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DOE OSTI2022

Inference for Nonparanormal Partial Correlation via Regularized Rank-Based Nodewise Regression

Abstract Partial correlation is a common tool in studying conditional dependence for Gaussian distributed data. However, partial correlation being zero may not be equivalent to conditional independence under non-Gaussian distributions. In this paper, we propose a statistical inference procedure for partial correlations under the high-dimensional nonparanormal (NPN) model where the observed data are normally distributed after certain monotone transformations. The NPN partial correlation is the partial correlation of the normal transformed data under the NPN model, which is a more general measure of conditional dependence. We estimate the NPN partial correlations by regularized nodewise regression based on the empirical ranks of the original data. A multiple testing procedure is proposed to identify the nonzero NPN partial correlations. The proposed method can be carried out by a simple coordinate descent algorithm for lasso optimization. It is easy-to-implement and computationally more efficient compared to the existing methods for estimating NPN graphical models. Theoretical results are developed to show the asymptotic normality of the proposed estimator and to justify the proposed multiple testing procedure. Numerical simulations and a case study on brain imaging data demonstrate the utility of the proposed procedure and evaluate its performance compared to the existing methods. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Machine learning for seismic low-frequency extrapolation

The cycle-skipping problem that plagues full waveform inversion (FWI) can be at least partially mitigated if low frequencies (which encode the kinematics of wave propagation in seismic data) are recorded. However, seismic sources and receivers are band-limited, so seismic data does not generally include signals down to 0 Hz. To improve our ability to solve the seismic inverse problem, one can synthesize this missing low-frequency (LF) content from the recorded high-frequency (HF) data using machine learning (ML) models. Deep learning models such as convolutional neural networks (CNNs) demonstrate impressive ability to perform low frequency extrapolation. However, such models require powerful hardware (GPU machines) and careful training. We assess the extrapolation capabilities of three different ML models that do not require GPU machines, namely, random forest, Gaussian process regression and gradient boosting, on both synthetic and real data. Experimental results on two synthetic data sets (generated from a low velocity lens embedded in a homogeneous medium, and the Marmousi model) demonstrate that FWI applied to the extrapolated data consistently improves inversion accuracy relative to FWI applied to the original data sets that do not contain low frequencies. Application of low-frequency extrapolation to real data from the Northwest Shelf of Australia demonstrates that tree-based ML models such as gradient boosting can outperform CNNs in terms of both accuracy and computational cost on non-GPU architectures.

58 GEOSCIENCES↗

DOE OSTI2022

Machine learning pipeline to predict defect behavior in metallic alloy systems

The interaction between defect and solute atoms is critical to the thermodynamic and kinetic behavior of metallic alloys under exposure to high-energy radiation, causing irradiation damage in materials. Radiation can generate non-equilibrium concentrations of point defects such as vacancies and interstitials. The excess point defects not only accelerate diffusional processes such as precipitation that cause radiation embrittlement, but also change the pathway of phase transformations, including nucleation processes. Understanding these defect behaviors is complicated by the challenge and complexity of addressing each possible local and discrete distribution of environments and chemical interactions around targeted defects-solute or solute-solute complexes. To resolve the challenge, machine learning regression techniques have emerged as powerful tools that can train and construct an energy model to accurately describe the chemical interactions of solutes and defects. In Fiscal Year 2022, the work focused on the workflow development and demonstration using machine learning regression, density functional theory, cluster expansion, and Monte Carlo simulation to predict the effects of ternary solute elements (e.g., aluminum and molybdenum) and point defects on the Cr-rich $\alpha^{\prime}$ precipitation in multicomponent FeCr model alloys. The computational outcomes include the prediction of the ternary phase diagram, vacancy formation energy for different compositions, and the effect of vacancies on the nucleation of Cr-rich clusters. The simulations predict a pronounced change of Cr solubility in bcc Fe by the addition of Al and the rejection of Al atoms from $\alpha^{\prime}$ precipitates. Additionally, the simulations show the formation of Cr-vacancy clusters as the initial nuclei for stable nucleation and growth of $\alpha^{\prime}$ particles. The results demonstrate important outcomes and applications of using machine learning pipeline to study model or commercial alloys with multicomponent solute species and point defects.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Robustness of the Stochastic Parameterization of Subgrid-Scale Wind Variability in Sea Surface Fluxes

