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NASA NTRS1993

The El Nino/Southern Oscillation and Future Soybean Prices

Recently, it was shown that the application of a method combining singular spectrum analysis (SSA) and the maximum entropy method to univariate indicators of the coupled ocean-atmosphere El Nino/Southern Oscillation (ENSO) phenomenon can be helpful in determining whether an El Nino (EN) or La Nina (LN) event will occur. SSA - a variant of principal component analysis applied in the time domain - filters out variability unrelated to ENSO and separates the quasi-biennial (QB), two-to-three year variability, from a lower-frequency (LF) four-to-six year EN-LN cycle; the total variance associated with ENSO combines the QB and LF modes. ENSO has been known to affect weather conditions over much of the globe. For example, EN events have been connected with unusually rainy weather over the Central and Western US, while the opposite phases of the oscillation (LN) have been plausibly associated with extreme dry conditions over much of the same geographical area...

Keppenne, C.↗

DOE OSTI2017

Automated X-Ray Diffraction of Irradiated Materials

Synchrotron-based X-ray diffraction (XRD) and small-angle Xray scattering (SAXS) characterization techniques used on unirradiated and irradiated reactor pressure vessel steels yield large amounts of data. Machine learning techniques, including PCA, offer a novel method of analyzing and visualizing these large data sets in order to determine the effects of chemistry and irradiation conditions on the formation of radiation induced precipitates. In order to run analysis on these data sets, preprocessing must be carried out to convert the data to a usable format and mask the 2-D detector images to account for experimental variations. Once the data has been preprocessed, it can be organized and visualized using principal component analysis (PCA), multi-dimensional scaling, and k-means clustering. In conclusion, from these techniques, it is shown that sample chemistry has a notable effect on the formation of the radiation induced precipitates in reactor pressure vessel steels.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy

Purpose: For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Methods: Considering the complex H&N structures and ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. Results: The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28% ± 1.46%) and margin error (0.49 ± 0.12 mm) showed good agreement between the automatic and manual results. The comparison with three other deformable model-based segmentation methods illustrated the superior shape tracking performance of the proposed method. Large interpatient variations of swallowing frequency, swallowing duration, and upper airway cross-sectional area were observed from the testing cine image sequences. Conclusions: The proposed motion tracking method can provide accurate upper airway motion tracking results, and enable automatic and quantitative identification and analysis of in-treatment H&N upper airway motion. By integrating explicit and implicit linked-shape representations within a hierarchical model-fitting process, the proposed tracking method can process complex H&N structures and low-contrast/resolution cine MRI images. Future research will focus on the improvement of method reliability, patient motion pattern analysis for providing more information on patient-specific prediction of structure displacements, and motion effects on dosimetry for better H&N motion management in radiation therapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Joint Bayesian Estimation of Quasar Continua and the Lyα Forest Flux Probability Distribution Function

We present a new Bayesian algorithm making use of Markov Chain Monte Carlo sampling that allows us to simultaneously estimate the unknown continuum level of each quasar in an ensemble of high-resolution spectra, as well as their common probability distribution function (PDF) for the transmitted Lyα forest flux. This fully automated PDF regulated continuum fitting method models the unknown quasar continuum with a linear principal component analysis (PCA) basis, with the PCA coefficients treated as nuisance parameters. The method allows one to estimate parameters governing the thermal state of the intergalactic medium (IGM), such as the slope of the temperature–density relation γ−1, while marginalizing out continuum uncertainties in a fully Bayesian way. Using realistic mock quasar spectra created from a simplified semi-numerical model of the IGM, we show that this method recovers the underlying quasar continua to a precision of ≃7% and ≃10% at z = 3 and z = 5, respectively. Given the number of principal component spectra, this is comparable to the underlying accuracy of the PCA model itself. Most importantly, we show that we can achieve a nearly unbiased estimate of the slope γ−1 of the IGM temperature–density relation with a precision of ±8.6% at z = 3 and ±6.1% at z = 5, for an ensemble of ten mock high-resolution quasar spectra. Applying this method to real quasar spectra and comparing to a more realistic IGM model from hydrodynamical simulations would enable precise measurements of the thermal and cosmological parameters governing the IGM, albeit with somewhat larger uncertainties, given the increased flexibility of the model.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Fault Detection and Diagnosis In Hall–Héroult Cells Based on Individual Anode Current Measurements Using Dynamic Kernel PCA

