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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 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

BEE - FY20 P6-3: Release BEEWorkflowManager, BEETaskManager, and client application 2.3.6.01 – LANL ATDM ST / STNS01-4 P6 Milestone Completion Documentation

Release BEEWorkflowManager, BEETaskManager, and client software. The BEEWorkflowManager daemon runs on the HPC cluster login node. It accepts workflows submitted by the BEE client. These workflows are specified using the Common Workflow Language (CWL) standard. The BEEWorkflowManager loads workflows into the Neo4j graph database to create the workflow directed acyclic graph (DAG), and submits the workflow tasks to the BEETaskManager for execution. The BEEWorkflowManager records the state of the workflow and its tasks, and communicates this state to the BEE client. The BEEWorkflowManager will start, pause, and cancel a running workflow and its tasks at the command of the BEE client. The BEETaskManager daemon runs on the HPC cluster login node. It accepts tasks from the BEEWorkflowManager, turns those tasks into HPC resource manager jobs (e.g. a slurm job script), and submits the job to the cluster resource manager. The BEETaskManager then tracks the status of the job (pending, running, complete) and updates the BEEWorkflowManager. The BEETaskManager will also cancel a queued or running job when commanded to do so by the BEEWorkflowManager. The first release of the BEETaskManager will support the Slurm resource manager and the Charliecloud linux container runtime.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Representing Complex Systems as Graphs for Debugging and Predictive Maintenance-Preliminary Thoughts

Representing complex systems as graphs enables use of mathematical tools to identify faults or predict failures. Graph nodes correspond to individual modules or subsystems, and edges link coupled system parts. ‘Probes’ measure the node outputs, monitoring the system health for unexpected behavior. Assuming one cannot probe every point, within a system, the fault correlates to a region—not necessarily the specific location. Bayesian networks trained to understand fault patterns can accurately identify the source. The diagnostic tool described aides debugging by pinpointing system failure causes. For predictive maintenance, probe data develop probability distribution functions describing subsystem mean time to failure. Unit lifetime can be estimated through these probability distributions. Two approaches include using Bayesian classifiers to infer the system failure source and developing maintenance schedules by treating systems as collections of random variables. When failure behavior does not follow a closed form function, use of similarity models is proposed.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Machine learning assisted search for Fe–Co–C ternary compounds with high magnetic anisotropy

We employ a machine learning (ML)-guided framework to explore rare earth free magnetic materials, specifically focusing on Fe–Co–C ternary compounds for potential use in permanent magnets. Utilizing a specifically trained crystal graph convolutional neural network model, we efficiently screen a vast space of nearly a million substitutional structures to select 620 promising structures for further investigation by first-principles calculation. We predict five low-energy metastable Fe–Co–C compounds with formation energy less than 150 meV/atom above the convex hull. These compounds exhibit high magnetization (Js > 1.0 T) and significant magnetic anisotropy (K1 > 1.0 MJ/m3), making them promising candidates for permanent magnet applications. The phonon calculations indicate these compounds are dynamically stable. Our ML-guided framework demonstrates the utility of rapidly identifying novel materials with tailored magnetic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Risk-Aware Measurement Synchronization and Recovery for DSSE With Heterogeneous Data Sources

Power distribution systems are increasingly integrating heterogeneous sensors with varying data reporting rates and types, which pose challenges to achieving observability at the desired temporal resolution of distribution system state estimation (DSSE). Multisensor failures caused by extreme events exacerbate these issues, introducing substantial uncertainties into DSSE. This article proposes a novel solution to these challenges by ensuring high-resolution system observability despite heterogeneous data sources and multisensor failures. First, a deep learning architecture combining long short-term memory (LSTM) and graph convolutional network (GCN) is employed to synchronize meters with different reporting rates, aiming to achieve system observability. A random-walk-model-based approach is introduced to generate pseudo-measurements while properly characterizing their uncertainties under multisensor failures. Finally, a disaster-risk-informed observability metric (RiOM) is defined to quantify the uncertainty associated with state estimation results. The proposed framework offers deeper insights into the system observability on the fly compared with conventional analysis. The effectiveness of the framework is demonstrated on an IEEE standard test case and a large-scale real-world distribution feeder in mid-Minnesota in the U.S.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Acoustic-based monitoring and machine learning of component status for microreactor applications