Abstract High-resolution numerical models have been used to develop statistical models of the enhancement of sea surface fluxes resulting from spatial variability of sea surface wind. In particular, studies have shown that flux enhancement is not a deterministic function of the resolved state. Previous studies focused on single geographical areas or used a single high-resolution numerical model. This study extends the development of such statistical models by considering six different high-resolution models, four different geographical regions, and three different 10-day periods, allowing for a systematic investigation of the robustness of both the deterministic and stochastic parts of the data-driven parameterization. Results indicate that the deterministic part, based on regressing the unresolved normalized flux onto resolved-scale normalized flux and precipitation, is broadly robust across different models, regions, and time periods. The statistical features of the stochastic part of the model (spatial and temporal autocorrelation and parameters of a Gaussian process fit to the regression residual) are also found to be robust and not strongly sensitive to the underlying model, modeled geographical region, or time period studied. Best-fit Gaussian process parameters display robust spatial heterogeneity across models, indicating potential for improvements to the statistical model. These results illustrate the potential for the development of a generic, explicitly stochastic parameterization of sea surface flux enhancements dependent on wind variability.

Endo, Kota↗

DOE OSTI2022

Different CT slice thickness and contrast‐enhancement phase in radiomics models on the differential performance of lung adenocarcinoma

Abstract Background To investigate the effects of computed tomography (CT) reconstruction slice thickness and contrast‐enhancement phase on the differential diagnosis performance of radiomic signature in lung adenocarcinoma. Methods A total of 187 patients who had been pathologically confirmed with lung adenocarcinoma and nonadenocarcinoma were divided into a training cohort ( n = 149) and validation cohort ( n = 38). All the patients underwent contrast‐enhanced CT and the images were reconstructed with different slice thickness. The radiomic features were extracted from different slice thickness and scan phase. The logistic regression (LR) algorithm was used to build a machine learning model for each group. The area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve and DeLong test was used to evaluate its discriminating performance. Results Finally, 34 image features and five semantic features were selected to establish a radiomics model. Based on the three contrast‐enhanced CT phases and four reconstruction slice thickness, 12 groups of radiomics models showed good discrimination ability with the AUCs range from 0.9287 to 0.9631, sensitivity range from 0.8349 to 0.9083, specificity range from 0.825 to 0.925 in the training group. Similar results were observed in the validation group. However, there was no statistical significance between the different CT scan phase groups and different slice thickness ( p > 0.05). Conclusions The radiomic analysis of contrast‐enhanced CT can be used for the differential diagnosis of lung adenocarcinoma. Moreover, different slice thickness and contrast‐enhanced scan phase did not affect the discriminating ability in the radiomics models.

Wang, Yang↗

DOE OSTI2021

A seamless multiscale operator neural network for inferring bubble dynamics

Modelling multiscale systems from nanoscale to macroscale requires the use of atomistic and continuum methods and, correspondingly, different computer codes. Here, we develop a seamless method based on DeepONet, which is a composite deep neural network (a branch and a trunk network) for regressing operators. In particular, we consider bubble growth dynamics, and we model tiny bubbles of initial size from 100 nm to 10 $\mathrm {\mu }\textrm {m}$ , modelled by the Rayleigh–Plesset equation in the continuum regime above 1 $\mathrm {\mu }\textrm {m}$ and the dissipative particle dynamics method for bubbles below 1 $\mathrm {\mu }\textrm {m}$ in the atomistic regime. After an offline training based on data from both regimes, DeepONet can make accurate predictions of bubble growth on-the-fly (within a fraction of a second) across four orders of magnitude difference in spatial scales and two orders of magnitude in temporal scales. The framework of DeepONet is general and can be used for unifying physical models of different scales in diverse multiscale applications.