Individual anode current signals in aluminum reduction cells provide localized cell conditions in the vicinity of each anode, which contain more information than the conventionally measured cell voltage and line current. One common use of this measurement is to identify process faults that can cause significant changes in the anode current signals. While this method is simple and direct, it ignores the interactions between anode currents and other important process variables. This paper presents an approach that applies multivariate statistical analysis techniques to individual anode currents and other process operating data, for the detection and diagnosis of local process abnormalities in aluminum reduction cells. Specifically, since the Hall–Héroult process is time-varying with its process variables dynamically and nonlinearly correlated, dynamic kernel principal component analysis with moving windows is used. The cell is discretized into a number of subsystems, with each subsystem representing one anode and cell conditions in its vicinity. The fault associated with each subsystem is identified based on multivariate statistical control charts. The results show that the proposed approach is able to not only effectively pinpoint the problematic areas in the cell, but also assess the effect of the fault on different parts of the cell.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Kernels for scalable data analysis in science: Towards an architecture-portable future

In this paper, we pose and address some of the unique challenges in the analysis of scientific Big Data on supercomputing platforms. Our approach identifies, implements and scales numerical kernels that are critical to the instantiation of theory-inspired analytic workflows on modern computing architectures. We present the benefits of scalable kernels towards constructing algorithms such as principal component analysis and non-negative matrix factorization on an image-analysis use case at the Oak Ridge Leadership Computing Facility (OLCF). Based on experience with the use-case, we conclude that piecing scalable analytic kernels into user-defined analytic workflows are a flexible, modular and agile way to enable architecture-portable productivity for the data-intensive sciences.

Sukumar, Sreenivas R.↗

NASA NTRS2020

Statistical Analysis of Factors Riving Surface Ozone Variability over Continental South Africa

Statistical relationships between surface ozone (O3) concentration, precursor species and meteorological conditions in continental South Africa were examined from data obtained from measurement stations in north-eastern South Africa. Three multivariate statistical methods were applied in the investigation, i.e. multiple linear regression (MLR), principal component analysis (PCA) and –regression (PCR), and generalised additive model (GAM) analysis. The daily maximum 8-h moving average O3 concentrations were considered in these statistical models (dependent variable). MLR models indicated that meteorology and precursor species concentrations are able to explain ~50% of the variability in daily maximum O3 levels. MLR analysis revealed that atmospheric carbon monoxide (CO), temperature and relative humidity were the strongest factors affecting the daily O3 variability. In summer, daily O3 variances were mostly associated with relative humidity, while winter O3 levels were mostly linked to temperature and CO. PCA indicated that CO, temperature and relative humidity were not strongly collinear. GAM also identified CO, temperature and relative humidity as the strongest factors affecting the daily variation of O3. Partial residual plots found that temperature, radiation and nitrogen oxides most likely have a non-linear relationship with O3,while the relationship with relative humidity and CO is probably linear. An inter-comparison between O3 levels modelled with the three statistical models compared to measured O3 concentrations showed that the GAM model offered a slight improvement over the MLR model. These findings emphasise the critical role of regional-scale O3 precursors coupled with meteorological conditions in daily variances of O3 levels in continental South Africa.

multiple linear regression (MLR)↗

NASA NTRSDate not supplied

Training and Validation of Spectral Gap Filling Algorithm for Cpf-Ceres Intercalibration

