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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

mvBayesPy

SAND2025-11476O The mvBayesPy tool is a Python package that performs multivariate Bayesian analysis on generic data. It includes tools for regression modeling, diagnosis, basis decomposition, sensitivity analysis and visualization. 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.

Tucker, James [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2023

Scalable Volume Visualization for Big Scientific Data Modeled by Functional Approximation

Considering the challenges posed by the space and time complexities in handling extensive scientific volumetric data, various data representations have been developed for the analysis of large-scale scientific data. Multivariate functional approximation (MFA) is an innovative data model designed to tackle substantial challenges in scientific data analysis. It computes values and derivatives with high-order accuracy throughout the spatial domain, mitigating artifacts associated with zero- or first-order interpolation. However, the slow query time through MFA makes it less suitable for interactively visualizing a large MFA model. In this work, we develop the first scalable interactive volume visualization pipeline, MFA-DVV, for the MFA model encoded from large-scale datasets. Our method achieves low input latency through distributed architecture, and its performance can be further enhanced by utilizing a compressed MFA model while still maintaining a high-quality rendering result for scientific datasets. We conduct comprehensive experiments to show that MFA-DVV can decrease the input latency and achieve superior visualization results for big scientific data compared with existing approaches.

big scientific dataset↗
DOE OSTI2026

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗
DOE OSTI2021

Survey on stochastic distribution systems: A full probability density function control theory with potential applications

Complex systems seen either in general engineering practice or economics are subjected to ever increased uncertainties that are mostly represented as random variables or parameters, and the characteristics of random variables are represented by their probability density functions (PDFs). Controlling their PDFs means to shape their stochastic distributions and in general it would provide a full treatment for system analysis and operational control and optimization. This leads to the development of stochastic distribution control (SDC) systems theory in the past decades, where the original aim of the controller design is to realize a shape control of the distributions of certain random variables in their PDFs sense for some engineering processes. Indeed, once the PDFs of these random variables or parameters are used to describe their distribution characters, the control task is to obtain control signals so that the output PDFs of stochastic systems are made to follow their target PDFs. The subject of SDC was initially originated for non-Gaussian stochastic control systems design but has found a wide spectrum of applications in general systems in terms of data-driven modeling, analysis, signal processing (filtering), data mining via multivariable statistics, decision-making (optimization) for systems subjected to uncertainties and even in economics. In this context, SDC constitutes an effective primer tool for complex system analysis, control and operational optimizations. In this review paper, a detailed survey of the developments on the research of SDC systems will be made together with their wide spectrum applications and future perspectives.

42 ENGINEERING↗
DOE OSTI2024

Development of an Attenuated Total Reflectance–Ultraviolet–Visible Probe for the Online Monitoring of Dark Solutions

Optical spectroscopy is a valuable tool for on-line monitoring of a variety of processes. Ultraviolet-visible (UV-vis) spectroscopy in particular, can monitor the concentration of analytes as well as identify speciation and oxidation state. However, it can be difficult to impossible to employ UV-vis based sensors on chemical systems that are very dark (i.e., high optical density) as exceedingly short pathlengths are required (for transmission approaches) or effective means of backscattering are needed (for reflectance approaches). Examples of processes that would benefit significantly from the use of optical sensors and encounter these challenges include used nuclear fuel recycling and molten salts with high concentrations of dissolved uranium. Utilizing an attenuated total reflectance (ATR) UV-vis approach can overcome these challenges and allow for the measurement of solutions orders of magnitude more concentrated than transmission UV-vis. However, determining ideal sensor specifications for varied processes can be time consuming and expensive. Here, in this study, we evaluate the ability for a novel ATR-UV-vis probe to measure very concentrated solutions of Co(II) and Ni(II) nitrate as well as organic dyes (methylene blue, acid red 1, and crystal violet). This sensor design provides a modular method for exploring possible “pathlengths” by altering the exposed ATR fiber length. Also studied were approaches to loading and measuring the sensor cell. These results are compared to a traditional 1 cm cuvette measured by transmission UV-vis. It was found that the ATR-UV-vis probe was capable of measuring solutions 600 times more concentrated than the 1 cm cuvette. Advanced data analysis in the form of multivariate curve resolution (MCR) was used to analyze the speciation of methylene blue over a large concentration range. The application of this novel ATR-UV-vis probe to the interrogation of dark solutions is a promising avenue for use in on-line monitoring of nuclear processes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Novel principal component analysis tool based on python for analysis of complex spectra of time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface analysis tool, which can simultaneously provide elemental, isotopic, and molecular information with part per million (ppm) sensitivity. However, each spectrum may be composed of hundreds of ion signals, which makes the spectra data complex. Principal component analysis (PCA) is a multivariate analysis technique that has been widely used to figure out the variances among samples in ToF-SIMS spectra data analysis and is showing great success in the explanation of complex ToF-SIMS spectra. So far, several software tools have been developed for PCA of ToF-SIMS spectra; however, none of them are freely available. Such a situation leads to some difficulties in extending applications of PCA to various research fields. More importantly, it has long been challenging for common researchers to understand PCA plots and extract chemical differences among samples. In this work, we developed a new and flexible software tool (named “advanced spectra pca toolbox”) based on python for PCA of complex ToF-SIMS spectra along with an easy-to-read manual. It can generate data analysis reports automatically to explain chemical differences among samples, allowing less experienced researchers to easily understand tricky PCA results. Moreover, it is expandable and compatible with artificial intelligence/machine learning functions. Pure goethite and different lignin adsorbed goethite samples were used as a model system to demonstrate our new software tool, proving that our software tool can be readily used in complex spectra data processing. Our new software tool is open-source, convenient, flexible, and expandable. We expect this open-source tool will benefit the ToF-SIMS community.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗
DOE OSTI2022

