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DOE OSTI2024

To have value, comparisons of high-throughput phenotyping methods need statistical tests of bias and variance

The gap between genomics and phenomics is narrowing. The rate at which it is narrowing, however, is being slowed by improper statistical comparison of methods. Quantification using Pearson’s correlation coefficient ( r ) is commonly used to assess method quality, but it is an often misleading statistic for this purpose as it is unable to provide information about the relative quality of two methods. Using r can both erroneously discount methods that are inherently more precise and validate methods that are less accurate. These errors occur because of logical flaws inherent in the use of r when comparing methods, not as a problem of limited sample size or the unavoidable possibility of a type I error. A popular alternative to using r is to measure the limits of agreement (LOA). However both r and LOA fail to identify which instrument is more or less variable than the other and can lead to incorrect conclusions about method quality. An alternative approach, comparing variances of methods, requires repeated measurements of the same subject, but avoids incorrect conclusions. Variance comparison is arguably the most important component of method validation and, thus, when repeated measurements are possible, variance comparison provides considerable value to these studies. Statistical tests to compare variances presented here are well established, easy to interpret and ubiquitously available. The widespread use of r has potentially led to numerous incorrect conclusions about method quality, hampering development, and the approach described here would be useful to advance high throughput phenotyping methods but can also extend into any branch of science. The adoption of the statistical techniques outlined in this paper will help speed the adoption of new high throughput phenotyping techniques by indicating when one should reject a new method, outright replace an old method or conditionally use a new method.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Statistical Validation of Multiple Related Data Sets—Case Study Using Interstellar Boundary Explorer Satellite Data

Abstract Space scientists often face the question of whether data collected by different instruments are measurements of the same source population. This paper proposes a statistical validation method for evaluating the agreement between such related data sets. It offers a detailed case study focused on validating a new data set from the Interstellar Boundary Explorer (IBEX) mission, which serves as a practical how-to guide for similar analyses. Since 2008, the IBEX satellite has been gathering data on heliospheric energetic neutral atoms (ENAs) while being exposed to various sources of background noise, such as cosmic rays and solar energetic particles. The IBEX mission initially released only a qualified triple-coincidence (qABC) data product, which was designed to provide observations of ENAs free of background contamination. Further measurements revealed that the qABC data were in fact susceptible to contamination, having relatively low ENA counts and high background rates. To mitigate this issue, the mission team recently considered releasing a certain qualified double-coincidence (qBC) data product, which has roughly twice the detection rate of the qABC data product. This paper presents a simulation-based validation of the new qBC data product against the already-released qABC data product. The results show that the qBCs can plausibly be said to be measuring the same source population as the qABCs up to an average absolute deviation of 3.6%. Visual diagnostics provide additional confirmation of source rate coherence across data products. The framework introduced here is general and can be applied to other validation problems both within and outside the field of space physics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Survey of Image Denoising Methods for Medical Image Classification

Medical imaging devices, such as X-ray machines, inherently produce images that suffer from visual noise. Our objectives were to (i.) determine the effect of image denoising on a medical image classification task, and (ii.) determine if there exists a correlation between image denoising performance and medical image classification performance. We performed the medical image classification task on chest X-rays using the DenseNet-121 convolutional neural network (CNN) and used the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) metrics as the image denoising performance measures. We first found that different denoising methods can make a statistically significant difference in classification performance for select labels. We also found that denoising methods affect fine-tuned models more than randomly-initialized models and that fine-tuned models have significantly higher and more uniform performance than randomly-initialized models. Lastly, we found that there is no significant correlation between PSNR and SSIM values and classification performance for our task.

Michael, Peter↗

DOE OSTI2020

Barcoded protein array for multiplex single-molecule interaction profiling

Methods for attaching barcodes to polypeptides are provided. Methods for detecting molecular interactions at the single molecule level are provided. Embodiments of the invention are directed to a ONA barcoded protein array technology for parallel protein interaction profiling on a single molecule basis. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Novel methods are described herein that measure protein interactions based on the statistical analysis of co-localized polonies arising from barcoding DNAs of interacting proteins.

