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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Quantitative methods and modeling to assess COVID–19–interrupted in vivo pharmacokinetic bioequivalence studies with two reference batches

The coronavirus disease 2019 (COVID-19) has presented unprecedented challenges to the generic drug development, including interruptions in bioequivalence (BE) studies. Per guidance published by the US Food and Drug Administration (FDA) during the COVID-19 public health emergency, any protocol changes or alternative statistical analysis plan for COVID-19-interrupted BE study should be accompanied with adequate justifications and not lead to biased equivalence determination. In this study, we used a modeling and simulation approach to assess the potential impact of study outcomes when two different batches of a Reference Standard (RS) were to be used in an in vivo pharmacokinetic BE study due to the RS expiration during the COVID-19 pandemic. Simulations were performed with hypothetical drugs under two scenarios: (1) uninterrupted study using a single batch of an RS, and (2) interrupted study using two batches of an RS. The acceptability of BE outcomes was evaluated by comparing the results obtained from interrupted studies with those from uninterrupted studies. The simulation results demonstrated that using a conventional statistical approach to evaluate BE for COVID-19-interrupted studies may be acceptable based on the pooled data from two batches. An alternative statistical method which includes a “batch” effect to the mixed effects model may be used when a significant “batch” effect was found in interrupted four-way crossover studies. However, such alternative method is not applicable for interrupted two-way crossover studies. Overall, the simulated scenarios are only for demonstration purpose, the acceptability of BE outcomes for the COVID19-interrupted studies could be case-specific.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

coloring v.1.0

SAND2024-02435O The software coloring allows applications written in the C++ language to generate publication-quality 2D plots. Its functionality is similar to Microsoft Excel's chart functionality or the Python language's matplotlib package. The value of coloring is that it is written purely in C++ and thus can be compiled on systems where Python is not available and linked into high performance computing software. For drawing shapes onto an image, coloring uses the mathematical definition of quadratic Bezier splines and uses Newton's method to search for the closest point on a spline to a given query point. This is then used to do accurate sub-pixel sampling to get clean, non-pixelated images. For working with the actual plot data, coloring has basic statistical methods such as finding maxima and minima as well as axis scaling such as logarithms. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Ibanez, Daniel↗
DOE OSTI2026

Emerging anomaly detection techniques for electronic health records: A survey

Background Anomaly detection in electronic health records (EHRs) is a cornerstone of biomedical informatics, with direct implications for patient safety, clinical decision-making, and the prevention of healthcare fraud. Once guided primarily by simple rule-based methods, the field has advanced rapidly, driven by increased computing power, richer and more detailed health data, and the rise of machine learning and deep learning techniques. The objective of this paper is to provide a comprehensive overview of modern approaches to detecting anomalies in EHRs, outlining their strengths, limitations, and relevance to key healthcare challenges. We review traditional statistical methods alongside newer ML- and DL-based strategies and hybrid models, with particular attention to how these techniques support transparency and build clinical trust. Methods This paper presents a thorough and critical survey through systematic review (PRISMA-based) of the latest anomaly detection strategies in time-sequence data domains within electronic health record systems. Results We explore a broad spectrum of methodologies, including statistical models, supervised and unsupervised learning approaches, hybrid frameworks, and state-of-the-art ML-based techniques that collectively advance the precision and scalability of detecting anomalies in complex clinical datasets. In addition to mapping current capabilities, we address the enduring challenges that hinder widespread implementation and provide a forward-looking perspective on the future of anomaly detection in the data-rich landscape of modern healthcare. Summary The advancement in AI-based approaches is reported along with the basic principles of the individual approaches and their applicability. The increased availability of high-quality data, advancements in DL approaches, and enhanced computation power are leading to more frequent adaptation of DL-based approaches. Emerging DL-based approaches that have been adapted in other domains or recently applied in the EHR domain are also discussed in detail. Although DL-based approaches can improve model predictions by incorporating comorbidities, their application is limited in low-frequency data domains (e.g., when the total available data remains in the single digits). Therefore, the user must carefully consider the application based on data availability.

