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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Evaluating the Performance of Random Forest and Iterative Random Forest Based Methods when Applied to Gene Expression Data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3. We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

iRF-Loop, expression network, Populus Trichocarpa↗
DOE OSTI2025

Randomized Federated Learning Methods for Nonsmooth, Nonconvex, and Hierarchical Optimization (Final Technical Report)

This final technical report summarizes the outcomes of a DOE-funded project on federated scientific machine learning (FL) under nonsmooth, nonconvex, and hierarchical optimization settings. The project develops new mathematical models, algorithms, and theoretical guarantees for decentralized stochastic, bilevel, and minimax optimization problems arising in DOE mission-relevant applications. A unified framework of randomized and zeroth-order federated optimization methods is introduced, providing provable convergence, communication efficiency, and sample-complexity guarantees. The report documents algorithmic design, theoretical analysis, and empirical validation of the proposed federated learning methods. The project also contributes to workforce development through graduate training and dissemination of results via publications and seminars.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Fusion Imaging to Guide Thoracic Endovascular Aortic Repair (TEVAR): A Randomized Comparison of Two Methods, 2D/3D Versus 3D/3D Image Fusion

Purpose: To compare the accuracy of two-dimensional (2D) versus three-dimensional (3D) image fusion for thoracic endovascular aortic repair (TEVAR) image guidance. Materials and Methods: Between December 2016 and March 2018, all eligible patients who underwent TEVAR were prospectively included in a single-center study. Image fusion methods (2D/3D or 3D/3D) were randomly assigned to guide each TEVAR and compared in terms of accuracy, dose area product (DAP), volume of contrast medium injected, fluoroscopy time and procedure time. Results: Thirty-two patients were prospectively included; 18 underwent 2D/3D and 14 underwent 3D/3D TEVAR. The 3D/3D method allowed more accurate positioning of the aortic mask on top of the fluoroscopic images (proximal landing zone error vector: 1.7 ± 3.3 mm) than was achieved by the 2D/3D method (6.1 ± 6.1 mm; p = 0.03). The 3D/3D image fusion method was associated with significantly lower DAP than the 2D/3D method (50.5 ± 30.1 Gy cm{sup 2} for 3D/3D vs. 99.5 ± 79.1 Gy cm{sup 2} for 2D/3D; p = 0.03). The volume of contrast medium injected was significantly lower for the 3D/3D method than for the 2D/3D method (50.6 ± 22.9 ml vs. 98.4 ± 47.9 ml; p = 0.002). Conclusion: Higher image fusion accuracy and lower contrast volume and irradiation dose were observed for 3D/3D image fusion than for 2D/3D during TEVAR. Level of Evidence: II, Randomized trial.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

Randomized Algorithms for Symmetric Nonnegative Matrix Factorization

Symmetric Nonnegative Matrix Factorization (SymNMF) is a technique in data analysis and machine learning that approximates a matrix with a product of a nonnegative, low-rank matrix and it transpose. To design faster and more scalable algorithms for SymNMF we develop two randomized algorithms for its computation. The first method uses randomized matrix sketching to compute an initial low-rank approximation to the input matrix and proceeds to uses this as a low-rank input to rapidly compute a SymNMF. The second methods uses randomized leverage score sampling to approximately solve constrained least squares problems. Many successful methods for SymNMF rely on (approximately) solving sequences of constrained least squares problems. Here, we prove theoretically that leverage score sampling can approximately solve constrained least squares problems to e-accuracy. Finally we demonstrate both methods work in practice by applying them to graph clustering tasks on large real world data sets. These experiments show that our methods approximately maintain solution quality and achieve significant speed ups for both large dense and large sparse problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Application of the locally self-consistent embedding approach to the Anderson model with non-uniform random distributions