Church, George M.↗

DOE OSTI2022

Quantitative assessment of fitting errors associated with streak camera noise in Thomson scattering data analysis

Thomson scattering measurements in high energy density experiments are often recorded using optical streak cameras. In the low-signal regime, noise introduced by the streak camera can become an important and sometimes the dominant source of measurement uncertainty. In this paper, we present a formal method of accounting for the presence of streak camera noise in our measurements. We present a phenomenological description of the noise generation mechanisms and present a statistical model that may be used to construct the covariance matrix associated with a given measurement. This model is benchmarked against simulations of streak camera images. We demonstrate how this covariance may then be used to weight fitting of the data and provide quantitative assessments of the uncertainty in the fitting parameters determined by the best fit to the data and build confidence in the ability to make statistically significant measurements in the low-signal regime, where spatial correlations in the noise become apparent. These methods will have general applicability to other measurements made using optical streak cameras.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Fast Extraction and Characterization of Fundamental Frequency Events from a Large PMU Dataset using Big Data Analytics

A novel method for fast extraction of fundamental frequency events (FFE) based on measurements of frequency and rate of change of frequency by Phasor Measurement Units (PMU) is introduced. The method is designed to work with exceptionally large historical PMU datasets. Statistical analysis was used to extract the features and train Random Forest and Catboost classifiers. The method is capable of fast extraction of FFE from a historical dataset containing measurements from hundreds of PMUs captured over multiple years. The reported accuracy of the best algorithm for classification expressed as Area Under the receiver operating Characteristic curve reaches 0.98, which was obtained in out-of-sample evaluations on 109 system-wide events over 2 years observed at 43 PMUs. Then Minimum Volume Enclosing Ellipsoid Algorithm was used to further analyze the events. 93.72% events were correctly characterized, where average duration of the event as seen by the PMU was 9.93 sec.

Baembitov, Rashid↗

DOE OSTI2026

Quantitative measurements of dislocations in metals for advancing predictive simulations

LLNL applications require scientists to predict how materials evolve under various thermomechanical conditions. While this is achieved through physics-based simulations, uncertainty in the predictions of mechanical properties remains a serious challenge that limits the predictive capabilities of models because we lack methods to compare predictions of atomic-scale defects (dislocations) with experimental measurements. High energy X-ray diffraction (HEXRD) is the most relevant technique that can provide the necessary statistical information on dislocations. However, this technique is not yet quantitative because we lack a precise understanding of the relationship between X-ray diffraction patterns and the underlying material dislocation content and arrangements. To address this need, we used our novel computational X-ray diffraction method to simulate the effect of dislocations on the diffraction patterns. We compared virtual and experimental diffraction patterns. Results allowed us to clearly establish the relationship between X-ray diffraction patterns and the underlying dislocation structures, proving that it is feasible to quantitatively measure dislocation statistics with HEXRD. This project delivered a method that can provide the missing piece to LLNL’s mechanical property simulations in advanced metals by obtaining experimentally long-needed quantitative dislocation data, which could fully enable predictive capabilities.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Precise Modeling of a Complex Solenoidal Magnetic Field Using a Combination of Analytic Functions and a PINN

We demonstrate an iterative approach to modeling a sparsely measured magnetic field in a large-bore solenoid. This approach uses a hybrid of traditional and machine learning techniques. The traditional technique is a linear least-squares fit using a series solution to Laplace's equation, while the machine learning technique involves the training of a physics-informed neural network (PINN) on the least-squares fit residuals. We use a newly defined activation function "DELTAsnake," a modification to the snake activation function proposed by Ziyin et al. that allows for stronger curvature and non-monotonicity. The combined model approximately obeys Maxwell's equations to a level sufficient for producing high quality physics simulations and analysis. Our approach is applied to a highly realistic calculation of the expected magnetic field in the Mu2e experiment's Detector Solenoid which includes a simple model for the expected statistical measurement uncertainties. Using ten toy measurement simulations, we demonstrate the capabilities of our model in comparison to the least-squares method alone; the least-squares method alone results in a reduced chi-squared statistic of ${2.15 \pm 0.01}$, while our approach improves the reduced chi-square to ${1.034 \pm 0.005}$. Furthermore, for an average toy simulation, we show that the range of the RMS of the three field component residuals reduces from ${0.07-0.37}$ Gauss to ${0.05-0.07}$ Gauss. We find that this novel method is robust against a realistic systematic uncertainty deriving from Hall probe calibration bias and can be used to significantly reduce the number of measurements required to achieve an accurate model.