Modeling of Supercritical CO2 Shell-and-Tube Heat Exchangers Under Extreme Conditions. Part I: Correlation Development

Abstract High-temperature supercritical CO2 Brayton cycles are promising possibilities for future stationary power generation and hybrid electric propulsion applications. Heat exchangers are critical components in supercritical CO2 thermal cycles and require accurate correlations and comprehensive performance modeling under extreme temperatures and pressures. In this paper (Part I), new Colburn and friction factor correlations are developed to quantify shell-side heat transfer and friction characteristics of flow within heat exchangers in the shell-and-tube configuration. Using experimental and computational fluid dynamics (CFD) data sets from existing literature, multivariate regression analysis is conducted to achieve correlations that capture the effect of multiple critical geometric parameters. These correlations offer superior accuracy and versatility as compared to previous studies and predict the thermohydraulic performance of about 90% of the existing experimental and CFD data within ±15%. Supplementary thermohydraulic performance data are acquired from CFD simulations with supercritical CO2 as working fluid to validate the developed correlations and demonstrate its capability to be applied to supercrtical CO2 heat exchangers.

Engineering↗
DOE OSTI2020

Non-Gaussianity in the weak lensing correlation function likelihood – implications for cosmological parameter biases

ABSTRACT We study the significance of non-Gaussianity in the likelihood of weak lensing shear two-point correlation functions, detecting significantly non-zero skewness and kurtosis in 1D marginal distributions of shear two-point correlation functions in simulated weak lensing data. We examine the implications in the context of future surveys, in particular LSST, with derivations of how the non-Gaussianity scales with survey area. We show that there is no significant bias in 1D posteriors of Ωm and σ8 due to the non-Gaussian likelihood distributions of shear correlations functions using the mock data (100 deg2). We also present a systematic approach to constructing approximate multivariate likelihoods with 1D parametric functions by assuming independence or more flexible non-parametric multivariate methods after decorrelating the data points using principal component analysis (PCA). While the use of PCA does not modify the non-Gaussianity of the multivariate likelihood, we find empirically that the 1D marginal sampling distributions of the PCA components exhibit less skewness and kurtosis than the original shear correlation functions. Modelling the likelihood with marginal parametric functions based on the assumption of independence between PCA components thus gives a lower limit for the biases. We further demonstrate that the difference in cosmological parameter constraints between the multivariate Gaussian likelihood model and more complex non-Gaussian likelihood models would be even smaller for an LSST-like survey. In addition, the PCA approach automatically serves as a data compression method, enabling the retention of the majority of the cosmological information while reducing the dimensionality of the data vector by a factor of ∼5.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Autonomous adaptive data acquisition for scanning hyperspectral imaging

Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Information-Theoretic Exploration of Multivariate Time-Varying Image Databases

