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DOE OSTI2020

Solving differential equations using deep neural networks

Recent work on solving partial differential equations (PDEs) with deep neural networks (DNNs) is presented. The paper reviews and extends some of these methods while carefully analyzing a fundamental feature in numerical PDEs and nonlinear analysis: irregular solutions. First, the Sod shock tube solution to the compressible Euler equations is discussed and analyzed. This analysis includes a comparison of a DNN-based approach with conventional finite element and finite volume methods, and demonstrates that the DNN is competitive in terms of degrees of freedom required for a given accuracy. Further, the DNN-based approach is extended to consider performance improvements and simultaneous parameter space exploration. Next, a shock solution to compressible magnetohydrodynamics (MHD) is solved for, and used in a scenario where experimental data is utilized to enhance a PDE system that is a priori insufficient to validate against the observed/experimental data. This is accomplished by enriching the model PDE system with source terms that are then inferred via supervised training with synthetic experimental data. The resulting DNN framework for PDEs enables straightforward system prototyping and natural integration of large data sets (be they synthetic or experimental), all while simultaneously enabling single-pass exploration of an entire parameter space.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes

Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana . A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.

09 BIOMASS FUELS↗

DOE OSTI2019

Public charging infrastructure for plug-in electric vehicles: What is it worth?

A lack of charging infrastructure is an important barrier to the growth of the plug-in electric vehicle (PEV) market. Public charging infrastructure has tangible and intangible value, such as reducing range anxiety or building confidence in the future of the PEV market. Quantifying the value of public charging infrastructure can inform analysis of investment decisions and can help predict the impact of charging infrastructure on future PEV sales. Estimates of willingness to pay (WTP) based on stated preference surveys are limited by consumers' lack of familiarity with PEVs. As an alternative, we focus on quantifying the tangible value of public PEV chargers in terms of their ability to displace gasoline use for PHEVs and to enable additional electric (e-) vehicle miles for BEVs, thereby mitigating the limitations of shorter range and longer recharging time. Simulation studies provide data that can be used to quantify e-miles enabled by public chargers and the value of additional e-miles can be inferred from econometric estimates of WTP for increased vehicle range. Functions are synthesized that estimate the WTP for public charging infrastructure by plug-in hybrid and battery electric vehicles, conditional on vehicle range, annual vehicle travel, pre-existing charging infrastructure, energy prices, vehicle efficiency, and household income. A case study based on California's public charging network in 2017 indicates that, to the purchaser of a new BEV with a 100-mile range and home recharging, existing public fast chargers are worth about $1500 for intraregional travel, and fast chargers along intercity routes are valued at over $6500.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Simulation-based inference for parameter estimation of complex watershed simulators

High-resolution, spatially distributed process-based (PB) simulators are widely employed in the study of complex catchment processes and their responses to a changing climate. However, calibrating these PB simulators using observed data remains a significant challenge due to several persistent issues, including the following: (1) intractability stemming from the computational demands and complex responses of simulators, which renders infeasible calculation of the conditional probability of parameters and data, and (2) uncertainty stemming from the choice of simplified representations of complex natural hydrologic processes. Here, we demonstrate how simulation-based inference (SBI) can help address both of these challenges with respect to parameter estimation. SBI uses a learned mapping between the parameter space and observed data to estimate parameters for the generation of calibrated simulations. To demonstrate the potential of SBI in hydrologic modeling, we conduct a set of synthetic experiments to infer two common physical parameters – Manning's coefficient and hydraulic conductivity – using a representation of a snowmelt-dominated catchment in Colorado, USA. We introduce novel deep-learning (DL) components to the SBI approach, including an “emulator” as a surrogate for the PB simulator to rapidly explore parameter responses. We also employ a density-based neural network to represent the joint probability of parameters and data without strong assumptions about its functional form. While addressing intractability, we also show that, if the simulator does not represent the system under study well enough, SBI can yield unreliable parameter estimates. Approaches to adopting the SBI framework for cases in which multiple simulator(s) may be adequate are introduced using a performance-weighting approach. The synthetic experiments presented here test the performance of SBI, using the relationship between the surrogate and PB simulators as a proxy for the real case.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1989