The Climate Absolute Radiance and Refractivity Observatory (CLARREO) Pathfinder (CPF) mission is set to launch an SI-traceable reflective solar (RS) spectrometer aboard the International Space Station to measure Earth-reflected solar radiation with a radiometric uncertainty of 0.3% (k=1). The CPF intercalibration team has devised a cutting-edge methodology to accurately transfer the benchmark CPF calibration reference to the shortwave (SW) channel (200-5000 nm) of the Clouds and the Earth’s Radiant Energy System (CERES) instrument. The spectral range of CPF measurements spans from 350-2300 nm, while the CERES SW channel measures the Earth-reflected broadband solar radiances between 200 nm to 5 μm. To conduct precise CPF-CERES intercalibration analysis, the CPF-like spectral radiances outside the CPF spectral range need to be estimated to match the CERES SW spectral range. In response, the team has developed a fast algorithm that leverages spectrally redundant information within the CPF-measured portion through principal component analysis (PCA) and utilizes pre-established spectral correlation relationships among wavelengths to extend the CPF spectrum below 350 nm and above 2300 nm. Our results show that the algorithm achieves excellent accuracy in generating the missing energy in the UV and IR portions. The RMS error in the UV region is less than 4.5x10-3 W/m2/sr/nm, while in the IR region, it is smaller than 8x10-5 W/m2/sr/nm. Our methodology was validated using measured EMIT radiance data, which covers the spectral range from 0.381 μm to 2.493 μm. We employed EMIT radiances within the wavelength range of 0.43 – 2.25 μm to generate radiances for both the shorter wavelength range (0.381 – 0.43 μm) and longer wavelength range (2.25 – 2.493 μm). The generated radiances agree very well with the measured EMIT radiances. The standard deviation in the integrated broadband radiances was about 0.1%, and the bias is less than 0.004% for over 1.5 million EMIT measured samples. These statistics show that the spectral gap filling algorithm is robust and effective in substantially reducing the spectral difference-induced uncertainty in the CPF-CERES intercalibration samples.

Qiguang Yang↗

DOE OSTI2016

TU-D-207B-05: Intra-Tumor Partitioning and Texture Analysis of DCE-MRI Identifies Relevant Tumor Subregions to Predict Early Pathological Response of Breast Cancer to Neoadjuvant Chemotherapy

Purpose: To predict early pathological response of breast cancer to neoadjuvant chemotherapy (NAC) based on quantitative, multi-region analysis of dynamic contrast enhancement magnetic resonance imaging (DCE-MRI). Methods: In this institution review board-approved study, 35 patients diagnosed with stage II/III breast cancer were retrospectively investigated using DCE-MR images acquired before and after the first cycle of NAC. First, principal component analysis (PCA) was used to reduce the dimensionality of the DCE-MRI data with a high-temporal resolution. We then partitioned the whole tumor into multiple subregions using k-means clustering based on the PCA-defined eigenmaps. Within each tumor subregion, we extracted four quantitative Haralick texture features based on the gray-level co-occurrence matrix (GLCM). The change in texture features in each tumor subregion between pre- and during-NAC was used to predict pathological complete response after NAC. Results: Three tumor subregions were identified through clustering, each with distinct enhancement characteristics. In univariate analysis, all imaging predictors except one extracted from the tumor subregion associated with fast wash-out were statistically significant (p< 0.05) after correcting for multiple testing, with area under the ROC curve or AUCs between 0.75 and 0.80. In multivariate analysis, the proposed imaging predictors achieved an AUC of 0.79 (p = 0.002) in leave-one-out cross validation. This improved upon conventional imaging predictors such as tumor volume (AUC=0.53) and texture features based on whole-tumor analysis (AUC=0.65). Conclusion: The heterogeneity of the tumor subregion associated with fast wash-out on DCE-MRI predicted early pathological response to neoadjuvant chemotherapy in breast cancer.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

An Efficient Sampling-Based Method for Sensitivity and Uncertainty Analysis Through RAVEN