Anomaly detection↗
DOE OSTI2015

Applying compressive sensing to TEM video: A substantial frame rate increase on any camera

One of the main limitations of imaging at high spatial and temporal resolution during in-situ transmission electron microscopy (TEM) experiments is the frame rate of the camera being used to image the dynamic process. While the recent development of direct detectors has provided the hardware to achieve frame rates approaching 0.1 ms, the cameras are expensive and must replace existing detectors. In this paper, we examine the use of coded aperture compressive sensing (CS) methods to increase the frame rate of any camera with simple, low-cost hardware modifications. The coded aperture approach allows multiple sub-frames to be coded and integrated into a single camera frame during the acquisition process, and then extracted upon readout using statistical CS inversion. Here we describe the background of CS and statistical methods in depth and simulate the frame rates and efficiencies for in-situ TEM experiments. Depending on the resolution and signal/noise of the image, it should be possible to increase the speed of any camera by more than an order of magnitude using this approach.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Tumor-Infiltrating Lymphocytes in a Contemporary Cohort of Women with Ductal Carcinoma In Situ (DCIS)

Background: Growing evidence suggests that the tumor immune microenvironment influences breast cancer development and prognosis. Density of tumor-infiltrating lymphocytes (TILs) within invasive breast cancer is correlated with response to therapy, especially in triple-negative disease. The clinical relevance and outcomes of TILs within ductal carcinoma in situ (DCIS) are less understood. Methods: Our institutional database of 668 patients with pure DCIS from 2010 to 2018 was queried. TILs were evaluated by International TILs Working Group guidelines. Percentage of TILs was assessed from the densest focus (hotspot) in one high-power field of stroma touching the basement membrane. Statistical methods included cluster analyses (to define sparse versus dense TILs), logistic, and Cox regression models. Results: Sixty-nine patients with DCIS and TILs were evaluated, of whom 54 (78%) were treated by breast-conserving surgery. Thirteen (19%) patients had ipsilateral recurrence. Each recurrence (n = 13) was matched to four controls (n = 56) based on date of surgery. Median follow-up was 6.7 years. TILs were defined as sparse (< 45%) or dense (≥ 45%). Dense TILs were associated with younger age (p = 0.045), larger tumor size (p < 0.001), high nuclear grade (p = 0.010), comedo histology (p = 0.033), necrosis (p = 0.027), estrogen receptor (ER) negativity (p = 0.037), and ipsilateral recurrence (p = 0.001). Nine patients with dense TILs had mean time to recurrence of 73.5 months compared with four patients with sparse TILs with mean time to recurrence of 97.9 months (p = 0.003). Conclusions: Dense TILs were significantly associated with age, tumor size, nuclear grade, comedo histology, necrosis, and ER status and was a significant predictor of recurrence in patients with pure DCIS.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

High-Resolution, Non-Invasive Imaging of Upper Vocal Tract Articulators Compatible with Human Brain Recordings

A complete neurobiological understanding of speech motor control requires determination of the relationship between simultaneously recorded neural activity and the kinematics of the lips, jaw, tongue, and larynx. Many speech articulators are internal to the vocal tract, and therefore simultaneously tracking the kinematics of all articulators is nontrivial-especially in the context of human electrophysiology recordings. Here, we describe a noninvasive, multi-modal imaging system to monitor vocal tract kinematics, demonstrate this system in six speakers during production of nine American English vowels, and provide new analysis of such data. Classification and regression analysis revealed considerable variability in the articulator-to-acoustic relationship across speakers. Non-negative matrix factorization extracted basis sets capturing vocal tract shapes allowing for higher vowel classification accuracy than traditional methods. Statistical speech synthesis generated speech from vocal tract measurements, and we demonstrate perceptual identification. We demonstrate the capacity to predict lip kinematics from ventral sensorimotor cortical activity. These results demonstrate a multi-modal system to non-invasively monitor articulator kinematics during speech production, describe novel analytic methods for relating kinematic data to speech acoustics, and provide the first decoding of speech kinematics from electrocorticography. These advances will be critical for understanding the cortical basis of speech production and the creation of vocal prosthetics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-CD-207B-12: Quantification of Clinical Feedback On Image Quality Differences Between Two CT Scanner Models