Formation of Fourier phase shifts in the solar Ni I 6768 A line

A formalism is developed to understand better how Doppler shifts of spectrum lines as inferred from phase shifts in the Fourier transforms of line profiles are related to the underlying velocity structures which they are intended to measure. With a standard model atmosphere and a simplified, quasi-LTE treatment of line formation, the formalism is applied to the Ni I 6768 A line, which has been selected for use with a network of imaging interferometers under development by the Global Oscillations Network Group for research in helioseismology. Fourier phase shifts are found to be a remarkably linear measure of velocity even in the presence of gradients and unresolved lateral variations in the assumed velocity field. An assumed outward increase in amplitude of a model oscillatory velocity is noticeably reflected in the center-to-limb behavior of the simulated velocity measure, and a sample model of solar granulation is found to have a strong influence on the formation of the Fourier phase.

Jones, Harrison P.↗

DOE OSTI2025

Direct NeTS sampling of nuclear graphite $S(α, β, T)$ in Serpent

For advanced reactor applications, Neural Thermal Scattering (NeTS) modules were developed to predict the thermal scattering law (TSL or $S(α, β, T)$) of a nuclear graphite neutron moderator. NeTS are multi-layer, feedforward artificial neural networks, which act as universal function approximators designed for TSL datasets. In this case, a 4-layer neural network with 164 neurons per layer is trained using FLASSH evaluated data in PyTorch and serialized as a torchscript dictionary to predict $S(α, β, T)$ on-the-fly. Relative, absolute and maximum percent deviations of NeTS from File 7 data generated using the FLASSH code are on the order of 0.01%, 0.1% and 1%, respectively, with low inference latencies of 0.000172 s per $S(α, β, T)$ at a given temperature. Capturing the full dimensionality of possible inelastic neutron-lattice interactions, NeTS functionality is embedded in the Serpent Monte Carlo code, where $S(α, β, T)_{NeTS}$ sampling is conducted on-the-fly and compared to ACE look-up-tables for predicting TREAT criticality. k-eff differences between sampling algorithms of 6 pcm are observed and are within the order of Monte Carlo uncertainty. Compared to discrete and continuous-energy ACE files (30 MB and 131 MB per temperature), the NeTS format is on the order of 200–300 kB for a continuous-temperature, interpolation-free representation of $S(α, β, T)$ and cross sections. NeTS-in-Serpent runtimes comparable with ACE look-up tables are achieved by scaling NeTS for high performance computing architectures with hybrid OpenMP + MPI parallelization. This work validates a novel, self-contained reactor physics framework for predictive cross sections, and demonstrates a general methodology for embedding modern machine learning libraries within existing neutronic analysis frameworks.

Nuclear Criticality Safety Program (NCSP)↗

NASA NTRS1988

Geodetic measurement of deformation east of the San Andreas Fault in Central California

The shear strain rates in the Diablo Range of California have been calculated, and the slip rate along the Calaveras and Paicines faults in Central California have been estimated, on the basis of triangulation and trilateration data from two geodetic networks located between the western edge of the Great Valley and the San Andreas Fault. The orientation of the principal compressive strain predicted from the azimuth of the major structures in the region is N 25 deg E, leading to an average shear strain value that corresponds to a relative shortening rate of 4.5 + or - 2.4 mm/yr. It is inferred that the measured strain is due to compression across the fold of this area. The hypothesized uniform, fault-normal compression within the Coast Ranges is not supported by these results.