This report provides a description and assessment of recent efforts to couple acoustic-based experimental measurements and characterization with machine learning models in order to enhance structural health monitoring capabilities for nuclear microreactors. With resilient embedded sensors in development by others supported by programs funded by the US Department of Energy’s Office of Nuclear Energy, the work described herein builds upon ongoing efforts to improve non-destructive testing technology that relates measured acoustic signatures to component stresses and/or structural defects, using a combination of new experimental measurements and machine learning architectures. The experimental procedure remained similar to that developed for the previous year’s demonstration of damage detection by the authors, with the same damaged sample tested under similar applied stress conditions. Notably, a new mounting fixture was designed and implemented to improve measurement consistency and a more sophisticated laser Doppler vibrometer was employed to make high-fidelity vibration measurements. Two nominally identical sets of training data were collected for each experimental setup to better understand the repeatability of the experiment and to better test the generality of trained neural network models. Additionally, we obtained new high-quality 3D mode shapes of the damaged test article at various stress and excitation levels, providing greater insights into the physical response of the sample during testing. Previously, we demonstrated that a machine learning model based on a convolutional neural network can predict structural details of an artificially introduced interface (intact, rough cut, smooth cut), and the applied torque level. In this study, we have transitioned to graph-based neural network architectures to better develop and test a flexible framework that is more suitable to being transferred away from controlled benchtop experiments and into more applied settings where less-structured data inputs may be expected. In general, performance testing of a graph neural network on frequency-domain representations of the data indicates strong and consistent identification of test conditions for datasets recorded on damaged components. With goals of predicting damage location and other changing experimental conditions using limited datasets, predictive models using a graph neural network architecture correctly predicted the applied torque level with an accuracy of 85% using only a single measurement point and predicted within one torque level in 95% of test windows. Predictions of damage location had limited success due to the symmetry and minimal number of the damage scenarios presented during model training. Results were ambiguous as to whether the model could detect the location of the artificial damage, or if it was instead learning the location of a given measurement point on the part and subsequently detecting which points were closest to the location of the damage. This finding will be factored into upcoming planned work on damaged graphite components, where new experimental tests with a larger number and variety of damage scenarios are expected to provide improved validation of recent developments in monitoring methodology.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

ERAD: A Graph-Based Tool for Energy Resilience Analysis of Electric Distribution Systems

Understanding the impact of extreme events on people's ability to access energy is crucial for designing resilient energy systems. In the event of a disaster, damage to the electric system and related infrastructure (e.g., downed power lines, flooded equipment, hacked communication systems, damaged roads, etc.) can impact people's access to critical services, including not just electricity but also shelter, food, healthcare, and more. There is a key need to understand such impacts better and evaluate options to improve energy resilience. The Energy Resilience Analysis for Electric Distribution Systems (ERAD) tool is a free and open-source software package designed to help researchers and decision-makers analyze and improve energy system resilience.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Abstract Causal query estimation in biomolecular networks commonly selects a ‘valid adjustment set’, i.e. a subset of network variables that eliminates the bias of the estimator. A same query may have multiple valid adjustment sets, each with a different variance. When networks are partially observed, current methods use graph-based criteria to find an adjustment set that minimizes asymptotic variance. Unfortunately, many models that share the same graph topology, and therefore same functional dependencies, may differ in the processes that generate the observational data. In these cases, the topology-based criteria fail to distinguish the variances of the adjustment sets. This deficiency can lead to sub-optimal adjustment sets, and to miss-characterization of the effect of the intervention. We propose an approach for deriving ‘optimal adjustment sets’ that takes into account the nature of the data, bias and finite-sample variance of the estimator, and cost. It empirically learns the data generating processes from historical experimental data, and characterizes the properties of the estimators by simulation. We demonstrate the utility of the proposed approach in four biomolecular Case studies with different topologies and different data generation processes. The implementation and reproducible Case studies are at https://github.com/srtaheri/OptimalAdjustmentSet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials

Abstract This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

ResDesign: Resilient by Design Platform for CPS Assessment and Validation

ResDesign project has developed integrated capabilities to help cyber physical system modelers and analysts to evaluate vulnerabilities and resilience of such systems using co-simulation-based attack testbed, graph-based visualization and monitoring tool, and Bayesian optimization-based co-design capability. The project demonstrates a collection of attack scenarios and use cases in an integrated software environment.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

..delta..-Learning of High-Fidelity Electronic Structure Using Graph Neural Networks with Modified Node-Level Features

In this work, we present a ..delta..-learning approach for predicting the eigenvalues calculated with the hybrid functional HSE06 (..epsilon..nkHSE) for a set of metal and nitrogen doped graphene catalysts (MNCs) from Perdew-Burke-Ernzerhof (PBE) inputs. The model presented here incorporates electronic scalar features along with structural information in a graph neural network (GNN). In particular, the PBE eigenvalues for different bands and k-points and orbital-resolved projectors are combined with the applied potential as node-level features along with structural information within the Atomistic Line Graph Neural Network (ALIGNN) architecture. These features enable flexibility for systems with electrified interfaces, such as in electrocatalysts and achieves mean absolute error (MAE) of less than 0.1 eV. The machine learning model reported here achieves a strong generalization to left-out adsorbates (MAE = 0.074 eV) and leave-one-chemical-space-out (MAE = 0.08 eV) and completely left-out metals (MAE = 0.072 eV), confirming the robustness of the machine learning (ML) model in predicting ..epsilon..nkHSE.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Grassmannian Diffusion Maps--Based Dimension Reduction and Classification for High-Dimensional Data