Mechanics↗

DOE OSTI2021

Modeling freight mode choice using machine learning classifiers: a comparative study using Commodity Flow Survey (CFS) data

This study explores the usefulness of machine learning classifiers for modeling freight mode choice. We investigate eight commonly used machine learning classifiers, namely Naïve Bayes, Support Vector Machine, Artificial Neural Network, K-Nearest Neighbors, Classification and Regression Tree, Random Forest, Boosting and Bagging, along with the classical Multinomial Logit model. US 2012 Commodity Flow Survey data are used as the primary data source; we augment it with spatial attributes from secondary data sources. The performance of the classifiers is compared based on prediction accuracy results. The current research also examines the role of sample size and training-testing data split ratios on the predictive ability of the various approaches. In addition, the importance of variables is estimated to determine how the variables influence freight mode choice. The results show that the tree-based ensemble classifiers perform the best. Specifically, Random Forest produces the most accurate predictions, closely followed by Boosting and Bagging. With regard to variable importance, shipment characteristics, such as shipment distance, industry classification of the shipper and shipment size, are the most significant factors for freight mode choice decisions.

42 ENGINEERING↗

DOE OSTI2020

Probabilistic neural networks for fluid flow surrogate modeling and data recovery

We consider the use of probabilistic neural networks for fluid flow surrogate modeling and data recovery. This framework is constructed by assuming that the target variables are sampled from a Gaussian distribution conditioned on the inputs. Consequently, the overall formulation sets up a procedure to predict the hyperparameters of this distribution which are then used to compute an objective function given training data. We demonstrate that this framework has the ability to provide for prediction confidence intervals based on the assumption of a probabilistic posterior, given an appropriate model architecture and adequate training data. The applicability of the present framework to cases with noisy measurements and limited observations is also assessed. To demonstrate the capabilities of this framework, we consider canonical regression problems of fluid dynamics from the viewpoint of reduced-order modeling and spatial data recovery for four canonical data sets. The examples considered in this study arise from (i) the shallow-water equations, (ii) a two-dimensional cylinder flow, (iii) the wake of a NACA0012 airfoil with a Gurney flap, and (iv) the NOAA sea surface temperature data set. Furthermore, the present results indicate that the probabilistic neural network not only produces a machine-learning-based fluid flow surrogate model but also systematically quantifies the uncertainty therein to assist with model interpretability.

42 ENGINEERING↗

DOE OSTI2020

Comparison of linear regression, k-nearest neighbour and random forest methods in airborne laser-scanning-based prediction of growing stock

Abstract In this study, for five sites around the world, we look at the effects of different model types and variable selection approaches on forest yield modelling performances in an area-based approach (ABA). We compared ordinary least squares regression (OLS), k-nearest neighbours (kNN) and random forest (RF). Our objective was to test if there are systematic differences in accuracy between OLS, kNN and RF in ABA predictions of growing stock volume. The analyses are based on a 5-fold cross-validation at five study sites: an eucalyptus plantation, a temperate forest and three different boreal forests. Two completely independent validation datasets were also available for two of the boreal sites. For the kNN, we evaluated multiple measures of distance including Euclidean, Mahalanobis, most similar neighbour (MSN) and an RF-based distance metric. The variable selection approaches we examined included a heuristic approach (for OLS, kNN and RF), exhaustive search among all combinations (OLS only) and all variables together (RF only). Performances varied by model type and variable selection approaches among sites. OLS and RF had similar accuracies and were more efficient than any of the kNN variants. Variable selection did not affect RF performance. Heuristic and exhaustive variable selection performed similarly for OLS. kNN fared the poorest amongst model types, and kNN with RF distance was prone to overfitting when compared with a validation dataset. Additional caution is therefore required when building kNN models for volume prediction though ABA, being preferable instead to opt for models based on OLS with some variable selection, or RF with all variables together.

Cosenza, Diogo N.↗

NASA NTRS2021

Application of Gaussian Mixture Regression for the Correction of Low Cost PM2.5 Monitoring Data in Accra, Ghana