Kampa, Cole [Caltech] (ORCID:0000000192972920)↗

DOE OSTI2021

Estimation of sensor measurement errors in reactor coolant systems using multi-sensor fusion

A nuclear power plant is typically instrumented with a variety of sensors to continually monitor its variables, and their sensor’s measurements may be used to assess the plant state and initiate safety actions, if needed. Errors in sensor measurements, due to factors such as calibration drifts, critically affect such state assessments. Here, we address a problem of estimating sensor errors using physics-informed machine learning methods that use measurements collected under known plant conditions. For a given sensor, we propose an information fusion method that uses measurements from other sensors to estimate its output assuming it is error-free and provides its difference from an actual measurement as an error estimate. We present the ensemble of trees and support vector machine fusers, and evaluate their performance using measurements collected over an emulated test loop of a pressurized water reactor. The plant variables are related to each other through the underlying physical laws under inertial constraints that place bounds on their derivatives, which analytically justify the applicability of machine learning methods for computing these fusers. Under twenty scenarios, we assess their sensor error estimates for pressure sensors of the heat exchanger of a reactor’s primary coolant system. Multiple types of errors are captured by both fusers under externally induced calibration drifts, blockages, minor leaks and air gaps in sensing lines, and electromagnetic interference; the root mean square error of the estimation of error is under 2.2% percent of the maximum measurement. We present generalization equations, in the framework of statistical learning theory, for these methods that characterize the confidence probability that the estimation error is bounded by a specified parameter in future test scenarios.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Temporal evolution of the light emitted by a thin, laser-ionized plasma source

We present an experimental and simulation-based investigation of the temporal evolution of light emission from a thin, laser-ionized helium plasma source. We demonstrate an analytic model to calculate the approximate scaling of the time-integrated, on-axis light emission with the initial plasma density and temperature, supported by the experiment, which enhances the understanding of plasma light measurement for plasma wakefield accelerator (PWFA) plasma sources. Our model simulates the plasma density and temperature using a split-step Fourier code and a particle-in-cell code. A fluid simulation is then used to model the plasma and neutral density, and the electron temperature as a function of time and position. We then show the numerical results of the space-and-time-resolved light emission and that collisional excitation is the dominant source of light emission. We validate our model by measuring the light emitted by a laser-ionized plasma using a novel statistical method capable of resolving the nanosecond-scale temporal dynamics of the plasma light using a cost-effective camera with microsecond-scale timing jitter. This method is ideal for deployment in the high radiation environment of a particle accelerator that precludes the use of expensive nanosecond-gated cameras. Our results show that our models can effectively simulate the dynamics of a thin, laser-ionized plasma source. In addition, this work provides a detailed understanding of the plasma light measurement, which is one of the few diagnostic signals available for the direct measurement of PWFA plasma sources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Advanced Laboratory and Field Arrays: Debris Modeling, Detection,& Mitigation (Task 1)

The statement of project objectives for this task was: develop tools, methods and models to assess, and mitigate the risk of damage to MHK infrastructure from woody debris. Develop the capability to detect woody debris using sonar and/or physical methods for purposes of characterizing debris statistics in river (at UAF’s Tanana River Test Site) and near-shore wave (at Yakutat, AK) environments and to activate debris mitigation measures. Develop debris impact risk maps and tables using statistics on debris size, geometry, type, prevalence, mobility and location. Improve and apply the COUPi discrete element method (DEM) to develop models of debris movement and impact on MHK infrastructure to evaluate risk of damage, and interference, to operations from debris. The proposed final deliverable for the task was a set of tools or techniques for providing estimates of the probability of debris impact, and resulting impact forces, on MHK infrastructure as a function of debris size, type, wave regime, and current velocity. Such estimates are required to assess damage risks to operational MHK infrastructure.