Purpose: This work sought to quantify a radiology team’s assessment of image quality differences between two CT scanner models currently in clinical use, with emphasis on noise and low-contrast detectability (LCD). Methods: A water phantom and a Kagaku anthropomorphic body phantom were scanned on GE Discovery CT750 HD and LightSpeed VCT scanners (4 each) with identical scan parameters and reconstructed to 2.5mm/5.0mm thicknesses. Images of water phantom were analyzed at the scanner console with a built-in LCD tool that uses statistical methods to compute requisite CT-number contrast for 95% confidence in detection of a user-defined object size. LCD value was computed for 5mm, 3mm, and 1mm objects. Analysis of standard deviation and LCD values were performed on Kagaku phantom images within liver, stomach, and spleen. LCD value was computed for 4mm, 3mm, and 1mm objects using a benchmarked MATLAB implementation of the GE scanner-console tool. Results: Water LCD values were larger (poorer performance) for all HD scanners compared to VCT scanners. Mean scanner model difference in requisite CT-number contrast for 5mm, 3mm, and 1mm objects for 5.0mm/2.5mm images was 3.0%/3.4% (p=0.02/p=0.10), 5.3%/5.7% (0.00002/0.02), and 8.5%/8.2% (0.0004/0.002), respectively. Mean standard deviations within Kagaku phantom ROIs were greater in HD compared to VCT images, with mean differences for the liver, stomach, and spleen for 5.0mm/2.5mm of 16%/12% (p=0.04/0.10), 8%/12% (0.15/0.11), and 16%/15% (0.05/0.11), respectively. Mean LCD value difference between HD and VCT scanners over all ROIs for 4mm, 3m, and 1mm objects and 5.0mm/2.5mm was 34%/9%, 16%/8%, and 18%/10%, respectively. HD scanners outperformed VCT scanners only for the 4mm stomach object. Conclusion: Using both water and anthropomorphic phantoms, it was shown that HD scanners are outperformed by VCT scanners with respect to noise and LCD in a consistent and in most cases statistically significant manner. The relationship between statistical and clinical significance demands further work.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Model Independent Approach to the Single Photoelectron Calibration of Photomultiplier Tubes

The accurate calibration of photomultiplier tubes is critical in a wide variety of applications for which it is necessary to know the absolute number of detected photons or precisely determine the resolution of the signal. Conventional calibration methods rely on fitting the photomultiplier response to a low intensity light source with analytical approximations to the single photoelectron distribution. We show that this approach often leads to biased estimates due to an inability to model the full distribution accurately, especially at low charge values. We present a simple statistical method to extract the relevant single photoelectron calibration parameters (first two central moments) without making any assumptions about the underlying single photoelectron distribution. We illustrate the use of this method through the calibration of a Hamamatsu R11410 photomultiplier tube and study the accuracy and precision of the method using Monte Carlo simulations. The method is found to have significantly reduced bias compared to conventional methods and works under a wide range of light intensities, making it suitable for the simultaneous calibration of large arrays of photomultiplier tubes where uniform illumination may not be possible.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Nuclear Forensics for Irradiated Materials using Kernel Regression Models