Sensitivity analysis (SA) and uncertainty quantification (UQ) are now widely recognized as essential parts of analyses for complex nuclear systems. Plenty of well-established methodologies are already available for performing SA and UQ, such as Monte Carlo analysis, adjoint-based method, and variance decomposition. The focus of this summary is on developing an efficient sampling-based approach to perform SA and UQ through RAVEN. RAVEN (Risk Analysis and Virtual control Environment) is a software framework able to perform SA and UQ, currently under development at the Idaho National Laboratory. In literature, a number of approaches have been developed to accelerate the process of SA and UQ for large complex systems, such as principal component analysis (PCA) of input space, input-output correlation analysis, and intersection subspace methods. The fundamental idea is to identify the dominant active directions in the parameter space prior to conducting SA and UQ. The premise is that the number of active directions is much less than the dimensionality of input space. In this work, the PCA or Karhunen-Loeve expansion or SVD method is implemented in RAVEN to identify the active directions. This approach is also combined with the forward sampling approaches, such as Monte Carlo, Grid, Latin Hypercube, and Response Surface Design sampling approaches that are currently available in RAVEN, to perform SA and UQ more efficiently. The summary is organized as follows. In the following section, we present the PCA-based forward sampling approach. The effectiveness and efficiency are discussed in the numerical results section. The paper then ends with a concluding summary. In this summary, we have presented PCA-based forward sampling approach to perform SA and UQ. The goal is to reduce the computational overhead for repetitive executions of complex nuclear systems that are generally required when performing SA and UQ. The control of correlations between input parameters is implemented in RAVEN to better represent the input relationships. In addition, we are currently examining our implementations with more realistic models, and we are also focusing on implementation of some new high-dimensional input reduction techniques in RAVEN. (authors)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Topological Data Analysis for Particulate Gels

Soft gels, formed via the self-assembly of particulate materials, exhibit intricate multiscale structures that provide them with flexibility and resilience when subjected to external stresses. Here, this work combines particle simulations and topological data analysis (TDA) to characterize the complex multiscale structure of soft gels. Our TDA analysis focuses on the use of the Euler characteristic, which is an interpretable and computationally scalable topological descriptor that is combined with filtration operations to obtain information on the geometric (local) and topological (global) structure of soft gels. We reduce the topological information obtained with TDA using principal component analysis (PCA) and show that this provides an informative low-dimensional representation of the gel structure. We use the proposed computational framework to investigate the influence of gel preparation (e.g., quench rate, volume fraction) on soft gel structure and to explore dynamic deformations that emerge under oscillatory shear in various response regimes (linear, nonlinear, and flow). Our analysis provides evidence of the existence of hierarchical structures in soft gels, which are not easily identifiable otherwise. Moreover, our analysis reveals direct correlations between topological changes of the gel structure under deformation and mechanical phenomena distinctive of gel materials, such as stiffening and yielding. In summary, we show that TDA facilitates the mathematical representation, quantification, and analysis of soft gel structures, extending traditional network analysis methods to capture both local and global organization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

The activation of carbon dioxide by first row transition metals (Sc – Zn)

The activation of CO2 by chloride-tagged first-row transition metal anions [ClM]- (M=Sc–Zn), was examined by mass spectrometry, quantum chemical calculations, and statistical analysis. The direct formation of [ClM(CO2)]- complexes was demonstrated in the reaction between [ClM] - and neutral CO2. In addition, the reverse reaction was investigated by energy-variable collisionally induced dissociation (CID) of the corresponding [ClM(CO2)]- anions generated in-source. Five different mono- and bi-dentate binding motifs present in the ion/CO2 complexes were identified by quantum chemical calculations and the relative stability of the each of these isomers was established and analyzed for all first-row transition metals based on the experimental and theoretical ion/molecule binding energies. It was found that the early first row transition metals form strong covalent bonds with the neutral CO2 molecule, while the late in particular copper and zinc are weakly bonded. Using simple valence bond Lewis diagrams, the binding motifs and their relative stabilities across the first row were described in a quantitative manner based on the electronic structure of the individual metals. This analysis provides an explanation for the change of most favorite bonding motif of the transition metals with CO2 along the 1st transition metal row. The nature of the activated CO2 complex and the relationship between its stability and other structural and spectral properties was also analyzed by Principal Component Analysis (PCA) and Artificial Neural Networks.

