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All sources NASA NTRS DOE OSTI

DOE OSTI2022

InClass nets: independent classifier networks for nonparametric estimation of conditional independence mixture models and unsupervised classification

Abstract Conditional independence mixture models (CIMMs) are an important class of statistical models used in many fields of science. We introduce a novel unsupervised machine learning technique called the independent classifier networks (InClass nets) technique for the nonparameteric estimation of CIMMs. InClass nets consist of multiple independent classifier neural networks (NNs), which are trained simultaneously using suitable cost functions. Leveraging the ability of NNs to handle high-dimensional data, the conditionally independent variates of the model are allowed to be individually high-dimensional, which is the main advantage of the proposed technique over existing non-machine-learning-based approaches. Two new theorems on the nonparametric identifiability of bivariate CIMMs are derived in the form of a necessary and a (different) sufficient condition for a bivariate CIMM to be identifiable. We use the InClass nets technique to perform CIMM estimation successfully for several examples. We provide a public implementation as a Python package called RainDancesVI.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRSDate not supplied

A Method for Validating Causal Diagrams of Human Health Risk in Space Flight

The complexity of cause-and-effect relationships between spaceflight hazards and resulting health conditions clouds understanding of the totality of human system risk in space. In response, NASA has introduced Directed Acyclic Graphs (causal diagrams) into the human systems risk management process. These diagrams allow for a common understanding of the mechanisms that lead from unique hazards of spaceflight to the health outcomes important to agencies and astronauts. However, the paucity of available biomedical data from spaceflight creates a need for methods of validating causal models that can accommodate data from spaceflight model analogs. Here we outline one approach utilizing open-access rodent bone datasets from the Ames Life Sciences Data Archive. The properties of directed acyclic graphs themselves can provide an epistemological and statistical framework for validation of a priori causal representations of human system risk in space flight. The assumed causal connections on the graph creates sets of logical implications: variables that – if the causal diagram is correct – should be correlated, as well as sets that should be conditionally independent. By testing these implied correlations and conditional independencies both statistically and heuristically, we can provide evidence for or against specific causal pathways on the causal diagram. In addition to validation of expert-generated causal diagrams, machine learning techniques can learn the most likely structure of a causal diagram from a given dataset. Comparison with and reconciliation between machine-learned causal diagrams and expert-generated diagrams is another technique for challenging assumptions and improving our understanding of causal mechanisms. Accurately representing complex causation is essential to systemic understanding of human health risks in space travel. Having a robust system of validating causal diagrams helps us arrive at more accurate representations of causal systems. This process will be integral to developing the countermeasures necessary for extended exploration of the moon and Mars.

Robert Reynolds↗

NASA NTRS1991

The asymptotic spectra of banded Toeplitz and quasi-Toeplitz matrices

Toeplitz matrices occur in many mathematical, as well as, scientific and engineering investigations. This paper considers the spectra of banded Toeplitz and quasi-Toeplitz matrices with emphasis on non-normal matrices of arbitrarily large order and relatively small bandwidth. These are the type of matrices that appear in the investigation of stability and convergence of difference approximations to partial differential equations. Quasi-Toeplitz matrices are the result of non-Dirichlet boundary conditions for the difference approximations. The eigenvalue problem for a banded Toeplitz or quasi-Toeplitz matrix of large order is, in general, analytically intractable and (for non-normal matrices) numerically unreliable. An asymptotic (matrix order approaches infinity) approach partitions the eigenvalue analysis of a quasi-Toeplitz matrix into two parts, namely the analysis for the boundary condition independent spectrum and the analysis for the boundary condition dependent spectrum. The boundary condition independent spectrum is the same as the pure Toeplitz matrix spectrum. Algorithms for computing both parts of the spectrum are presented. Examples are used to demonstrate the utility of the algorithms, to present some interesting spectra, and to point out some of the numerical difficulties encountered when conventional matrix eigenvalue routines are employed for non-normal matrices of large order. The analysis for the Toeplitz spectrum also leads to a diagonal similarity transformation that improves conventional numerical eigenvalue computations. Finally, the algorithm for the asymptotic spectrum is extended to the Toeplitz generalized eigenvalue problem which occurs, for example, in the stability of Pade type difference approximations to differential equations.

