-year project funded by the ARPA-E PERFORM program, a collaborative team is working towards developing an integrated risk management framework that will leverage flexibility from distributed and bulk resources to cost-effectively and reliably manage delivery risk of intermittent resources. Two concepts are at the core of the proposed integrated risk management framework: (A) flexibility options, which are a novel type of options and enable wholesale electricity market participants to hedge uncertainty by buying flexibility. (B) DER flexibility scores, which provide a way for utilities or aggregators to classify assets in groups with different likelihood of delivering contracted flexibility. This report presentation will focus on the proposed ISO-product "flexibility options," which is complementary to ramp and other products being introduced by ISOs/RTOs to manage net load uncertainties. Participating resources with imbalance risk can buy flexibility options to hedge their production, whereas grid-connected resources that can provide physical flexibility can offer flexibility options. We will present basics of the formulation for a day-ahead ISO market that matches buyers and sellers of this hedge in coordination with existing capabilities to schedule energy and ancillary services, and outline how their settlements mitigate the impact of imbalance risk.

24 POWER TRANSMISSION AND DISTRIBUTION↗