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NASA NTRS2002

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Weber, Ryan↗

DOE OSTI2023

Efficient Probabilistic Prediction and Uncertainty Quantification of Tropical Cyclone–Driven Storm Tides and Inundation

Abstract This study proposes and assesses a methodology to obtain high-quality probabilistic predictions and uncertainty information of near-landfall tropical cyclone–driven (TC-driven) storm tide and inundation with limited time and resources. Forecasts of TC track, intensity, and size are perturbed according to quasi-random Korobov sequences of historical forecast errors with assumed Gaussian and uniform statistical distributions. These perturbations are run in an ensemble of hydrodynamic storm tide model simulations. The resulting set of maximum water surface elevations are dimensionality reduced using Karhunen–Loève expansions and then used as a training set to develop a polynomial chaos (PC) surrogate model from which global sensitivities and probabilistic predictions can be extracted. The maximum water surface elevation is extrapolated over dry points incorporating energy head loss with distance to properly train the surrogate for predicting inundation. We find that the surrogate constructed with third-order PCs using elastic net penalized regression with leave-one-out cross validation provides the most robust fit across training and test sets. Probabilistic predictions of maximum water surface elevation and inundation area by the surrogate model at 48-h lead time for three past U.S. landfalling hurricanes (Irma in 2017, Florence in 2018, and Laura in 2020) are found to be reliable when compared to best track hindcast simulation results, even when trained with as few as 19 samples. The maximum water surface elevation is most sensitive to perpendicular track-offset errors for all three storms. Laura is also highly sensitive to storm size and has the least reliable prediction. Significance Statement The purpose of this study is to develop and evaluate a methodology that can be used to provide high-quality probabilistic predictions of hurricane-induced storm tide and inundation with limited time and resources. This is important for emergency management purposes during or after the landfall of hurricanes. Our results show that sampling forecast errors using quasi-random sequences combined with machine learning techniques that fit polynomial functions to the data are well suited to this task. The polynomial functions also have the benefit of producing exact sensitivity indices of storm tide and inundation to the forecasted hurricane properties such as path, intensity, and size, which can be used for uncertainty estimation. The code implementing the presented methodology is publicly available on GitHub.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Decoding the proton’s gluonic density with lattice QCD-informed machine learning

We present a first machine learning-based decoding of the gluonic structure of the proton from lattice QCD using a variational autoencoder inverse mapper (VAIM). Harnessing the power of generative AI, we predict the parton distribution function (PDF) of the gluon given information on the reduced pseudo-Ioffe-time distributions (RpITDs) as calculated from an ensemble with lattice spacing a ≈ 0.09 fm and a pion mass of M π ≈ 310 MeV. The resulting gluon PDF is consistent with phenomenological global fits within uncertainties, particularly in the intermediate-to-high-x region where lattice data are most constraining. A subsequent correlation analysis confirms that the VAIM learns a meaningful latent representation, highlighting the potential of generative AI to bridge lattice QCD and phenomenological extractions within a unified analysis framework.

Gluon parton distribution function↗

DOE OSTI2023

Deep neural network uncertainty quantification for LArTPC reconstruction

We evaluate uncertainty quantification (UQ) methods for deep learning applied to liquid argon time projection chamber (LArTPC) physics analysis tasks. As deep learning applications enter widespread usage among physics data analysis, neural networks with reliable estimates of prediction uncertainty and robust performance against overconfidence and out-of-distribution (OOD) samples are critical for their full deployment in analyzing experimental data. While numerous UQ methods have been tested on simple datasets, performance evaluations for more complex tasks and datasets are scarce. Here we assess the application of selected deep learning UQ methods on the task of particle classification using the PiLArNet monte carlo 3D LArTPC point cloud dataset. We observe that UQ methods not only allow for better rejection of prediction mistakes and OOD detection, but also generally achieve higher overall accuracy across different task settings. We assess the precision of uncertainty quantification using different evaluation metrics, such as distributional separation of prediction entropy across correctly and incorrectly identified samples, receiver operating characteristic curves (ROCs), and expected calibration error from observed empirical accuracy. We conclude that ensembling methods can obtain well calibrated classification probabilities and generally perform better than other existing methods in deep learning UQ literature.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Arctic Tipping Points Triggering Global Change (LDRD Final Report)