13 HYDRO ENERGY↗

DOE OSTI2024

Optimal Zeno Dragging for Quantum Control: A Shortcut to Zeno with Action-Based Scheduling Optimization

The quantum Zeno effect asserts that quantum measurements inhibit simultaneous unitary dynamics when the “collapse” events are sufficiently strong and frequent. This applies in the limit of strong continuous measurement or dissipation. It is possible to implement a dissipative control that is known as “Zeno dragging” by dynamically varying the monitored observable, and hence also the eigenstates, which are attractors under Zeno dynamics. This is similar to adiabatic processes, in that the Zeno-dragging fidelity is highest when the rate of eigenstate change is slow compared to the measurement rate. We demonstrate here two theoretical methods for using such dynamics to achieve control of quantum systems. The first, which we shall refer to as “shortcut to Zeno,” is analogous to the shortcuts to adiabaticity (counterdiabatic driving) that are frequently used to accelerate unitary adiabatic evolution. In the second approach, we apply the Chantasri-Dressel-Jordan stochastic action [PRA 88, 042110 (2013)], and demonstrate that the extremal-probability readout paths derived from this are well suited to setting up a Pontryagin-style optimization of the Zeno-dragging schedule. A fundamental contribution of the latter approach is to show that an action suitable for measurement-driven control optimization can be derived quite generally from statistical arguments. Implementing these methods on the Zeno dragging of a qubit, we find that both approaches yield the same solution, namely, that the optimal control is a unitary that matches the motion of the Zeno-monitored eigenstate. We then show that such a solution can be more robust than a unitary-only operation and we comment on solvable generalizations of our qubit example embedded in larger systems. These methods open up new pathways toward systematically developing dynamic control of Zeno subspaces to realize dissipatively stabilized quantum operations. Published by the American Physical Society 2024

Physics↗

DOE OSTI2020

Solvent Hold Tank Sample Results for MCU-19-366- 367-368 (April 2019), MCU-19-469-470-471 (May 2019), MCU-19-524-525-526 (June 2019): Quarterly Report

A trend summary of three sets of Solvent Hold Tank (SHT) monthly samples MCU-19-366-367-368 (April), MCU-19-469-470-471 (May), and MCU-19-524-525-526 (June) are reported. Most of the conclusions are based on the June SHT sample (MCU-19-524-525-526). Analyses of the June SHT sample (MCU-19-524- 525-526) indicated that the Modifier (Cs-7SB) and the Extractant (MaxCalix) concentrations were below their nominal recommended concentrations (169,000 mg/L and 46,900 mg/L respectively) by 4% and 2% respectively but consistent with previously observed levels during normal runs. The Suppressor (N,N’,N”– tris(3,7-dimethyloctyl)guanidine or TiDG) concentration has decreased since the March 2019 measurement to 793 mg/L, which is above the minimum recommended concentration (479 mg/L). The Semi-Volatile Organic Analysis (SVOA) did not detect any impurities. However, the Fourier Transform Hydrogen Nuclear Magnetic Resonance (FT-HNMR) analysis detected presence of phthalates at a few ppm. The impurity concentration was highest in the April sample and consistently detected in the May and June samples (but always registered as a few ppm or less). Another impurity observed in the samples was mercury. Based on the June SHT sample, up to 25 ± 5 micrograms of mercury per mL of solvent was detected (as the average of the Direct Mercury Analysis (DMA) and X-Ray Fluorescence (XRF) methods). The higher mercury concentration in the solvent (as determined in the last three-monthly samples) is possibly due to the higher mercury concentration in Salt Batches 9 and 10. The gamma concentration (~2.90E4 dpm/mL) measured in the June 2019 SHT samples was consistent with previous values observed when the Modular Caustic-Side Solvent Extraction Unit (MCU) was operating continuously (for example, between December 2016 and January 2017). Statistical analysis of the different analytical methods detected a bias between the FT-HNMR and the High Performance Liquid Chromatography (HPLC) methods when measuring the MaxCalix and Modifier concentrations; the FT-HNMR gave a higher concentration possibly due to peak overlapping in the measured data. A bias was detected when measuring total mercury by the DMA method versus the XRF method with the XRF method reported higher mercury concentrations. The laboratory will continue to monitor the quality of the solvent for any new impurities or degradation of the solvent components.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