Highlights: • Typical Medium Theory (TMT) for the Anderson Localization. • Locally Self-Consistent Multiple Scattering Method (LSMS) for Random Disordered Systems. • Linear Scaling Computational Method for Random Disordered Systems. We apply the recently developed embedding scheme for the locally self-consistent method to random disorder electrons systems. The method is based on the locally self-consistent multiple scattering theory and the typical medium theory. The locally self-consistent multiple scattering theory divides a system into many small designated local interaction zones. The subsystem within each local interaction zone is embedded in a self-consistent field from the typical medium theory. This approximation allows the study of random systems with large numbers of sites. We present results for the three dimensional Anderson model with different random disorder potential distributions. Using the typical density of states as an indicator of Anderson localization, we find that the method can capture the localization for commonly studied disorder potentials. These include the uniform distribution, the Gaussian distribution, and even the unbounded Cauchy distribution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Devices and methods for increasing the speed and efficiency at which a computer is capable of modeling a plurality of random walkers using a particle method

A method for increasing a speed or energy efficiency at which a computer is capable of modeling a plurality of random walkers. The method includes defining a virtual space in which a plurality of virtual random walkers will move among different locations in the virtual space. The method also includes either assigning a corresponding set of ringed neurons in a spiking neural network to a corresponding virtual random walker, or assigning a corresponding set of ringed neurons to a point in the virtual space. Movement of a given virtual random walker is tracked by decoding differences between states of individual neurons in a corresponding given set of ringed neurons. A virtual random walk of the plurality of virtual random walkers is executed using the spiking neural network.

Aimone, James Bradley↗
DOE OSTI2022

Devices and methods for increasing the speed and efficiency at which a computer is capable of modeling a plurality of random walkers using a density method

A method for increasing a speed or energy efficiency at which a computer is capable of modeling a plurality of random walkers. The method includes defining a virtual space in which a plurality of virtual random walkers will move among different locations in the virtual space, wherein the virtual space comprises a plurality of vertices and wherein the different locations are ones of the plurality of vertices. A corresponding set of neurons in a spiking neural network is assigned to a corresponding vertex such that there is a correspondence between sets of neurons and the plurality of vertices, wherein a spiking neural network comprising a plurality of sets of spiking neurons is established. A virtual random walk of the plurality of virtual random walkers is executed using the spiking neural network, wherein executing includes tracking how many virtual random walkers are at each vertex at a given time increment.

Aimone, James Bradley↗
DOE OSTI2022

The Global LAnd Surface Satellite (GLASS) evapotranspiration product Version 5.0: Algorithm development and preliminary validation

An accurate estimation of spatially and temporally continuous global terrestrial evapotranspiration (ET) is essential in the assessment of surface energy, water and carbon cycles. The Global LAnd Surface Satellite (GLASS) ET product Version 4.0 (v4.0) based on the Bayesian model averaging (BMA) method was generated to estimate global terrestrial ET. However, certain uncertainty for the GLASS ET product v4.0 limits its application. In this study, we introduced the deep neural networks (DNN) merging framework to improve terrestrial ET estimation for GLASS ET product Version 5.0 (v5.0) generation by integrating five satellite-derived ET products [Moderate Resolution Imaging Spectroradiometer (MODIS) ET product (MOD16), Shuttleworth–Wallace dual-source ET product (SW), Priestley–Taylor-based ET product (PT-JPL), modified satellite-based Priestley–Taylor ET product (MS-PT) and simple hybrid ET product (SIM)]. We compared the performance of DNN method against other merging methods, including GLASS ET algorithm v4.0 (BMA), the gradient boosting regression tree (GBRT) method and the random forest (RF) method, based on 195 global eddy covariance (EC) flux towers covering observations from 2000 through 2015. Validations indicated that the DNN had the highest accuracy among four merging methods across different land cover types, yielding the highest average determination coefficients (R 2 , 0.62), root-mean-squared-error (RMSE, 24.1 W/m 2 ) and Kling–Gupta efficiency (KGE, 0.77) with a of 99% confidence interval. Compared with GLASS ET algorithm v4.0, the DNN improved on the R 2 by approximately 7% (p < 0.01) and the KGE by 10%. Based on the DNN, we then generated 8-day GLASS ET product v5.0 globally with a 1 km spatial resolution from 2001 to 2015 driven by GLASS vegetation and surface net radiation (R n ) datasets and Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA2) datasets. Finally, this global terrestrial ET product provides a valuable dataset for monitoring regional and global water resources and environmental changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Random Forests as a Viable Method to Select and Discover High-redshift Quasars