The Arctic is warming and feedbacks in the coupled Earth system may be driving the Arctic to tipping events that could have critical downstream impacts for the rest of the globe. In this project we have focused on analyzing sea ice variability and loss in the coupled Earth system Summer sea ice loss is happening rapidly and although the loss may be smooth and reversible, it has significant consequences for other Arctic systems as well as geopolitical and economic implications. Accurate seasonal predictions of sea ice minimum extent and long-term estimates of timing for a seasonally ice-free Arctic depend on a better understanding of the factors influencing sea ice dynamics and variation in this strongly coupled system. Under this project we have investigated the most influential factors in accurate predictions of September Arctic sea ice extent using machine learning models trained separately on observational data and on simulation data from five E3SM historical ensembles. Monthly averaged data from June, July, and August for a selection of ice, ocean, and atmosphere variables were used to train a random forest regression model. Gini importance measures were computed for each input feature with the testing data. We found that sea ice volume is most important earlier in the season (June) and sea ice extent became a more important predictor closer to September. Results from this study provide insight into how feature importance changes with forecast length and illustrates differences between observational data and simulated Earth system data. We have additionally performed a global sensitivity analysis (GSA) using a fully coupled ultra- low resolution configuration E3SM. To our knowledge, this is the first global sensitivity analysis involving the fully-coupled E3SM Earth system model. We have found that parameter variations show significant impact on the Arctic climate state and atmospheric parameters related to cloud parameterizations are the most significant. We also find significant interactions between parameters from different components of E3SM. The results of this study provide invaluable insight into the relative importance of various parameters from the sea ice, atmosphere and ocean components of the E3SM (including cross-component parameter interactions) on various Arctic-focused quantities of interest (QOIs).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Leveraging AI and Spatial Data to Unlock Pipeline Integrity Insights: NETL’s Advanced Infrastructure Integrity Model (AIIM)

Maintaining the integrity of natural gas infrastructure plays a critical role in ensuring energy security. Robust, data-driven foundational AI models for pipeline integrity can help address risk management and mitigation issues. Trusted foundational models can help with industry adoption and accelerate innovation by enhancing integrity predictions, reduce costs, and informing infrastructure build-out. The AIIM dashboard was released in 2022 and utilizes multi-ML models for ensemble-type insights. It was expanded to include analytics on reported incidents. It was developed as an ESRI Dashboard to support data visualization & interrogation and contains pipeline data and model results.

Advanced Infrastructure Integrity Model (AIIM)↗

NASA NTRS1987

Atmospheric correlation-time measurements and effects on coherent Doppler lidar

The time for which the backscatter from an ensemble of atmospheric aerosol particles remains coherent was studied by using a pulsed TEA CO2 lidar with coherent detection. Experimental results are compared with predictions by using model pulse shapes appropriate for TEA CO2 laser transmitters. The correlation time of the backscatter return signal is important in studies of atmospheric turbulence and its effects on optical propagation and backscatter. Techniques for its measurement are discussed and evaluated.

Ancellet, Gerard M.↗

NASA NTRS1991

The effect of anisotropic emission from thick accretion disks on the luminosity functions of active galactic nuclei

High-luminosity active galactic nuclei (AGNs) powered by accretion onto a massive black hole (or other compact object) may have bolometric luminosities dominated by thermal emission from a geometrically thick accretion disk. Radiation from these disks is strongly anisotropic, which has important consequences for the observed luminosity distribution, and therefore for systematic biases in flux-limited samples. The effect of anisotropic emission from an ensemble of AGNs with random oriented thick disks radiating at or near the Eddington limit is calculated. Because of their higher luminosities, it is predicted face-on disks should constitute an increasing fraction of observed high-redshift, high-luminosity AGNs. Comparison of the results with observed quasar luminosity functions suggests a narrow mass distribution with an upper limit of about a billion solar masses for high-redshift quasars.