Blaziak, Kacper↗

DOE OSTI2016

Mini-apps for high performance data analysis

Scaling-up scientific data analysis and machine learning algorithms for data-driven discovery is a grand challenge that we face today. Despite the growing need for analysis from science domains that are generating `Big Data' from instruments and simulations, building high-performance analytical workflows of data-intensive algorithms have been daunting because: (i) the `Big Data' hardware and software architecture landscape is constantly evolving, (ii) newer architectures impose new programming models, and (iii) data-parallel kernels of analysis algorithms and their performance facets on different architectures are poorly understood. To address these problems, we have: (i) identified scalable data-parallel kernels of popular data analysis algorithms, (ii) implemented `Mini-Apps' of those kernels using different programming models (e.g. Map Reduce, MPI, etc.), (iii) benchmarked and validated the performance of the kernels in diverse architectures. In this paper, we discuss two of those Mini-Apps and show the execution of principal component analysis built as a workflow of the Mini-Apps. We show that Mini-Apps enable scientists to (i) write domain-specific data analysis code that scales on most HPC hardware and (ii) and offers the ability (most times with over a 10x speed-up) to analyze data sizes 100 times the size of what off-the-shelf desktop/workstations of today can handle.

Sukumar, Sreenivas R.↗

DOE OSTI2016

On-demand data analytics in HPC environments at leadership computing facilities: Challenges and experiences

Harney, John↗

DOE OSTI2020

XRF-MAPS

x-ray fluorescence (XRF) imaging typically involves the creation and analysis of 3D data sets, where at each scan position a full energy dispersive x-ray spectrum is recorded. This allows one to later process the data in a variety of different approaches, e.g., by spectral region of interest (ROI) summation with or without background subtraction, principal component analysis, or fitting. XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets.

GLOWACKI, ARTHURT↗

DOE OSTI2022

Modeling the Spectral Diversity of Quasars in the Sixteenth Data Release from the Sloan Digital Sky Survey

Abstract We present a new approach to capturing the broad diversity of emission-line and continuum properties in quasar spectra. We identify populations of spectrally similar quasars through pixel-level clustering on 12,968 high signal-to-noise ratio (S/N) spectra from the Sloan Digital Sky Survey (SDSS) in the redshift range of 1.57 < z < 2.4. Our clustering analysis finds 396 quasar spectra that are not assigned to any population, 15 misclassified spectra, and 6 quasars with incorrect redshifts. We compress the quasar populations into a library of 684 high-S/N composite spectra, anchored in redshift space by the Mg ii emission line. Principal component analysis on the library results in an eigenspectrum basis spanning 1067–4007 Å. We model independent samples of SDSS quasar spectra with the eigenbasis, allowing for a free redshift parameter. Our models achieve a median reduced χ 2 on non–broad absorption line quasar spectra that is reduced by 8.5% relative to models using the eigenspectra from the SDSS spectroscopic pipeline. A significant contribution to the relative improvement is from the ability to reconstruct the range of emission-line variation. The redshift estimates from our model are consistent with the Mg ii emission-line redshift with an average offset that displays 51.4% less redshift-dependent variation relative to the SDSS eigenspectra. Our method for developing quasar spectra models can improve automated classification and predict the intrinsic spectrum in regions affected by intervening absorbers such as Ly α , C iv , and Mg ii , thus benefiting studies of large-scale structure.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2010

Soil Components in Heterogeneous Impact Glass in Martian Meteorite EETA79001

Martian soil composition can illuminate past and ongoing near-surface processes such as impact gardening [2] and hydrothermal and volcanic activity [3,4]. Though the Mars Exploration Rovers (MER) have analyzed the major-element composition of Martian soils, no soil samples have been returned to Earth for detailed chemical analysis. Rao et al. [1] suggested that Martian meteorite EETA79001 contains melted Martian soil in its impact glass (Lithology C) based on sulfur enrichment of Lithology C relative to the meteorite s basaltic lithologies (A and B) [1,2]. If true, it may be possible to extract detailed soil chemical analyses using this meteoritic sample. We conducted high-resolution (~0.3 m/pixel) element mapping of Lithology C in thin section EETA79001,18 by energy dispersive spectrometry (EDS). We use these data for principal component analysis (PCA).

Schrader, C. M.↗

DOE OSTI2020

Metabolomics analysis reveals differences in evolution between maize and rice

SUMMARY Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.

Deng, Min↗