Modern scientific simulations produce very large datasets, making interactive exploration of such data computationally prohibitive. An increasingly common data reduction technique is to store visualizations and other data extracts in a database. The Cinema project is one such approach, storing visualizations in an image database for post hoc exploration and interactive image-based analysis. This work focuses on developing efficient algorithms that can quantify various types of multivariate dependencies existing within multi-variable datasets. It applies specific mutual information measures for the quantification of salient regions from multivariate image data. Here, using such information measures, the opacity of the images is modulated so that the salient regions are automatically highlighted and the domain scientists can interactively explore the most relevant regions for scientific discovery.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Application of Partial Least Squares Approaches to Pyroprocessing ER Data

Multivariate approaches show promise for application to process monitoring for safeguards of pyroprocessing. Past MPACT work explored the application of Principal Component Analysis (PCA) to detect off-normal conditions in pyroprocessing electrorefiner (ER) data from in the Hot Fuel Examination Facility (HFEF) at Idaho National Laboratory (INL) known as the Scalable Pyrochemical Recycling testbed (SPyRe) ER. PCA, however, does not consider the output variables. In FY24, multivariate analysis was extended from PCA to Partial Least Squares (PLS) analysis. PLS maximizes the variance between both the input signals and output variables. In the case of this work, PLS was applied in two different manners: Predictive PLS and Discriminant PLS. Predictive PLS maximizes the covariance between the process variables of the ER and the measured U concentration from in-situ voltammetry. Discriminant PLS maximizes the covariance between the process variables and a set of training process “states” such as known off-normal conditions. By projecting into the latent variable space in PLS, the process variables can be regressed onto the outputs and predictions can be made for new data sets. In this work, by applying predictive PLS, a penalized non-linear PLS approach was able to make predictions of concentration based on test and training data and detect when operations were off-normal. However, the predictive PLS does not classify the signals to which off-normal operations are attributable. Discriminant PLS can be used to classify off-normal operations but is inadequate to properly classify specific off-normal classes like power supply faults when the Discriminant PLS model is only specifically trained to detect that off-normal class. When all faults are trained against the observation data, all three operational classes are accurately classified and distinguished. Thus, future application of latent variable techniques should not select any given method, but should use a mixture of PCA, Predictive PLS, and Discriminant PLS.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

The Fe 4+ / 3+ Redox Mechanism in NaFeO 2 : A Simultaneous Operando Nuclear Resonance and X-ray Scattering Study

Simultaneous operando Nuclear Forward Scattering and transmission X-ray diffraction and 57 Fe Mössbauer spectroscopy measurements were carried out in order to investigate the electrochemical mechanism of NaFeO 2 vs. Na metal using a specifically designed in situ cell. The obtained data were analysed using an alternative and innovative data analysis approach based on chemometric tools such as Principal Component Analysis (PCA) and Multivariate Curve Resolution - Alternating Least Squares (MCR-ALS). This approach, which allows the unbiased extraction of all possible information from the operando data, enabled the stepwise reconstruction of the independent “real” components permitting the description of the desodiation mechanism of NaFeO 2 . This wealth of information allows a clear description of the electrochemical reaction at the redox-active iron centres, and thus an improved comprehension of the cycling mechanisms of this material vs. sodium.

25 ENERGY STORAGE↗
DOE OSTI2020

Capabilities of multivariate Bayesian inference toward seismic hazard assessment

Multivariate Bayesian analysis can bring significant benefits to seismic hazard analysis: Its multivariate feature enables computing scalar and vector hazard without making any approximations; Correlations between intensity measures are implicitly modeled, permitting direct simulation of ground motion selection tools such as the conditional mean spectrum and the generalized conditioning intensity measure; and Its updating feature enables a seamless integration of new ground motion data into the hazard results. Here, we first develop a multivariate Bayesian ground motion model through the NGA-West2 database. The model functional form considers fault-type, magnitude, and distance dependencies, and also the linear and the rock intensity dependent site response. We use a hybrid Markov Chain Monte Carlo sampling to perform Bayesian inference consisting of Gibbs step and a multilevel Metropolis-Hastings step. We then perform several checks on the model and note that its performance is satisfactory. Finally, we illustrate the merits of this multivariate Bayesian analysis, which include: ground motion model updating with ground motion data recorded in the last four years not part of the NGA-West2 database; computation of scalar and vector seismic hazard using the un-updated and updated ground motion models for Los Angeles, CA; and simulation of the conditional mean spectrum under scalar and vector IM conditioning while accounting for different sources of aleatoric and epistemic uncertainties.