Urry, C. M.↗

NASA NTRS2003

Resonance Effects in the NASA Transonic Flutter Cascade Facility

Investigations of unsteady pressure loadings on the blades of fans operating near the stall flutter boundary are carried out under simulated conditions in the NASA Transonic Flutter Cascade facility (TFC). It has been observed that for inlet Mach numbers of about 0.8, the cascade flowfield exhibits intense low-frequency pressure oscillations. The origins of these oscillations were not clear. It was speculated that this behavior was either caused by instabilities in the blade separated flow zone or that it was a tunnel resonance phenomenon. It has now been determined that the strong low-frequency oscillations, observed in the TFC facility, are not a cascade phenomenon contributing to blade flutter, but that they are solely caused by the tunnel resonance characteristics. Most likely, the self-induced oscillations originate in the system of exit duct resonators. For sure, the self-induced oscillations can be significantly suppressed for a narrow range of inlet Mach numbers by tuning one of the resonators. A considerable amount of flutter simulation data has been acquired in this facility to date, and therefore it is of interest to know how much this tunnel self-induced flow oscillation influences the experimental data at high subsonic Mach numbers since this facility is being used to simulate flutter in transonic fans. In short, can this body of experimental data still be used reliably to verify computer codes for blade flutter and blade life predictions? To answer this question a study on resonance effects in the NASA TFC facility was carried out. The results, based on spectral and ensemble averaging analysis of the cascade data, showed that the interaction between self-induced oscillations and forced blade motion oscillations is very weak and can generally be neglected. The forced motion data acquired with the mistuned tunnel, when strong self-induced oscillations were present, can be used as reliable forced pressure fluctuations provided that they are extracted from raw data sets by an ensemble averaging procedure.

Lepicovsky, J.↗

NASA NTRS2019

Near Real-Time Sub/Seasonal Prediction of Aerosol at NASA Global Modeling and Assimilation Office

A new version of the coupled modeling and analysis system used to produce near real time subseasonal to seasonal forecasts was released over a year ago by the NASA/Goddard Global Modeling and Assimilation Office. The model runs at approximately 1/2 degree globally in the atmosphere and ocean, contains a realistic description of the cryosphere, and includes an interactive aerosol model. The data assimilation used to produce initial conditions is weakly coupled, in which the atmosphere-only assimilated state is coupled to an ocean data assimilation system using a Local Ensemble Transform Kalman Filter. Here will briefly describe the new system, and show results of aerosol-derived air quality from an extensive series of retrospective forecasts. The interactive aerosol is shown to improve seasonal time scale prediction skill during some "forecasts of oppurtunity". Plans for a future version of the system with predicted biomass burning from fires will also be discussed.

Molod, Andrea M.↗

DOE OSTI2025

Lattice QCD Calculation of the Subtraction Function in Forward Compton Amplitude

The subtraction function plays a pivotal role in calculations involving the forward Compton amplitude, which is crucial for predicting the Lamb shift in muonic atoms, as well as the proton-neutron mass difference. In this Letter, we present a lattice QCD calculation of the subtraction function using two domain wall fermion gauge ensembles near the physical pion mass. We utilize a recently proposed subtraction point, demonstrating its advantage in mitigating statistical and systematic uncertainties by eliminating the need for ground-state subtraction. Our results reveal significant contributions from N⁢π intermediate states to the subtraction function. Incorporating these contributions, we compute the proton, neutron, and nucleon isovector subtraction functions at photon momentum transfer Q 2 ϵ[0,2] GeV 2 . For the proton subtraction function, we compare our lattice results with chiral perturbation theory prediction at low Q 2 and with the results from the perturbative operator-product expansion at high Q 2 . Finally, using these subtraction functions as input, we determine their contribution to two-photon exchange effects in the Lamb shift and isovector nucleon electromagnetic self-energy.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Challenges of COVID-19 Case Forecasting in the US, 2020–2021