This work introduces the Grassmannian diffusion maps (GDMaps), a novel nonlinear dimensionality reduction technique that defines the affinity between points through their representation as low-dimensional subspaces corresponding to points on the Grassmann manifold. Here, the method is designed for applications, such as image recognition and data-based classification of constrained high-dimensional data where each data point itself is a high-dimensional object (i.e., a large matrix) that can be compactly represented in a lower-dimensional subspace. The GDMaps is composed of two stages. The first is a pointwise linear dimensionality reduction wherein each high-dimensional object is mapped onto the Grassmann manifold representing the low-dimensional subspace on which it resides. The second stage is a multipoint nonlinear kernel-based dimension reduction using diffusion maps to identify the subspace structure of the points on the Grassmann manifold. To this end, an appropriate Grassmannian kernel is used to construct the transition matrix of a random walk on a graph connecting points on the Grassmann manifold. Spectral analysis of the transition matrix yields low-dimensional Grassmannian diffusion coordinates embedding the data into a low-dimensional reproducing kernel Hilbert space. Further, a novel data classification/recognition technique is developed based on the construction of an overcomplete dictionary of reduced dimension whose atoms are given by the Grassmannian diffusion coordinates. Three examples are considered. First, a "toy" example shows that the GDMaps can identify an appropriate parametrization of structured points on the unit sphere. The second example demonstrates the ability of the GDMaps to revealing the intrinsic subspace structure of high-dimensional random field data. In the last ex- ample, a face recognition problem is solved considering face images subject to varying illumination conditions, changes in face expressions, and occurrence of occlusions. The technique presented high recognition rates (i.e., 95% in the best case) using a fraction of the data required by conventional methods.

42 ENGINEERING↗
DOE OSTI2025

RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

PerCon SFA project data dentification of spatially resolved biomarkers of drought in Sorghum bicolor rhizosphere molecular-microbe interactions using a novel root cartography "RhizoGrid" system for sampling plants under drought and control conditions across 10 equally sized root zone environments (4 quadrants each). Each quadrant was sampled and processed for 16S amplicon, metabolomics, and X-ray computed tomography (XCT). Data download includes experimental metadata and results files for 16S rRNA sequence analysis of microbial community assembly (processed data files), liquid chromatography mass spectrometry (LC-MS) metabolomics analysis of microbial community root exudates (processed data files), X-ray computed tomography (XCT) spatial gradient analysis (raw and processed data files) of microbial community composition, and related computational modeling outputs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning

To expedite new molecular compound development, a long-sought goal within the chemistry community has been to predict molecules’ bulk properties of interest a priori to synthesis from a chemical structure alone. In this work, we demonstrate that machine learning methods can indeed be used to directly learn the relationship between chemical structures and bulk crystalline properties of molecules, even in the absence of any crystal structure information or quantum mechanical calculations. We focus specifically on a class of organic compounds categorized as energetic materials called high explosives (HE) and predicting their crystalline density. An ongoing challenge within the chemistry machine learning community is deciding how best to featurize molecules as inputs into machine learning models—whether expert handcrafted features or learned molecular representations via graph-based neural network models—yield better results and why. We evaluate both types of representations in combination with a number of machine learning models to predict the crystalline densities of HE-like molecules curated from the Cambridge Structural Database, and we report the performance and pros and cons of our methods. Our message passing neural network (MPNN) based models with learned molecular representations generally perform best, outperforming current state-of-the-art methods at predicting crystalline density and performing well even when testing on a data set not representative of the training data. However, these models are traditionally considered black boxes and less easily interpretable. Here, to address this common challenge, we also provide a comparison analysis between our MPNN-based model and models with fixed feature representations that provides insights as to what features are learned by the MPNN to accurately predict density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Almost-Rigidity of Frameworks

Here, we extend the mathematical theory of rigidity of frameworks (graphs embedded in d-dimensional space) to consider nonlocal rigidity and flexibility properties. We provide conditions on a framework under which (I) as the framework flexes continuously it must remain inside a small ball, a property we call “almost-rigidity”; (II) any other framework with the same edge lengths must lie outside a much larger ball; (III) if the framework deforms by some given amount, its edge lengths change by a minimum amount; (IV) there is a nearby framework that is prestress stable, and thus rigid. The conditions can be tested efficiently using semidefinite programming. The test is a slight extension of the test for prestress stability of a framework, and gives analytic expressions for the radii of the balls and the edge length changes. Examples illustrate how the theory may be applied in practice, and we provide an algorithm to test for rigidity or almost-rigidity. We briefly discuss how the theory may be applied to tensegrities. © 2020 Wiley Periodicals LLC.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