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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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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Inference of bipolar neutrino flavor oscillations near a core-collapse supernova based on multiple measurements at Earth

Neutrinos in compact-object environments, such as core-collapse supernovae, can experience various kinds of collective effects in flavor space, engendered by neutrino-neutrino interactions. These include “bipolar” collective oscillations, which are exhibited by neutrino ensembles where different flavors dominate at different energies. Considering the importance of neutrinos in the dynamics and nucleosynthesis in these environments, it is desirable to ascertain whether an Earth-based detection could contain signatures of bipolar oscillations that occurred within a supernova envelope. To that end, we, in this study, continue examining a cost-function formulation of statistical data assimilation (SDA) to infer solutions to a small-scale model of neutrino flavor transformation. SDA is an inference paradigm designed to optimize a model with sparse data. Our model consists of two monoenergetic neutrino beams with different energies emanating from a source and coherently interacting with each other and with a matter background, with radially varying interaction strengths. We attempt to infer flavor transformation histories of these beams using simulated measurements of the flavor content at locations “in vacuum” (that is, far from the source), which could in principle correspond to Earth-based detectors. Within the scope of this small-scale model, we found that: (i) based on such measurements, the SDA procedure is able to infer whether bipolar oscillations had occurred within the protoneutron star envelope, and (ii) if the measurements sample the full amplitude of the neutrino oscillations in vacuum, then the amplitude of the prior bipolar oscillations is well predicted. This result intimates that the inference paradigm can well complement numerical integration codes, via its ability to infer flavor evolution at physically inaccessible locations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Implementation of a Binary Neural Network on a Passive Array of Magnetic Tunnel Junctions

The increasing scale of neural networks and their growing application space have produced demand for more energy- and memory-efficient artificial-intelligence-specific hardware. Avenues to mitigate the main issue, the von Neumann bottleneck, include in-memory and near-memory architectures, as well as algorithmic approaches. In this report we leverage the low-power and the inherently binary operation of magnetic tunnel junctions (MTJs) to demonstrate neural network hardware inference based on passive arrays of MTJs. In general, transferring a trained network model to hardware for inference is confronted by degradation in performance due to device-to-device variations, write errors, parasitic resistance, and nonidealities in the substrate. To quantify the effect of these hardware realities, we benchmark 300 unique weight matrix solutions of a two-layer perceptron to classify the Wine dataset for both classification accuracy and write fidelity. Despite device imperfections, we achieve software-equivalent accuracy of up to 95.3% with proper tuning of network parameters in 15 x 15 MTJ arrays having a range of device sizes. The success of this tuning process shows that new metrics are needed to characterize the performance and quality of networks reproduced in mixed signal hardware.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Bayesian differential programming for robust systems identification under uncertainty

This paper presents a machine learning framework for Bayesian systems identification from noisy, sparse and irregular observations of nonlinear dynamical systems. The proposed method takes advantage of recent developments in differentiable programming to propagate gradient information through ordinary differential equation solvers and perform Bayesian inference with respect to unknown model parameters using Hamiltonian Monte Carlo sampling. This allows an efficient inference of the posterior distributions over plausible models with quantified uncertainty, while the use of sparsity-promoting priors enables the discovery of interpretable and parsimonious representations for the underlying latent dynamics. A series of numerical studies is presented to demonstrate the effectiveness of the proposed methods, including nonlinear oscillators, predator–prey systems and examples from systems biology. Taken together, our findings put forth a flexible and robust workflow for data-driven model discovery under uncertainty. All codes and data accompanying this article are available at https://bit.ly/34FOJMj .