Sauber, Jeanne↗

DOE OSTI2021

Data-driven Stellar Models

We developed a data-driven model to map stellar parameters ( T eff , log g , and [Fe/H]) accurately and precisely to broadband stellar photometry. This model must, and does, simultaneously constrain the passband-specific dust reddening vector in the Milky Way, R. The model uses a neural network to learn the (de-reddened) absolute magnitude in one band and colors across many bands, given stellar parameters from spectroscopic surveys and parallax constraints from Gaia. To demonstrate the effectiveness of this approach, we train our model on a data set with spectroscopic parameters from LAMOST, APOGEE, and GALAH, Gaia parallaxes, and optical and near-infrared photometry from Gaia, Pan-STARRS 1, Two Micron All Sky Survey and Wide-field Infrared Survey Explorer. Testing the model on these data sets leads to an excellent fit and a precise—and by construction—accurate prediction of the color–magnitude diagrams in many bands. This flexible approach rigorously links spectroscopic and photometric surveys, and also results in an improved, T eff -dependent R. As such, it provides a simple and accurate method for predicting photometry in stellar evolutionary models. Our model will form a basis to infer stellar properties, distances, and dust extinction from photometric data, which should be of great use in 3D mapping of the Milky Way. Our trained model can be obtained at doi:10.5281/zenodo.3902382.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Geometric GNNs for charged particle tracking at GlueX

Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a point cloud and can be structured as graphs, graph neural networks (GNNs) emerge as an intuitive and effective choice for this task. In this study, we evaluate the GNN model for track finding on the data from the GlueX experiment at Jefferson Lab. We use simulation data to train the model and test on both simulation and real GlueX measurements. We demonstrate that GNN-based track finding outperforms the currently used traditional method at GlueX in terms of segment-based efficiency at a fixed purity while providing faster inferences. We show that the GNN model can achieve significant speedup by processing multiple events in batches, which exploits the parallel computation capability of graphical processing units (GPUs). Finally, we compare the GNN implementation on GPU and field-programmable gate array and describe the trade-off.

batched GNN pipeline↗

DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Source-Resolved Inversion of Elemental Carbon Emissions in California Using Log-Space Bayesian Inference

Elemental carbon (EC), operationally quantified by thermal-optical analysis, is widely used as a proxy for black carbon (BC) relevant to short-term climate forcing and public health. Current EC emission inventories remain highly uncertain, with persistent discrepancies between bottom-up and top-down estimates. In this study, we develop a source-resolved, log-space Bayesian inversion framework applied to estimate California’s statewide EC emissions in 2019. By integrating surface EC measurements from the EPA’s Air Quality System network with high-resolution source contributions simulated by a chemical transport model, we identify a one-third underestimation in the existing statewide EC inventory, requiring an increase of the total from a prior of 8.58 [5.49–13.75] Gg year–1 to a posterior estimate of 12.78 [10.71–15.37] Gg year–1. This discrepancy is primarily driven by substantial underestimations in the power and industrial and off-road mobile sectors. Furthermore, population-weighted exposure analysis reveals a marked sectoral divergence between emission mass and health burden: off-road mobile sources dominate both emissions and exposure, accounting for 31% of statewide exposure, while residential wood combustion contributes 26% of total exposure despite comprising only 19% of total emissions, due to its source proximity to population. These findings underscore the need to update sector-specific EC speciation profiles and demonstrate that mitigation strategies targeting off-road mobile sources and residential wood combustion are critical for reducing EC-related health impacts in California.

Zhang, Jie↗

DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Cosmological parameter estimation with a joint-likelihood analysis of the cosmic microwave background and big bang nucleosynthesis

Here, we present a joint-likelihood analysis of big bang nucleosynthesis (BBN) and cosmic microwave background (CMB) data, consistently combining likelihoods and taking into account uncertainties in nuclear reaction rates for the first time. Bayesian inference is performed on the baryon abundance and the effective number of neutrino species, 𝑁 eff , using a CMB Boltzmann solver in combination with LINX , a new flexible and efficient BBN code. We marginalize over Planck nuisance parameters and nuclear rates to find 𝑁 eff =3.0⁢8$^{+0.15}_{−0.14}$, 2.9⁢4$^{+0.16}_{−0.15}$, or 2.96$^{+0.13}_{−0.14}$, for three separate reaction networks. This framework enables robust testing of the lambda cold dark matter paradigm and its variants with CMB and BBN data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1979

Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

Holmquist, R.↗

NASA NTRS1994

NASA Goddard Earth Sciences Graduate Student Program

The evolution of synoptic-scale dynamics associated with a middle and upper tropospheric cloud event that occurred on 26 November 1991 is examined. The case under consideration occurred during the FIRE CIRRUS-II Intensive Field Observing Period held in Coffeyville, KS during Nov. and Dec., 1991. Using data from the wind profiler demonstration network and a temporally and spatially augmented radiosonde array, emphasis is given to explaining the evolution of the kinematically-derived ageostrophic vertical circulations and correlating the circulation with the forcing of an extensively sampled cloud field. This is facilitated by decomposing the horizontal divergence into its component parts through a natural coordinate representation of the flow. Ageostrophic vertical circulations are inferred and compared to the circulation forcing arising from geostrophic confluence and shearing deformation derived from the Sawyer-Eliassen Equation. It is found that a thermodynamically indirect vertical circulation existed in association with a jet streak exit region. The circulation was displaced to the cyclonic side of the jet axis due to the orientation of the jet exit between a deepening diffluent trough and building ridge. The cloud line formed in the ascending branch of the vertical circulation with the most concentrated cloud development occurring in conjunction with the maximum large-scale vertical motion. The relationship between the large scale dynamics and the parameterization of middle and upper tropospheric clouds in large-scale models is discussed and an example of ice water contents derived from a parameterization forced by the diagnosed vertical motions and observed water vapor contents is presented.

Ackerman, Thomas P.↗

NASA NTRS1994

Extended field observations of cirrus clouds using a ground-based cloud observing system

Ackerman, Thomas P.↗

NASA NTRS2008

Model Effects on GLAS-Based Regional Estimates of Forest Biomass and Carbon

ICESat/GLAS waveform data are used to estimate biomass and carbon on a 1.27 million sq km study area. the Province of Quebec, Canada, below treeline. The same input data sets and sampling design are used in conjunction with four different predictive models to estimate total aboveground dry forest biomass and forest carbon. The four models include nonstratified and stratified versions of a multiple linear model where either biomass or (square root of) biomass serves as the dependent variable. The use of different models in Quebec introduces differences in Provincial biomass estimates of up to 0.35 Gt (range 4.942+/-0.28 Gt to 5.29+/-0.36 Gt). The results suggest that if different predictive models are used to estimate regional carbon stocks in different epochs, e.g., y2005, y2015, one might mistakenly infer an apparent aboveground carbon "change" of, in this case, 0.18 Gt, or approximately 7% of the aboveground carbon in Quebec, due solely to the use of different predictive models. These findings argue for model consistency in future, LiDAR-based carbon monitoring programs. Regional biomass estimates from the four GLAS models are compared to ground estimates derived from an extensive network of 16,814 ground plots located in southern Quebec. Stratified models proved to be more accurate and precise than either of the two nonstratified models tested.

Nelson, Ross↗

NASA NTRS2007

Decision Support Systems for Launch and Range Operations Using Jess

The virtual test bed for launch and range operations developed at NASA Ames Research Center consists of various independent expert systems advising on weather effects, toxic gas dispersions and human health risk assessment during space-flight operations. An individual dedicated server supports each expert system and the master system gather information from the dedicated servers to support the launch decision-making process. Since the test bed is based on the web system, reducing network traffic and optimizing the knowledge base is critical to its success of real-time or near real-time operations. Jess, a fast rule engine and powerful scripting environment developed at Sandia National Laboratory has been adopted to build the expert systems providing robustness and scalability. Jess also supports XML representation of knowledge base with forward and backward chaining inference mechanism. Facts added - to working memory during run-time operations facilitates analyses of multiple scenarios. Knowledge base can be distributed with one inference engine performing the inference process. This paper discusses details of the knowledge base and inference engine using Jess for a launch and range virtual test bed.

Thirumalainambi, Rajkumar↗