An implementation of neural simulation-based inference for parameter estimation in ATLAS

Neural simulation-based inference (NSBI) is a powerful class of machine-learning-based methods for statistical inference that naturally handles high-dimensional parameter estimation without the need to bin data into low-dimensional summary histograms. Such methods are promising for a range of measurements, including at the Large Hadron Collider, where no single observable may be optimal to scan over the entire theoretical phase space under consideration, or where binning data into histograms could result in a loss of sensitivity. This work develops a NSBI framework for statistical inference, using neural networks to estimate probability density ratios, which enables the application to a full-scale analysis. It incorporates a large number of systematic uncertainties, quantifies the uncertainty due to the finite number of events in training samples, develops a method to construct confidence intervals, and demonstrates a series of intermediate diagnostic checks that can be performed to validate the robustness of the method. As an example, the power and feasibility of the method are assessed on simulated data for a simplified version of an off-shell Higgs boson couplings measurement in the four-lepton final states. This approach represents an extension to the standard statistical methodology used by the experiments at the Large Hadron Collider, and can benefit many physics analyses.

frequentist statistics↗

DOE OSTI2024

A road map to cosmological parameter analysis with third-order shear statistics: III. Efficient estimation of third-order shear correlation functions and an application to the KiDS-1000 data

Context. Third-order lensing statistics contain a wealth of cosmological information that is not captured by second-order statistics. However, the computational effort it takes to estimate such statistics in forthcoming stage IV surveys is prohibitively expensive. Aims. We derive and validate an efficient estimation procedure for the three-point correlation function (3PCF) of polar fields such as weak lensing shear. We then use our approach to measure the shear 3PCF and the third-order aperture mass statistics on the KiDS-1000 survey. Methods We constructed an efficient estimator for third-order shear statistics that builds on the multipole decomposition of the 3PCF. We then validated our estimator on mock ellipticity catalogs obtained from N -body simulations. Finally, we applied our estimator to the KiDS-1000 data and presented a measurement of the third-order aperture statistics in a tomographic setup. Results. Our estimator provides a speedup of a factor of ∼100–1000 compared to the state-of-the-art estimation procedures. It is also able to provide accurate measurements for squeezed and folded triangle configurations without additional computational effort. We report a significant detection of tomographic third-order aperture mass statistics in the KiDS-1000 data (S/N = 6.69). Conclusions. Our estimator will make it computationally feasible to measure third-order shear statistics in forthcoming stage IV surveys. Furthermore, it can be used to construct empirical covariance matrices for such statistics.