Science & Technology - Other Topics↗
DOE OSTI2022

Computer Model Calibration with Time Series Data Using Deep Learning and Quantile Regression

Computer models play a key role in many scientific and engineering problems. One major source of uncertainty in computer model experiments is input parameter uncertainty. Computer model calibration is a formal statistical procedure to infer input parameters by combining information from model runs and observational data. The existing standard calibration framework suffers from inferential issues when the model output and observational data are high-dimensional dependent data, such as large time series, due to the difficulty in building an emulator and the nonidentifiability between effects from input parameters and data-model discrepancy. To overcome these challenges, we, in this work, propose a new calibration framework based on a deep neural network (DNN) with long short-term memory layers that directly emulates the inverse relationship between the model output and input parameters. Adopting the “learning with noise” idea, we train our DNN model to filter out the effects from data-model discrepancy on input parameter inference. We also formulate a new way to construct interval predictions for DNN using quantile regression to quantify the uncertainty in input parameter estimates. Through a simulation study and real data application with the Weather Research and Forecasting Model Hydrological modeling system (WRF-Hydro), we show our approach can yield accurate point estimates and well-calibrated interval estimates for input parameters.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

DeepLensSBI: Deep inference of simulated strong lenses in ground-based surveys

This code is used to train and test machine learning models and generate results and plots presented in 2501.08524 [astro-ph.IM]. The code is written in python. The goal of this work is to train ML models trained on simulated images of strong gravitational lenses. The trained model can then quickly infer properties of the lensed objects with uncertainty quantification.

Poh, Jason [Univ. of Chicago, IL (United States)] ↗
DOE OSTI2024

The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models

Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing (i) the KL divergence between prior and posterior and (ii) the Stein’s loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model

Abstract Motivation The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. Results In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantifying leaf symptoms of sorghum charcoal rot in images of field‐grown plants using deep neural networks

Abstract Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red‐green‐blue images of sorghum plants exhibiting symptoms of infection. EfficientNet‐B3 and a fully convolutional network emerged as the top‐performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet‐B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models’ validation scores increased linearly, and their inference time decreased exponentially. This trend could be attributed to larger patches containing more information, improving model performance, and fewer patches reducing the computational load, thus decreasing inference time. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a foundation for drone‐based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web‐based application where users can easily analyze their own images.

Gonzalez, Emmanuel M.↗
DOE OSTI2021

Finding Liebig’s law of the minimum

Abstract Liebig’s law of the minimum (LLM) is often used to interpret empirical biological growth data and model multiple substrates co‐limited growth. However, its mechanistic foundation is rarely discussed, even though its validity has been questioned since its introduction in the 1820s. Here we first show that LLM is a crude approximation of the law of mass action, the state of art theory of biochemical reactions, and the LLM model is less accurate than two other approximations of the law of mass action: the synthesizing unit model and the additive model. We corroborate this conclusion using empirical data sets of algae and plants grown under two co‐limiting substrates. Based on our analysis, we show that when growth is modeled directly as a function of substrate uptake, the LLM model improperly restricts the organism to be of fixed elemental stoichiometry, making it incapable of consistently resolving biological adaptation, ecological evolution, and community assembly. When growth is modeled as a function of the cellular nutrient quota, the LLM model may obtain good results at the risk of incorrect model parameters as compared to those inferred from the more accurate synthesizing unit model. However, biogeochemical models that implement these three formulations are needed to evaluate which formulation is acceptably accurate and their impacts on predicted long‐term ecosystem dynamics. In particular, studies are needed that explore the extent to which parameter calibration can rescue model performance when the mechanistic representation of a biogeochemical process is known to be deficient.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery

Methods that accelerate the evaluation of molecular properties are essential for chemical discovery. While some degree of ligand additivity has been established for transition metal complexes, it is underutilized in asymmetric complexes, such as the square pyramidal coordination geometries highly relevant to catalysis. To develop predictive methods beyond simple additivity, we apply a many-body expansion to octahedral and square pyramidal complexes and introduce a correction based on adjacent ligands (i.e., the cis interaction model). We first test the cis interaction model on adiabatic spin-splitting energies of octahedral Fe(II) complexes, predicting DFT-calculated values of unseen binary complexes to within an average of 1.4 kcal/mol. Uncertainty analysis reveals the optimal basis, comprising the homoleptic and mer symmetric complexes. We next show that the cis model (i.e., the cis interaction model solved for the optimal basis) infers both DFT- and CCSD(T)-calculated model catalytic reaction energies to within 1 kcal/mol on average. The cis model predicts low-symmetry complexes with reaction energies outside the range of binary complex reaction energies. We observe that trans interactions are unnecessary for most monodentate systems but can be important for some combinations of ligands, such as complexes containing a mixture of bidentate and monodentate ligands. Lastly, we demonstrate that the cis model may be combined with Δ-learning to predict CCSD(T) reaction energies from exhaustively calculated DFT reaction energies and the same fraction of CCSD(T) reaction energies needed for the cis model, achieving around 30% of the error from using the CCSD(T) reaction energies in the cis model alone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Robust inference of ecosystem soil water stress from eddy covariance data