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub ( https://covid19forecasthub.org ). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1–4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Degenerate parametric down-conversion facilitated by exciton-plasmon polariton states in a nonlinear plasmonic cavity

Abstract We study the effect of degenerate parametric down-conversion (DPDC) in an ensemble of two-level quantum emitters (QEs) coupled via near-field interactions to a single surface plasmon (SP) mode of a nonlinear plasmonic cavity. For this purpose, we develop a quantum driven-dissipative model capturing non-equilibrium dynamics of the system in which incoherently pumped QEs have transition frequency tuned near the second-harmonic response of the SPs. Considering the strong coupling regime, i.e. the SP-QE interaction rate exceeds system dissipation rates, we find a critical SP-QE coupling attributed to the phase transition between normal and lasing steady states. Examining fluctuations above the system’s steady states, we predict new elementary excitations, namely, the exciton-plasmon polaritons formed by the two-SP quanta and single-exciton states of QEs. The contribution of two-SP quanta results in the linear scaling of the SP-QE interaction rate with the number of QEs,  o , as opposed to the  o -scaling known for the Dicke and Tavis–Cummings models. We further examine how SP-QE interaction scaling affects the polariton dispersions and power spectra in the vicinity of the critical coupling. For this purpose, we compare the calculation results assuming a finite ensemble of QEs and the model thermodynamic limit. The calculated power spectra predict an interplay of coherent photon emission by QEs near the second-harmonic frequency and correlated photon-pair emission at the fundamental frequency by the SPs (i.e. the photonic DPDC effect).

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NASA NTRSDate not supplied

Extreme Precipitation in the Southern US Great Plains in the Spring of 2015: Mechanisms and Prediction

During May of 2015, the southern US Great Plains and adjacent Gulf Coast region experienced more than twice the long-term mean precipitation, making it the wettest May since 1895. We investigate the physical mechanisms associated with this event using a suite of large-ensemble regional replay AGCM simulations from the NASA-GEOS model. In these simulations, certain regions of the globe are constrained to closely follow observations while the remainder of the domain is free running, allowing for the isolation of the remote regions that were important for the event. Preliminary analysis provides evidence that the extreme southern US precipitation was linked in part to positive precipitation anomalies in the central and eastern tropical Pacific via a wave train, which ultimately caused anomalous moisture flux from the Gulf of Mexico. An analysis of Subseasonal Experiment (SubX) model output was conducted to explore the subseasonal prediction skill of the event. Several models are able the predict the presence of positive precipitation anomalies in or near the southern US at lead times exceeding 10 days, albeit with errors in the locations and magnitude of the heaviest precipitation anomalies. A more thorough investigation with version 2 of NASA’s GEOS-S2S model shows that the prediction skill stems from the model’s ability to reasonably predict the positive tropical Pacific precipitation anomalies and the initiation of the Rossby wave train that is believed to be linked to the event. The potential causes for limitations in the prediction skill of this event will be explored.

Great Plains↗

DOE OSTI2024

A method for examining ensemble averaging forms during the transition to turbulence in HED systems for application to RANS models