Beam, Richard M.↗

DOE OSTI2020

The Sylvester Graphical Lasso (SyGlasso)

This paper introduces the Sylvester graphical lasso (SyGlasso) that captures multiway dependencies present in tensor-valued data. The model is based on the Sylvester equation that defines a generative model. The proposed model complements the tensor graphical lasso that imposes a Kronecker sum model for the inverse covariance matrix by providing an alternative Kronecker sum model that is generative and interpretable. A nodewise regression approach is adopted for estimating the conditional independence relationships among variables. The statistical convergence of the method is established, and empirical studies are provided to demonstrate the recovery of meaningful conditional dependency graphs. Here we apply the SyGlasso to an electroencephalography (EEG) study to compare the brain connectivity of alcoholic and nonalcoholic subjects. Here, we demonstrate that our model can simultaneously estimate both the brain connectivity and its temporal dependencies.

Wang, Yu↗

DOE OSTI2022

Physics-constrained deep neural network method for estimating parameters in a redox flow battery

Here, in this paper, we present a physics-constrained deep neural network (PCDNN) method for parameter estimation in the zero-dimensional (0D) model of the vanadium redox flow battery (VRFB). In this approach, we use deep neural networks to approximate the model parameters as functions of the operating conditions. This method allows the integration of VRFB computational models as the physical constraints in the parameter learning process, leading to enhanced accuracy of parameter estimation and cell voltage prediction. Using an experimental dataset, we demonstrate that the PCDNN method can estimate model parameters for a range of operating conditions and improve the 0D model prediction of voltage compared to the 0D model prediction with constant operation-condition-independent parameters estimated with traditional inverse methods. We also demonstrate that the PCDNN approach has an improved generalization ability for estimating parameter values for operating conditions not used in the training process.

25 ENERGY STORAGE↗

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 OSTI2023

Dietary uptake of geosmin in rainbow trout ( Oncorhynchus mykiss )

Geosmin is a primary source of muddy/earthy ‘off-flavors’ in farmed fish, which may render their organoleptic quality unacceptable to consumers. Model systems of geosmin uptake typically comprise exposure to waterborne geosmin that is absorbed via the gills. The present research demonstrates dietary exposure as an alternative route of geosmin uptake in Rainbow Trout (Oncorhynchus mykiss) fillets. Trout (average initial weight of 355 g) were stocked in quadruplicate compartmentalized raceways (N = 4 compartments per treatment, n = 50 fish per compartment) supplied with first-use, flow-through water (4.5 complete turnovers per hour). Fish were fed diets containing 0 (control dose), 0.005 (low dose), 0.05 (medium dose), or 0.5 (high dose) mg geosmin/kg feed at 1% body weight/day for four weeks. Fillets (12 fillets/diet/week plus 12 pre-trial fillet samples) and weekly feed and water samples were analyzed via GC–MS to determine geosmin concentrations. Feeding behavior was documented daily according to a four-point scale. ANOVA with post-hoc Tukey tests and polynomial contrast, regression, correlation, and chi-squared statistical analyses were applied to data (α = 0.05 significance level). Palatability of feed did not hinder consumption of the geosmin-spiked feeds: although fish responded positively to all feeds, the most aggressive feeding behavior was observed among those fed medium and high dose feed. Geosmin was effectively imparted into fillets after one week, and no significant temporal effect was found after four weeks. Mean geosmin concentrations significantly increased in fillets from low (mean of 26 ng/kg geosmin) to medium (202 ng/kg) to high (441 ng/kg) dose feed groups during the trial. Polynomial contrasts and regression modeling validated this significant positive effect of dose on geosmin uptake, with an estimated 166 ng/kg rise in fillet-geosmin for every log 10 increase in feed concentration. Waterborne geosmin levels immediately post-feeding were conditionally independent of concentrations in feed and fillets, therefore dietary uptake was affirmed as the predominant mechanism of absorption in the present experimental system. Finally, based on these findings, geosmin-spiked feeds may be used to induce predictable, repeatable levels of this off-flavor compound in fillets and serve as a model system for further investigation of sensory quality and off-flavor mitigation strategies for farm-raised fish.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Implications of rootless geothermal models: Missing processes, parameter compensation, and imposter convection

Numerical models of geothermal systems commonly capture only the top of a reservoir. Deeper areas of the reservoir are simplified to a boundary at the base of the model domain. Commonly, the basal boundary is given either a heat source or a source of mass and enthalpy. Here we developed and present simple numerical experiments which demonstrate that these approaches do not produce the correct model behavior in comparison to a model that captures the entire convecting domain with a heat flux only. We describe a variety of incorrect types of model behavior that arise directly from the choice of boundary condition, independent of the specific parameterization of the model. Heat sources are sensitive to the thickness of the domain and parameters take unphysical values to compensate for the reduced height. The combined mass/heat boundary can produce temperatures that show similarities to circulating geothermal systems, but with incorrect fluid flow and a strong boundary layer focused at the base of the simulated clay cap. These errors likely cause parameters to adjust their values to compensate for the incorrect physics. We highlight these issues and show an example from a developed reservoir model. Initial calibrations to natural state temperature were unsuitable for history matching. The 3D model required parameter adjustments to achieve a more realistic production model. Appropriate mitigation measures should be considered to reduce parameter compensation and improve decision-support models.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Transcriptome-wide association analysis identifies candidate susceptibility genes for prostate-specific antigen levels in men without prostate cancer

Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility for prostate cancer (PCa) screening. Using genome-wide association study (GWAS) summary statistics from 95,768 PCa-free men, we conducted a transcriptome-wide association study (TWAS) to examine impacts of genetically predicted gene expression on PSA. Analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10 × 10 –6 ) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61 × 10 –6 ) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses identified 155 statistically significantly (p < 0.05/22,249 = 2.25 × 10 –6 ) genes. Out of 173 unique PSA-associated genes across analyses, we replicated 151 (87.3%) in a TWAS of 209,318 PCa-free individuals from the Million Veteran Program. Based on conditional analyses, we found 20 genes (11 single tissue, nine cross-tissue) that were associated with PSA levels in the discovery TWAS that were not attributable to a lead variant from a GWAS. Ten of these 20 genes replicated, and two of the replicated genes had colocalization probability of >0.5: CCNA2 and HIST1H2BN. Six of the 20 identified genes are not known to impact PCa risk. Fine-mapping based on whole blood and prostate tissue revealed five protein-coding genes with evidence of causal relationships with PSA levels. Of these five genes, four exhibited evidence of colocalization and one was conditionally independent of previous GWAS findings. These results yield hypotheses that should be further explored to improve understanding of genetic factors underlying PSA levels.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Holographic entropy cone beyond AdS/CFT

We extend all known area inequalities obeyed by Ryu-Takayanagi surfaces of anti–de Sitter boundary regions—the holographic entropy cone—to static generalized entanglement wedges of bulk regions in arbitrary spacetimes. The generalized holographic entropy cone is subject to a mutual independence condition on the bulk regions: each bulk input region must be outside the entanglement wedge of the union of all others. The condition captures when gravitating regions involve fundamentally distinct degrees of freedom despite the nonlocality inherent in the holographic principle.

Quantum gravity↗

DOE OSTI2020

Scaling properties of direct photon yields in heavy ion collisions

Abstract A recent analysis from the PHENIX collaboration of available direct photon measurement results in collisions of various systems such as Au+Au, Cu+Cu, and Pb+Pb, at different beam energies ranging from 39 to 2760 GeV, has shown a universal, within experimental uncertainties, multiplicity scaling, in which direct photon $$p_{T}$$ p T -spectra for transverse momenta up to 2 GeV/ c are scaled with charged hadron pseudorapidity density at midrapidity raised to power $$\alpha =1.25$$ α = 1.25 . On the other hand, those direct photon $$p_{T}$$ p T -spectra also exhibit geometrical scaling in the similar $$p_{T}$$ p T range. Assuming power-law dependence of the scaled photon spectra for both scaling laws, we formulate two independent conditions for the power $$\alpha $$ α , which overshoot experimental data by $$\sim 10\%$$ ∼ 10 % on average. We discuss possible sources that might improve this estimate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides

Abstract Background The oleaginous yeast Rhodotorula toruloides is a promising chassis organism for the biomanufacturing of value-added bioproducts. It can accumulate lipids at a high fraction of biomass. However, metabolic engineering efforts in this organism have progressed at a slower pace than those in more extensively studied yeasts. Few studies have investigated the lipid accumulation phenotype exhibited by R. toruloides under nitrogen limitation conditions. Consequently, there have been only a few studies exploiting the lipid metabolism for higher product titers. Results We performed a multi-omic investigation of the lipid accumulation phenotype under nitrogen limitation. Specifically, we performed comparative transcriptomic and lipidomic analysis of the oleaginous yeast under nitrogen-sufficient and nitrogen deficient conditions. Clustering analysis of transcriptomic data was used to identify the growth phase where nitrogen-deficient cultures diverged from the baseline conditions. Independently, lipidomic data was used to identify that lipid fractions shifted from mostly phospholipids to mostly storage lipids under the nitrogen-deficient phenotype. Through an integrative lens of transcriptomic and lipidomic analysis, we discovered that R. toruloides undergoes lipid remodeling during nitrogen limitation, wherein the pool of phospholipids gets remodeled to mostly storage lipids. We identify specific mRNAs and pathways that are strongly correlated with an increase in lipid levels, thus identifying putative targets for engineering greater lipid accumulation in R. toruloides . One surprising pathway identified was related to inositol phosphate metabolism, suggesting further inquiry into its role in lipid accumulation. Conclusions Integrative analysis identified the specific biosynthetic pathways that are differentially regulated during lipid remodeling. This insight into the mechanisms of lipid accumulation can lead to the success of future metabolic engineering strategies for overproduction of oleochemicals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