We present a method of selecting quasars up to redshift ≈6 with random forests, a supervised machine-learning method, applied to Pan-STARRS1 and WISE data. We find that, thanks to the increasing set of known quasars, we can assemble a training set that enables supervised machine-learning algorithms to become a competitive alternative to other methods up to this redshift. We present a candidate set for the redshift range 4.8–6.3, which includes the region around z = 5.5 where selecting quasars is difficult due to their photometric similarity to red and brown dwarfs. We demonstrate that, under our survey restrictions, we can reach a high completeness (66% ± 7% below redshift 5.6/83{sub -9}{sup +6}% above redshift 5.6) while maintaining a high selection efficiency (78{sub -8}{sup +10}%/94{sub -8}{sup +5}%). Our selection efficiency is estimated via a novel method based on the different distributions of quasars and contaminants on the sky. The final catalog of 515 candidates includes 225 known quasars. We predict the candidate catalog to contain additional 148{sub -33}{sup +41} new quasars below redshift 5.6 and 45{sub -8}{sup +5} above, and we make the catalog publicly available. Spectroscopic follow-up observations of 37 candidates led us to discover 20 new high redshift quasars (18 at 4.6 ≤ z ≤ 5.5, 2 z ~ 5.7). These observations are consistent with our predictions on efficiency. We argue that random forests can lead to higher completeness because our candidate set contains a number of objects that would be rejected by common color cuts, including one of the newly discovered redshift 5.7 quasars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Single-frame far-field diffractive imaging with randomized illumination

We introduce a single-frame diffractive imaging method called randomized probe imaging (RPI). In RPI, a sample is illuminated by a structured probe field containing speckles smaller than the sample’s typical feature size. Quantitative amplitude and phase images are then reconstructed from the resulting far-field diffraction pattern. The experimental geometry of RPI is straightforward to implement, requires no near-field optics, and is applicable to extended samples. When the resulting data are analyzed with a complimentary algorithm, reliable reconstructions which are robust to missing data are achieved. To realize these benefits, a resolution limit associated with the numerical aperture of the probe-forming optics is imposed. RPI therefore offers an attractive modality for quantitative X-ray phase imaging when temporal resolution and reliability are critical but spatial resolution in the tens of nanometers is sufficient. We discuss the method, introduce a reconstruction algorithm, and present two proof-of-concept experiments: one using visible light, and one using soft X-rays.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

A non‐intrusive domain‐decomposition model reduction method for linear steady‐state partial differential equations with random coefficients

Abstract Domain decomposition methods have been proved to be an effective strategy to reduce the dimension of parametric partial differential equations (PDEs). However, existing domain decomposition methods for parametric PDEs are usually intrusive, which means domain decomposition based solvers need to be implemented from scratch for each target parametric PDE. To address this issue, we develop a new non‐intrusive domain‐decomposition model reduction method for linear steady‐state PDEs with random‐field coefficients. As a variant of our previous work by Mu and Zhang, the new method only needs access to the final linear system, that is, the global stiffness matrix and the right hand side, of a deterministic PDE solver, in order to build a domain‐decomposition‐based reduced model without intrusive implementation from scratch. The key idea is to remove the interface condition between sub‐domains and rely on the correlation between columns of the linear system to couple the sub‐domains. The non‐intrusive feature enables the applicability of the proposed method to a broader class of uncertainty quantification problems, where many legacy codes/solvers can be fully reused by our method. Two numerical examples including diffusion equations with random diffusivity and convection‐dominated transport with random velocity, are provided to demonstrate the effectiveness and efficiency of our method.