Astronomy & Astrophysics↗

DOE OSTI2020

Measurement Uncertainty in One-Of-A-Kind Event Data Analysis

A golden standard in science is to repeat an experiment a statistically significant number of times, recording data using the same set of detectors and the same data analysis methodology. In such case experimental error includes both the range of true values generated by repetitions of the experiment, and measurement uncertainty caused by the detector. They are independent. It is a huge and too frequently used simplification, to assume that one can measure multiple repetitions of an identical experiment, resulting in identical true experimental value. Repetitions, as similar is it is experimentally achievable, have unavoidable built-in differences resulting in a range of the true values rather than in a single value. When modern, very sensitive and well calibrated measurement systems are used, this range is not negligible, and sometimes dominates over the measurement uncertainty. Range of true values depends on built-in differences in physics of the experiment. Stochastic physical processes result typically in a broader range of true values than non-stochastic processes do. Measurement uncertainty depends on a measurement method (properties of the detector not of the experiment). Modern measurement methods, including digital ones, frequently make the measurement uncertainty very small. When data from one–of –a kind experiment are analyzed, only the measurement uncertainty is reported. It provides no information about the range of true experimental values, neither about reliability of a reported data point. Reliability of a data point is in general independent from its measurement uncertainty. However, in practice reliable measurement methods frequently have high measurement uncertainty, while low reliability methods are applied to limit measurement uncertainty. Comparison of reliable data with high measurement uncertainty to not so reliable data measured with low uncertainty is discussed – in different scenarios different data analysis methods are applicable. Methods for data analysis from an experiment repeated statistically significant number of times are very well developed. They do not require a detailed expertise in physics of an experiment, nor in the properties of the measurement system used, and meaning of the reported uncertainty is well understood in any scientific community. It all changes when data from one-of-a-kind experiment is analyzed. Analyst’s expertise is required both in the physics of the experiment and in all aspects of the measurement system, all possible malfunctions. Data users must remember that only measurement uncertainty is reported from any one-of-a-kind experiment. Theory with simulations may provide estimation of expected built-in differences in the experiment, and by this of expected range of true values for a given experiment; yet measurement uncertainty can never be used in place of the range of true experimental values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Worldwide Physics-Based Lifetime Prediction of c-Si Modules Due to Solder-Bond Failure

Lifetime prediction of the fielded c-Si solar modules due to location-specific weather conditions has been an important topic of photovoltaic research and the economic viability of solar energy. Data analytic techniques such as the performance ratio method, Statistical clear sky model, and Suns-Vmp methods quantify the degradation from measured data of a solar farm, however, the nonlinear time-dependence and correlated degradations make it difficult to use the empirical degradation rates for ultimate lifetime projection. In this article, we propose a complementary physics-based model to predict the solder bond failure caused by mechanical stress associated with the variations of the temperature. Integrating the worldwide weather information from NASA/NSRDB databases, the model predicts the location-specific output-power degradation and the lifetime of a module due to solder bond failure. The model parameters are calibrated against qualification tests involving thermal cycling of specific batches of modules from a specific technology/manufacturer. The results may be summarized as: 1) Modules installed at higher latitudes show a longer lifetime due to reduced damage accumulation. 2) The reduction of temperature fluctuation close to large bodies of water, such as seashores, increases solder bond lifetime significantly. 3) Relatively speaking, modules installed close to the Tropic of Cancer/Capricorn (23.5 degrees North/South) suffer from a higher solder bond damage and have a shorter lifetime, suggesting a conservative design. This model should serve as a building block of a comprehensive reliability framework that can predict the lifetime of a module that experiences simultaneous and correlated degradation mechanisms involving yellowing, corrosion, and potential-induced degradation.

14 SOLAR ENERGY↗

DOE OSTI2023

Representative Phenomena of Cyclic Turbulent Combustion in High-Pressure Fuel Sprays

Abstract Cyclic variations in conventional diesel combustion engines can lead to large differences in engine out emissions even at steady operation. This study uses an optically accessible constant-pressure flow chamber to acquire fuel injections in quick succession to analyze mixing, auto-ignition, and combustion of diesel-surrogate n-heptane using multiple high-speed optical diagnostics. Prior studies have utilized fewer injections and/or they rely on analysis of ensemble average behavior. These approaches do not yield information on injection-to-injection variation or provide confidence in utilizing individual injection measurements for high-fidelity computational fluid dynamics(CFD) model validation. In this study, a large set of 500 injections is used to obtain global parameters including liquid length, vapor penetration length, ignition delay time, and lift-off length. Results for multiple injections are presented to illustrate large injection to injection variations. Potential sources for these variations are analyzed to conclude localized, small scale turbulence and rate of injection variations as the likely sources. Then, a statistical method based on z-scores is proposed and implemented to identify instantaneous injections that best represent the bulk data-set of jet boundaries measured independently by three different diagnostics. This synthesis of statistics-guided screening of data set and ensemble-average analysis offers higher confidence for CFD model validation relying upon both a representative single and average injection results.

42 ENGINEERING↗