58 GEOSCIENCES↗
DOE OSTI2023

Application of Principal Component Analysis to Electrochemical Reprocessing PM and NMAC

In this report, data from an electrorefiner (ER) for nuclear fuel reprocessing is evaluated for process monitoring (PM) conclusions. This data comes from tests performed at the Idaho National Laboratory in 2022. Multivariate approaches utilizing methods of Principal Component Analysis (PCA) is applied. This is based off established work in process monitoring for fault detection in industrial facilities. This report will discuss the background, methods, and results of the application and some of the conclusions and applications that can be drawn from them. PCA is applied to two different electrorefiner (ER) operations that occurred at Idaho National Laboratory between August and October 2022. The first operation occurred with little incident while the second had several noted faults in the equipment in operational logs. The data from the first run was used to train the data for “normal” operations and applied to both sets of data to determine when operations were in an “off-normal” condition and identify where the fault occurs through PCA. PCA was able to identify off-normal events and identify the cause for off-normal operations. These identified off-normal events matched with the events and their causes in the operational logs. However, small amounts of variance in the data led to false detection of “off-normal” events. Thus, careful selection of training data and a-posteriori conclusions based off operator assessments will both be required for application of PCA to PM applications. This work demonstrated that multivariate approaches and latent variables are applicable to pyroprocessing PM applications and can be further expanded in future work as quality variables such as salt concentration from sensors and sampling become available.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Factors associated with treatment limitations in two Swedish intensive care units: Prevalence and patient involvement

Abstract The aim was to study the prevalence, documentation, and patient involvement in treatment limitations (TLs) in two Swedish intensive care units (ICUs). All patients admitted to the ICUs of two Swedish regional hospitals in 2019 were screened for inclusion. Exclusion criteria included postanesthesia care <24 h. Patients were identified using the Swedish Intensive Care Registry (SIR) and data were extracted from SIR and hospital charts. Uni‐ and multivariable logistic analysis was performed to investigate associations with the presence of TLs. A total of 3090 patients were admitted to the two ICUs in 2019. After exclusion, 1019 patients were included in the study. 45.5% were women and the mean age was 62.9 years. 26.5% of the patients had one or several TLs. Age (OR 1.04 per one year increase 95% confidence interval (CI) 1.02–1.05), SAPS3‐score (OR 1.08 per one unit increase 95% CI 1.06–1.09) and ICU length of stay (OR 1.11 per one day increase 95% CI 1.05–1.17) were independently associated with an increased likelihood of receiving a TL. 17% of the patients were involved in the decision‐making process and in >30% of cases neither the patient nor next‐of‐kin were informed. Women were to a larger extent involved in the decision process than men (24.5 vs. 12.5% p < .05). When the intensivist documented why a TL was established, patient autonomy was four times more commonly stated as the motivation for the TL among women compared to men (15.5% vs. 3.8% p < .05). TLs were common in two Swedish ICUs but a substantial number of patients and next‐of‐kin were not involved in the decision‐making process or informed of the decision. Women were more often than men engaged in the decision to establish a TL.

Jönsson, Nino↗
DOE OSTI2021

Identification and correction of temporal and spatial distortions in scanning transmission electron microscopy

Scanning transmission electron microscopy (STEM) has become the technique of choice for quantitative characterization of atomic structure of materials, where the minute displacements of atomic columns from high-symmetry positions can be used to map strain, polarization, octahedra tilts, and other physical and chemical order parameter fields. The latter can be used as inputs into mesoscopic and atomistic models, providing insight into the correlative relationships and generative physics of materials on the atomic level. However, these quantitative applications of STEM necessitate understanding the microscope induced image distortions and developing the pathways to compensate them both as part of a rapid calibration procedure for in situ imaging, and the post-experimental data analysis stage. Here, we explore the spatiotemporal structure of the microscopic distortions in STEM using multivariate analysis of the atomic trajectories in the image stacks. Based on the behavior of principal component analysis (PCA), we develop the Gaussian process (GP)-based regression method for quantification of the distortion function. The limitations of such an approach and possible strategies for implementation as a part of in-line data acquisition in STEM are discussed. Here, the analysis workflow is summarized in a Jupyter notebook that can be used to retrace the analysis and analyze the reader's data.

36 MATERIALS SCIENCE↗