Zhang, Guannan↗
DOE OSTI2021

Immortal rays: Rethinking random ray neutron transport on GPU architectures

The Random Ray Method (TRRM) is a recently developed adaptation of the Method of Characteristics for neutral particle transport simulations. TRRM has demonstrated excellent performance on 3D nuclear reactor benchmark problems using CPU-based compute systems. When porting to GPU-based systems, however, new performance challenges arise that are unique to processors targeting massive fine-grained parallelism. For smaller problems, or for large problems that are domain decomposed across many computational nodes, the problem size per node has insufficient parallelism to saturate GPU node resources, thus greatly limiting speedup. In this study, we report on a newly developed “immortal ray” variant of TRRM. Here, the immortal ray technique exposes significantly more fine-grained parallelism by fundamentally reformulating the numerical details of ray discretization, resulting in performance tradeoffs with significant overall benefit on GPUs. For very small 2D simulation problems we found the new immortal ray variant allowed for up to a 4.4x speedup when run on a single GPU. For larger 3D simulation problems we found the new variant improved strong scaling by 3x when run on the Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Multivariate Testing of Sampling Techniques to Address Class Imbalance in Building Use Type Classification

This study addresses the challenges inherent in building use type classification, particularly focusing on the issue of class imbalance in the training datasets for machine learning classifiers. We comprehensively analyze the efficacy of various class-balancing sampling techniques. Employing Monte Carlo simulations and Bayesian optimization, we evaluated the performance of multiple sampling methods, including Random Oversampling, Random Undersampling, SMOTE, Borderline-SMOTE, and ADASYN, across a dataset encompassing nine southeastern coastal states of the United States. Our findings reveal that simple random over- and undersampling techniques outperform more sophisticated methods. Additionally, we show inherent value in creating an imbalance in training data to effectively train a machine learning classifier for distinguishing between residential and nonresidential buildings. This study provides valuable guidance for future research on building use type classification research and lays essential groundwork for developing attribute-rich building stock datasets.

Adams, Daniel↗
DOE OSTI2019

Unified feature association networks through integration of transcriptomic and proteomic data

High-throughput multi-omics studies and corresponding network analyses of multi-omic data have rapidly expanded their impact over the last 10 years. As biological features of different types (e.g. transcripts, proteins, metabolites) interact within cellular systems, the greatest amount of knowledge can be gained from networks that incorporate multiple types of -omic data. However, biological and technical sources of variation diminish the ability to detect cross-type associations, yielding networks dominated by communities comprised of nodes of the same type. We describe here network building methods that can maximize edges between nodes of different data types leading to integrated networks. We systematically rank several network inference methods and demonstrate that, in many cases, using a random forest method, GENIE3, produces the most integrated networks. This increase in integration does not come at the cost of accuracy as GENIE3 produces networks of approximately the same quality as the other network inference methods tested here. Using GENIE3, we also infer networks representing antibody-mediated Dengue virus cell invasion and receptor-mediated Dengue virus invasion. A number of functional pathways showed centrality differences between the two networks including genes responding to both GM-CSF and IL-4, which had a higher centrality value in an antibody-mediated vs. receptor-mediated Dengue network. Because a biological system involves the interplay of many different types of molecules, incorporating multiple data types into networks will improve their use as models of biological systems. The methods explored here are some of the first to specifically highlight and address the challenges associated with how such multi-omic networks can be assembled and how the greatest number of interactions can be inferred from different data types. The resulting networks can lead to the discovery of new host response patterns and interactions during viral infection, generate new hypotheses of pathogenic mechanisms and confirm disease associated mechanisms of disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

The co-expression extrapolation (COXEN) method has been successfully used in multiple studies to select genes for predicting the response of tumor cells to a specific drug treatment. Here, we enhance the COXEN method to select genes that are predictive of the efficacies of multiple drugs for building general drug response prediction models that are not specific to a particular drug. The enhanced COXEN method first ranks the genes according to their prediction power for each individual drug and then takes a union of top predictive genes of all the drugs, among which the algorithm further selects genes whose co-expression patterns are well preserved between cancer cases for building prediction models. We apply the proposed method on benchmark in vitro drug screening datasets and compare the performance of prediction models built based on the genes selected by the enhanced COXEN method to that of models built on genes selected by the original COXEN method and randomly picked genes. Models built with the enhanced COXEN method always present a statistically significantly improved prediction performance (adjusted p-value ≤ 0.05). Our results demonstrate the enhanced COXEN method can dramatically increase the power of gene expression data for predicting drug response.

60 APPLIED LIFE SCIENCES↗