Low-cost sensors (LCSs) for air quality monitoring have enormous potential to improve air quality data coverage in resource-limited parts of the world such as sub-Saharan Africa. LCSs, however, are affected by environment and source conditions. To establish high-quality data, LCSs must be collocated and calibrated with reference grade PM2.5 monitors. From March 2020, a low-cost PurpleAir PM2.5 monitor was collocated with a Met One Beta Attenuation Monitor 1020 in Accra, Ghana. While previous studies have shown that multiple linear regression (MLR) and random forest regression (RF) can improve accuracy and correlation between PurpleAir and reference data, MLR and RF yielded suboptimal improvement in the Accra collocation (R2 = 0.81 and R2 = 0.81, respectively). We present the first application of Gaussian mixture regression (GMR) to air quality data calibration and demonstrate improvement over traditional methods by increasing the collocated PM2.5 correlation and accuracy to R2 = 0.88 and MAE = 2.2 μg/cu. m. Gaussian mixture models (GMMs) are a probability density estimator and clustering method from which nonlinear regressions that tolerate missing inputs can be derived. We find that even when given missing inputs, GMR provides better correlation than MLR and RF performed with complete data. GMR also allows us to estimate calibration certainty. When evaluated, 95% confidence intervals agreed with reference PM2.5 data 96% of the time, suggesting that the model accurately assesses its own confidence. Additionally, clustering within the GMM is consistent with climate characteristics, providing confidence that the calibration approach can learn underlying relationships in data.

Sensors↗

NASA NTRS2006

The Goddard Snow Radiance Assimilation Project: An Integrated Snow Radiance and Snow Physics Modeling Framework for Snow/cold Land Surface Modeling

Microwave-based retrievals of snow parameters from satellite observations have a long heritage and have so far been generated primarily by regression-based empirical "inversion" methods based on snapshots in time. Direct assimilation of microwave radiance into physical land surface models can be used to avoid errors associated with such retrieval/inversion methods, instead utilizing more straightforward forward models and temporal information. This approach has been used for years for atmospheric parameters by the operational weather forecasting community with great success. Recent developments in forward radiative transfer modeling, physical land surface modeling, and land data assimilation are converging to allow the assembly of an integrated framework for snow/cold lands modeling and radiance assimilation. The objective of the Goddard snow radiance assimilation project is to develop such a framework and explore its capabilities. The key elements of this framework include: a forward radiative transfer model (FRTM) for snow, a snowpack physical model, a land surface water/energy cycle model, and a data assimilation scheme. In fact, multiple models are available for each element enabling optimization to match the needs of a particular study. Together these form a modular and flexible framework for self-consistent, physically-based remote sensing and water/energy cycle studies. In this paper we will describe the elements and the integration plan. All modules will operate within the framework of the Land Information System (LIS), a land surface modeling framework with data assimilation capabilities running on a parallel-node computing cluster. Capabilities for assimilation of snow retrieval products are already under development for LIS. We will describe plans to add radiance-based assimilation capabilities. Plans for validation activities using field measurements will also be discussed.

Kim, E.↗

NASA NTRS1998

A Monte Carlo Uncertainty Analysis of Ozone Trend Predictions in a Two Dimensional Model

We use Monte Carlo analysis to estimate the uncertainty in predictions of total O3 trends between 1979 and 1995 made by the Goddard Space Flight Center (GSFC) two-dimensional (2D) model of stratospheric photochemistry and dynamics. The uncertainty is caused by gas-phase chemical reaction rates, photolysis coefficients, and heterogeneous reaction parameters which are model inputs. The uncertainty represents a lower bound to the total model uncertainty assuming the input parameter uncertainties are characterized correctly. Each of the Monte Carlo runs was initialized in 1970 and integrated for 26 model years through the end of 1995. This was repeated 419 times using input parameter sets generated by Latin Hypercube Sampling. The standard deviation (a) of the Monte Carlo ensemble of total 03 trend predictions is used to quantify the model uncertainty. The 34% difference between the model trend in globally and annually averaged total O3 using nominal inputs and atmospheric trends calculated from Nimbus 7 and Meteor 3 total ozone mapping spectrometer (TOMS) version 7 data is less than the 46% calculated 1 (sigma), model uncertainty, so there is no significant difference between the modeled and observed trends. In the northern hemisphere midlatitude spring the modeled and observed total 03 trends differ by more than 1(sigma) but less than 2(sigma), which we refer to as marginal significance. We perform a multiple linear regression analysis of the runs which suggests that only a few of the model reactions contribute significantly to the variance in the model predictions. The lack of significance in these comparisons suggests that they are of questionable use as guides for continuing model development. Large model/measurement differences which are many multiples of the input parameter uncertainty are seen in the meridional gradients of the trend and the peak-to-peak variations in the trends over an annual cycle. These discrepancies unambiguously indicate model formulation problems and provide a measure of model performance which can be used in attempts to improve such models.