MFNets: Multifidelity data-driven networks for Bayesian learning and prediction

This paper presents a multifidelity uncertainty quantification framework called MFNets. We seek to address three existing challenges that arise when experimental and simulation data from different sources are used to enhance statistical estimation and prediction with quantified uncertainty. Specifically, we demonstrate that MFNets can (1) fuse heterogeneous data sources arising from simulations with different parameterizations, e.g simulation models with different uncertain parameters or data sets collected under different environmental conditions; (2) encode known relationships among data sources to reduce data requirements; and (3) improve the robustness of existing multi-fidelity approaches to corrupted data. MFNets construct a network of latent variables (LVs) to facilitate the fusion of data from an ensemble of sources of varying credibility and cost. These LVs are posited as explanatory variables that provide the source of correlation in the observed data. Furthermore, MFNets provide a way to encode prior physical knowledge to enable efficient estimation of statistics and/or construction of surrogates via conditional independence relations on the LVs. We highlight the utility of our framework with a number of theoretical results which assess the quality of the posterior mean as a frequentist estimator and compare it to standard sampling approaches that use single fidelity, multilevel, and control variate Monte Carlo estimators. We also use the proposed framework to derive the Monte Carlo-based control variate estimator entirely from the use of Bayes rule and linear-Gaussian models -- to our knowledge the first such derivation. Finally, we demonstrate the ability to work with different uncertain parameters across different models.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1973

A new technique for Auger analysis of surface species subject to electron-induced desorption

Pepper, S. V.↗

NASA NTRS1973

A new technique for Auger analysis of surface species subject to electron-induced desorption.

A method is presented to observe surface species subject to electron-induced desorption by Auger electron spectroscopy. The surface to be examined is moved under the electron beam at constant velocity, establishing a time-independent condition and eliminating the time response of the electron spectrometer as a limiting factor. The dependence of the Auger signal on the sample velocity, incident electron current, beam diameter, and desorption cross section is analyzed. It is shown that it is advantageous to analyze the moving sample with a high beam current, in contrast to the usual practice of using a low beam current to minimize desorption from a stationary sample. The method is illustrated by the analysis of a friction transfer film of PTFE, in which the fluorine is removed by electron-induced desorption. The method is relevant to surface studies in the field of lubrication and catalysis.

Pepper, S. V.↗

NASA NTRS1975

A dynamic model for the time evolution of the modulated cosmic ray spectrum

A recently developed model predicts an energy dependent phase lag in the modulated cosmic ray density U(t) given by U(t) approximately equal to US (t - tau) where US is the solution to the Fokker-Planck equation under time independent conditions and tau is the average time spent by particles inside the modulating region. The delay times tau are functions of modulating parameters R (the radius of the modulating cavity), V (the solar wind velocity), and K (the effective average diffusion-coefficient which is a function of energy). This model is applied to predict the time evolution of the modulated cosmic ray proton spectrum over a simulated solar cycle. A modulation produced mostly by varying R over the solar cycle is less consistent with the observations.

Ogallagher, J. J.↗

NASA NTRS1982

The possible modifications of the Hisse model for pure LANDSAT agricultural data

An idea, due to A. Feiveson, is presented for relaxing the assumption of class conditional independence of LANDSAT spectral measurements within the same patch (field). Theoretical arguments are given which show that any significant refinement of the model beyond Feiveson's proposal will not allow the reduction, essential to HISSE, of the pure data to patch summary statistics. A slight alteration of the new model is shown to be a reasonable approximation to the model which describes pure data elements from the same patch as jointly Guassian with a covariance function which exhibits exponential decay with respect to spatial separation.

Peters, C.↗

NASA NTRS1981

The possible modifications of the HISSE model for pure LANDSAT agricultural data

A method for relaxing the assumption of class conditional independence of LANDSAT spectral measurements within the same patch (field) is discussed. Theoretical arguments are given which show that any significant refinement of the model beyond this proposal will not allow the reduction, essential to HISSE, of the pure data to patch summary statistics. A slight alteration of the new model is shown to be a reasonable approximation to the model which describes pure data elements from the same patch as jointly Gaussian with a covariance function which exhibits exponential decay with respect to spatial separation.

Peters, C.↗