Eddy covariance data are invaluable for determining ecosystem water use strategies under soil water stress. However, existing stress inference methods require numerous subjective data processing and model specification assumptions whose effect on the inferred soil water stress signal is rarely quantified. These uncertainties may confound the stress inference and the generalization of ecosystem water use strategies across multiple sites and studies. In this research, we quantify the sensitivity of soil water stress signals inferred from eddy covariance data to the prevailing data and modeling assumptions (i.e., their robustness) to compile a comprehensive list of sites with robust soil water stress signals and assess the performance of current stress inference methods. To accomplish this, we identify the most prevalent assumptions from the literature and perform a digital factorial experiment to extract probability distributions of plausible soil water stress signals and model performance at 151 FLUXNET2015 and AmeriFlux-FLUXNET sites. Here, we develop a new framework that summarizes these probability distributions to classify and rank the robustness of each site’s soil water stress signal, which we display with a user-friendly heat map. We estimate that only 5%–36% of sites exhibit a robust soil water stress signal due to deficient model performance and poorly constrained ecosystem water use parameters. We also find that the lack of robustness is site-specific, which undermines grouping stress signals by broad ecosystem categories or comparing results across studies with differing assumptions. Lastly, existing stress inference methods appear better suited for eddy covariance sites with grass/annual vegetation. Our findings call for more careful and consistent inference of ecosystem water stress from eddy covariance data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Modeling the immune response to HIV infection

The interplay between immune response and HIV is intensely studied via mathematical modeling, with significant insights but few direct answers. Here in this short review, we highlight advances and knowledge gaps across different aspects of immunity. In particular, we identify the innate immune response and its role in priming the adaptive response as ripe for modeling. The latter have been the focus of most modeling studies, but we also synthesize key outstanding questions regarding effector mechanisms of cellular immunity and development of broadly neutralizing antibodies. Thus far, most modeling studies aimed to infer general immune mechanisms; we foresee that significant progress will be made next by detailed quantitative fitting of models to data, and prediction of immune responses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Modeling the Formation of the Family of the Dwarf Planet Haumea

The dwarf planet (136108) Haumea has an intriguing combination of unique physical properties: near-breakup spin, two regular satellites, and an unexpectedly compact family. While these properties point toward formation by a collision, there is no self-consistent and reasonably probable formation hypothesis that can connect the unusually rapid spin and low relative velocities of Haumea family members (“Haumeans”). We explore and test the proposed formation hypotheses (catastrophic collision, graze-and-merge, and satellite collision) in detail. We flexibly parameterize the properties of the collision (e.g., the collision location) and use simple models for the unique three-dimensional velocity ejection field expected from each model to generate simulated families. These are then compared to the observed Kuiper Belt objects using Bayesian parameter inference, including a mixture model that robustly allows for interlopers from the background population. After testing our methodology, we find that the best match to the observed Haumeans is an essentially isotropic ejection field with a typical velocity of 150 m s{sup −1}. The graze-and-merge formation hypothesis—in which Haumeans are shed due to excess angular momentum—is clearly disfavored because the observed Haumeans are not oriented in a plane. The satellite collision model is also disfavored. Including these new constraints, we present a detailed discussion of the formation hypotheses, including variations, some of which are tested. Some new hypotheses are proposed (a cratering collision and a collision where Haumea’s upper layers are “missing”) and scrutinized. We do not identify a satisfactory formation hypothesis, but we do propose several avenues of additional investigation. In the process of these analyses, we identify many new candidate Haumeans and dynamically confirm seven of them as consistent with the observed family. We also confirm that Haumeans have a shallow size distribution and discuss implications for the discovery and identification of new Haumeans.

79 ASTRONOMY AND ASTROPHYSICS↗