Considine, D. B.↗

DOE OSTI2023

Effects of Aluminum and Molybdenum on the Phase Stability of Iron-Chromium Alloys: A First-Principles Study

The interaction between solute atoms is critical to the thermodynamic behavior of Fe-Cr alloys, but the effects of non-dilute Al and Mo on the Fe-Cr phase stability and vacancy formation energy are not clearly understood. In this study, density functional theory, cluster expansion, and Monte Carlo simulation are used to predict the effects of ternary solute elements on the thermodynamic properties in multicomponent Fe-Cr alloys. The machine learning regression approach is applied to train and construct energy models that accurately describe the complex chemical interactions. The computational outcomes include the prediction of the partial ternary phase diagram, mixing enthalpy, and vacancy formation energy for different compositions. The phase boundary calculation predicts a pronounced change of Cr solubility in bcc Fe by the addition of Al and the rejection of Al atoms from a’ precipitates. The mixing enthalpy calculation shows that Mo may also reduce the Cr solubility in bcc Fe. Additionally, the simulations show that non-dilute Cr decreases the vacancy formation energy in bcc Fe, while adding Al results in a less significant effect. Finally, the results demonstrate important applications of using machine learning energy models to study model or commercial alloys with multicomponent solute species and point defects.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Degradation and Modeling of Large-Format Commercial Lithium-Ion Cells as a Function of Chemistry, Design, and Aging Conditions

Demand for large-format (>10 Ah) lithium-ion batteries has increased substantially in recent years, due to the growth of both electric vehicle and stationary energy storage markets. The economics of these applications is sensitive to the lifetime of the batteries, and end-of-life can either be due to energy or power limitations. Despite this, there is little information from cell manufacturers on the sensitivity of cell degradation to environmental conditions or battery use. This work reports accelerated aging test data from four commercial large-format lithium-ion batteries from three manufacturers, with varying design (thickness, casings, ...), chemistry (lithium-iron-phosphate (LFP) or lithium-nickel-manganese-cobalt-oxide positive electrodes (NMC), with graphite (Gr) negative electrodes), and capacity (50 to 250 Amp hours). The tested LFP|Gr cell is found to be relatively insensitive to cycling conditions like temperature or voltage window, while NMC|Gr cells have varying sensitivity. Degradation trends are further investigated by training predictive models: simple polynomial trend lines, a semi-empirical reduced-order model, and an empirical reduced-order model identified using machine-learning based on symbolic regression. Calendar and cycle life are simulated over a variety of conditions to directly compare the various batteries. Cell size and thickness are found to substantially impact sensitivity to temperature during cycle aging, while electrode chemistry impacts depth-of-discharge sensitivity. Real-world battery lifetime is evaluated by simulating residential energy storage and commercial frequency containment reserve systems in several U.S. climate regions. Predicted lifetime across cell types varies from 7 years to 20+ years, though all cells are predicted to have at least 10 year life in certain conditions.

battery lifetime↗

DOE OSTI2021

Statistical Uncertainty in Paleoclimate Proxy Reconstructions

A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.

58 GEOSCIENCES↗

DOE OSTI2026

Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction

Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Targeting KDM4 for treating PAX3-FOXO1–driven alveolar rhabdomyosarcoma

Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3–Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1 + RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1–governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1 + RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1–related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.

Cell Biology↗

DOE OSTI2021

The proton charge radius extracted from the initial-state radiation experiment at MAMI

Abstract We report on a comprehensive reinterpretation of the existing cross-section data for elastic electron-proton scattering obtained by the initial-state radiation technique, resulting in a significantly improved accuracy of the extracted proton charge radius. By refining the external energy corrections we have achieved an outstanding description of the radiative tail, essential for a detailed investigation of the proton finite-size effects on the measured cross sections. This development, together with a novel framework for determining the radius, based on a regression analysis of the cross sections employing a polynomial model for the form factor, led us to a new value for the charge radius, which is $$(0.878 \pm 0.011_\mathrm {stat.}\pm 0.031_\mathrm {sys.}\pm 0.002_\mathrm {mod.})\,\mathrm {fm}$$ ( 0.878 ± 0 . 011 stat . ± 0 . 031 sys . ± 0 . 002 mod . ) fm

Physics↗