The ultimate purpose of nuclear forensics is to locate the origin of nuclear and other radioactive materials out of regulatory control used in nuclear security events such as classical forensics. For this purpose, some specific characteristics of interdicted materials (referred to as 'signatures') should be defined to compare the known sample database. In some cases, involved with irradiated material, the signatures could be specific amount of fission product inventory depending on reactor operational histories such as reactor type, initial enrichment, burn up rate of nuclear fuel and cooling period after irradiation in the reactor. In order to make inference model for irradiated material for nuclear forensics, we suggested 3 ways as follows; (i) analyzing ORIGEN produced nuclear substances for the fission product inventory, (ii) classifying the range of reactor type, (iii) predicting the operational history from the fission product inventory. In terms of nuclear substance analysis, the construction of spent fuel database has been internationally carried out since ITWG (Nuclear Smuggling International Technical Working Group) was established in 1995. However, enough sample data cannot be obtained in Korea to determine reactor type and operational histories because analyzing nuclear substances have been limited due to the international regulation. Thus, this study does not mention how to obtain mass or ratios of nuclides for the spent fuel. We just have generated simulation sample data as a fission product inventory using ORIGEN to construct spent fuel database. When unidentified radioactive materials are discovered, it is assumed that mass or ratios of the nuclides are analyzed by certain methods which are available in Korea as well as other countries. Then, a reactor type is determined, and finally, regression model can locate the origin or source of the radioactive materials by inferring operational histories using the fission product inventory. There are some studies on the classification of reactor type using statistical methods. As a part of predicting the operational history, this paper focuses on the development of spent fuel inference algorithm for nuclear forensics to estimate reactor operational histories that reflect characteristics of a reactor from the fission product inventory. The spent fuel inference algorithm for nuclear forensics has been developed on the basis of Kernel Regression (KR) which can conditionally generate the estimated output data by giving weight depending on geometric distance between sample data and input data. Also the KR which comprises Auto-Associative KR and Inferential KR have some benefits that can estimate only using data without assumption for specific physical model and re-learning process. Auto-associative KR (AAKR) was used to sort out outliers of input data and Inferential KR (IKR) was carried out to predict the operational histories for spent fuel. All of regression algorithms were performed in R programming tool. From the validation of both AAKR and IKR, it is expected that kernel regression has enough accuracy to be applied to nuclear forensics for spent fuel. Once the nuclear substance is measured to fill the fission product inventory with a certain reactor type, this kernel regression algorithm would predict the operational histories of spent fuel with high accuracy. Finally, this information is expected to be useful to find the origin of irradiated materials. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2015

Determination of critical experiment correlations using the sampler sequence within scale 6.2 - 14602

The validation of neutron transport methods used in nuclear criticality safety analyses is required by consensus American National Standards Institute/American Nuclear Society (ANSI/ANS) standards. In the last decade, there has been an increased interest in correlations among critical experiments used in validation that have shared physical attributes and which impact the independence of each measurement. The statistical methods included in many of the frequently cited guidance documents on performing validation calculations incorporate the assumption that all individual measurements are independent, so little guidance is available to practitioners on the topic. Typical guidance includes recommendations to select experiments from multiple facilities and experiment series in an attempt to minimize the impact of correlations or common-cause errors in experiments. Recent efforts have been made both to determine the magnitude of such correlations between experiments and to develop and apply methods for adjusting the bias and bias uncertainty to account for the correlations. This paper describes recent work performed at Oak Ridge National Laboratory using the Sampler sequence from the SCALE code system to develop experimental correlations using a Monte Carlo sampling technique. Sampler will be available for the first time with the release of SCALE 6.2, and a brief introduction to the methods used to calculate experiment correlations within this new sequence is presented in this paper. Techniques to utilize these correlations in the establishment of upper subcritical limits are the subject of a companion paper and will not be discussed here. Example experimental uncertainties and correlation coefficients are presented for a variety of low-enriched uranium water-moderated lattice experiments selected for use in a benchmark exercise by the Working Party on Nuclear Criticality Safety Subgroup on Uncertainty Analysis in Criticality Safety Analyses. The results include studies on the effect of fuel rod pitch on the correlations, and some observations are also made regarding difficulties in determining experimental correlations using the Monte Carlo sampling technique. (authors)

42 ENGINEERING↗
DOE OSTI2024

Improved Subseasonal Forecasting of Extreme Polar Vortices Using Machine Learning