This paper discusses a strategy to initialize a two-dimensional (2D) Reynolds-averaged Navier–Stokes model [LANL's Besnard–Harlow–Rauenzahn (BHR) model] in order to describe an unsteady transitional Richtmyer–Meshkov (RM)-induced flow observed in on-going high-energy-density ensemble experiments performed on the OMEGA-EP facility. The experiments consist of a nominal single-mode perturbation (initial amplitude a 0 ≈ 10 and wavelength $λ$ = 100μm) with target-to-target variations in the surface roughness subjected to the RM instability with delayed Rayleigh–Taylor in a heavy-to-light configuration. Our strategy leverages high-resolution three-dimensional (3D) implicit large eddy simulations (ILES) simulations to initialize BHR-relevant parameters and subsequently validate the 2D BHR results against the 3D ILES simulations. A suite of five 3D ILES simulations corresponding to five experimental target profiles is undertaken to generate an ensemble dataset. Using ensemble averages from the 3D simulations to initialize the turbulent kinetic energy in the BHR model ( K 0 ) demonstrates the ability of the model to predict the time evolution of the interface as well as the density-specific-volume covariance, b . To quantify the sensitivity of the BHR results to the choice of K 0 and the initial turbulent length scale, S 0 , we execute a parameter sweep spanning four orders of magnitude for both S 0 and K 0 , generating a parameter space consisting of 26 simulations. The Pearson's correlation coefficient is used as a measure of discrepancy between the 2D BHR and 3D ILES simulations and reveals that the ranges 8≲S 0 ≲20 μm and 10 9 ≲K 0 ≲10 10 cm 2 /s 2 produce predictions that agree best with the 3D ILES results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Synthetic light-cone catalogues of modern redshift and weak lensing surveys with abacussummit

ABSTRACT The joint analysis of different cosmological probes, such as galaxy clustering and weak lensing, can potentially yield invaluable insights into the nature of the primordial Universe, dark energy, and dark matter. However, the development of high-fidelity theoretical models is a necessary stepping stone. Here, we present public high-resolution weak lensing maps on the light-cone, generated using the N-body simulation suite abacussummit, and accompanying weak lensing mock catalogues, tuned to the Early Data Release small-scale clustering measurements of the Dark Energy Spectroscopic Instrument. Available in this release are maps of the cosmic shear, deflection angle, and convergence fields at source redshifts ranging from z = 0.15 to 2.45 as well as cosmic microwave background convergence maps for each of the 25 base-resolution simulations ($L_{\rm box} = 2000\, h^{-1}\, {\rm Mpc}$ and Npart = 69123) as well as for the two huge simulations ($L_{\rm box} = 7500\, h^{-1}\, {\rm Mpc}$ and Npart = 86403) at the fiducial abacussummit cosmology. The pixel resolution of each map is 0.21 arcmin, corresponding to a healpix Nside of 16 384. The sky coverage of the base simulations is an octant until z ≈ 0.8 (decreasing to about 1800 deg2 at z ≈ 2.4), whereas the huge simulations offer full-sky coverage until z ≈ 2.2. Mock lensing source catalogues are sampled matching the ensemble properties of the Kilo-Degree Survey, Dark Energy Survey, and Hyper Suprime-Cam data sets. The mock catalogues are validated against theoretical predictions for various clustering and lensing statistics, such as correlation multipoles, galaxy–shear, and shear–shear, showing excellent agreement. All products can be downloaded via a Globus endpoint (see Data Availability section).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1987

The effect of increased horizontal resolution on GLA Fourth Order model forecasts

A benchmark series of ten-day weather forecasts has been run with the GLA Fourth Order GCM with both a 4 deg latitude by 5 deg longitude resolution and a 2 deg latitude by 2.5 deg longitude resolution. Ensemble statistics of forecast skill and maps of systematic error fields have been generated for both resolutions. The enhanced resolution added 24 hours of useful predictive skill to the sea level pressure forecasts and 6 hours to the 500 mb height forecasts, but 5 to 6 days into the forecasts the advantage of the finer resolution was lost. The systematic error fields showed that by 8 days the 'climate drift' of the 2 x 2.5 deg forecasts had become pronounced and had caused the loss of predictive skill relative to the 4 x 5 deg forecasts. Additional results indicate that a gravity wave drag parameterization scheme might alleviate the climate drift problem.

Helfand, H. M.↗