Our research was focused on forecasting the position and shape of the winter stratospheric polar vortex at a subseasonal timescale of 15 days in advance. To achieve this, we employed both statistical and neural network machine learning techniques. The analysis was performed on 42 winter seasons of reanalysis data provided by NASA giving us a total of 6,342 days of data. The state of the polar vortex for determined by using geometric moments to calculate the centroid latitude and the aspect ratio of an ellipse fit onto the vortex. Timeseries for thirty additional precursors were calculated to help improve the predictive capabilities of the algorithm. Feature importance of these precursors was performed using random forest to measure the predictive importance and the ideal number of precursors. Then, using the precursors identified as important, various statistical methods were tested for predictive accuracy with random forest and nearest neighbor performing the best. An echo state network, a type of recurrent neural network that features sparsely connected hidden layer and a reduced number of trainable parameters that allows for rapid training and testing, was also implemented for the forecasting problem. Hyperparameter tuning was performed for each methods using a subset of the training data. The algorithms were trained and tuned on the first 41 years of data, then tested for accuracy on the final year. In general, the centroid latitude of the polar vortex proved easier to predict than the aspect ratio across all algorithms. Random forest outperformed other statistical forecasting algorithms overall but struggled to predict extreme values. Forecasting from echo state network suggested a strong predictive capability past 15 days, but further work is required to fully realize the potential of recurrent neural network approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

The use of multiwavelets for uncertainty estimation in seismic surface wave dispersion.

This report describes a new single-station analysis method to estimate the dispersion and uncer- tainty of seismic surface waves using the multiwavelet transform. Typically, when estimating the dispersion of a surface wave using only a single seismic station, the seismogram is decomposed into a series of narrow-band realizations using a bank of narrow-band filters. By then enveloping and normalizing the filtered seismograms and identifying the maximum power as a function of frequency, the group velocity can be estimated if the source-receiver distance is known. However, using the filter bank method, there is no robust way to estimate uncertainty. In this report, I in- troduce a new method of estimating the group velocity that includes an estimate of uncertainty. The method is similar to the conventional filter bank method, but uses a class of functions, called Slepian wavelets, to compute a series of wavelet transforms of the data. Each wavelet transform is mathematically similar to a filter bank, however, the time-frequency tradeoff is optimized. By taking multiple wavelet transforms, I form a population of dispersion estimates from which stan- dard statistical methods can be used to estimate uncertainty. I demonstrate the utility of this new method by applying it to synthetic data as well as ambient-noise surface-wave cross-correlelograms recorded by the University of Nevada Seismic Network.

58 GEOSCIENCES↗
DOE OSTI2024

Measurement of the W-boson mass and width with the ATLAS detector using proton–proton collisions at $\sqrt{s}=7$ TeV

Proton-proton collision data recorded by the ATLAS detector in 2011, at a centre-of-mass energy of 7 TeV, have been used for an improved determination of the W-boson mass and a first measurement of the W-boson width at the LHC. Recent fits to the proton parton distribution functions are incorporated in the measurement procedure and an improved statistical method is used to increase the measurement precision. The measurement of the W-boson mass yields a value of m w = 80,366.5 ± 9.8 (stat.) ± 12.5 (syst.) MeV = 80,366.5 ± 15.9 MeV, and the width is measured as Γ w = 2202 ± 32 (stat.) ± 34 (syst.) MeV = 2202 ± 47 MeV. The first uncertainty components are statistical and the second correspond to the experimental and physics-modelling systematic uncertainties. Both results are consistent with the expectation from fits to electroweak precision data. The present measurement of m w is compatible with and supersedes the previous measurement performed using the same data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

High Throughput, High Precision Hot Testing Tool for HBLED Wafer Level Testing

The Socrates research effort developed an in depth understanding and demonstrated in a prototype tool new precise methods for teh characterization of color characteristics and flux from individual LEDs for the production of uniform quality lighting. This effort was focused on improving the color quality and consistency of solid state lighting and potentially reducing characterization costs for all LED product types. The patented laser hot testing method was demonstrated to be far more accurate than all current state of the art color and flux characterization methods in use by the solid state lighting industry today. A seperately patented LED grouping method (statistical binning) was demonstrated to be a useful approach to improving utilization of entire lots of large color and flux distributions of manufactured LEDs for high quality color solid-state lighting. At the conclusion of the research in late 2015 the solid-state lighting industry was however generally satisfied with its existing production methods for high quality color products for the small segment of customers that demand it, albeit with added costs.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Predicting Biomass Yields of Advanced Switchgrass Cultivars for Bioenergy and Ecosystem Services Using Machine Learning

The production of advanced perennial bioenergy crops within marginal areas of the agricultural landscape is gaining interest due to its potential to sustainably produce feedstocks for biofuels and bioproducts while also improving the sustainability and resilience of commodity crop production. However, predicting the biomass yields of this production system is challenging because marginal areas are often relatively small and spread around agricultural fields and are typically associated with various abiotic conditions that limit crop production. Machine learning (ML) offers a viable solution as a biomass yield prediction tool because it is suited to predicting relationships with complex functional associations. The objectives of this study were to (1) evaluate the accuracy of commonly applied ML algorithms in agricultural applications for predicting the biomass yields of advanced switchgrass cultivars for bioenergy and ecosystem services and (2) determine the most important biomass yield predictors. Datasets on biomass yield, weather, land marginality, soil properties, and agronomic management were generated from three field study sites in two U.S. Midwest states (Illinois and Iowa) over three growing seasons. The ML algorithms evaluated in the study included random forests (RFs), gradient boosting machines (GBMs), artificial neural networks (ANNs), K-neighbors regressor (KNR), AdaBoost regressor (ABR), and partial least squares regression (PLSR). Coefficient of determination (R 2 ) and mean absolute error (MAE) were used to evaluate the predictive accuracy of the tested algorithms. Results showed that the ensemble methods, RF (R 2 = 0.86, MAE = 0.62 Mg/ha), GBM (R 2 = 0.88, MAE = 0.57 Mg/ha), and GBM (R 2 = 0.78, MAE = 0.66 Mg/ha), were the most accurate in predicting biomass yields of the Independence, Liberty, and Shawnee switchgrass cultivars, respectively. This is in agreement with similar studies that apply ML to multi-feature problems where traditional statistical methods are less applicable and datasets used were considered to be relatively small for ANNs. Consistent with previous studies on switchgrass, the most important predictors of biomass yield included average annual temperature, average growing season temperature, sum of the growing season precipitation, field slope, and elevation. This study helps pave the way for applying ML as a management tool for alternative bioenergy landscapes where understanding agronomic and environmental performance of a multifunctional cropping system seasonally and interannually at the sub-field scale is critical.

09 BIOMASS FUELS↗
DOE OSTI2019

Progress in Accurate Chemical Kinetic Modeling, Simulations, and Parameter Estimation for Heterogeneous Catalysis

Chemical kinetic modeling in heterogeneous catalysis is gaining ground in its ability to provide qualitatively or even quantitatively accurate prediction of real-world behavior because of new advances in the physical and chemical representations of catalytic systems, estimation of relevant kinetic parameters, and capabilities in kinetic modeling. This Perspective chronicles current trends and future areas of advancement in chemical kinetic modeling, simulation, and parameter estimation: ranging from elementary step calculations to multiscale modeling to the role of advanced statistical methods for incorporating uncertainties in predictions. Multiple new or growing methodologies are covered, examples are provided, and forward-looking topics for advancement are noted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Understanding End‐of‐Century Snowpack Changes Over California's Sierra Nevada

Abstract This study uses dynamical and statistical methods to understand end‐of‐century mean changes to Sierra Nevada snowpack. Dynamical results reveal that middle‐elevation watersheds experience considerably more rain than snow during winter, leading to substantial snowpack declines by spring. Despite some high‐elevation watersheds receiving slightly more snow in January and February, the warming signal still dominates across the wet season and leads to notable declines by springtime. A statistical model is created to mimic dynamical results for 1 April snowpack, allowing for an efficient downscaling of all available general circulation models from the Coupled Model Intercomparison Project phase 5. For all general circulation models and emission scenarios, dramatic 1 April snowpack loss occurs at elevations below 2,500 m, despite increased precipitation in many general circulation models. Only 36% (±12%) of historical 1 April total snow water equivalent volume remains at the century's end under a “business‐as‐usual” emission scenario, with 70% (±12%) remaining under a realistic “mitigation” scenario.

Sun, Fengpeng↗