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Results for “embedded model error”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A Bayesian Calibration Framework with Embedded Model Error for Model Diagnostics

We study the utility and performance of a Bayesian model error embedding construction in the context of molecular dynamics modeling of metallic alloys, where we embed model error terms in existing interatomic potential model parameters. To alleviate the computational burden of this approach, we propose a framework combining likelihood approximation and Gaussian process surrogates. Here we leverage sparse Gaussian process techniques to construct a hierarchy of increasingly accurate but more expensive surrogate models. This hierarchy is then exploited by multilevel Markov chain Monte Carlo methods to efficiently sample from the target posterior distribution. We illustrate the utility of this approach by calibrating an interatomic potential model for a family of gold-copper alloys. In particular, this case study highlights effective means for dealing with computational challenges with Bayesian model error embedding in large-scale physical models, and the utility of embedded model error for model diagnostics.

Bayesian inference↗
DOE OSTI2024

Quantification of modeling uncertainty in the Rayleigh damping model

Understanding and accurately characterizing energy dissipation mechanisms in civil structures during earthquakes is an important element of seismic assessment and design. The most commonly used model is attributed to Rayleigh. This paper proposes a systematic approach to quantify the uncertainty associated with Rayleigh's damping model. Bayesian calibration with embedded model error is employed to treat the coefficients of the Rayleigh model as random variables using modal damping ratios. Through a numerical example, we illustrate how this approach works and how the calibrated model can address modeling uncertainty associated with the Rayleigh damping model.

42 ENGINEERING↗
DOE OSTI2022

Quantifying modeling uncertainty in simplified beam models for building response prediction

The use of simple models for response prediction of building structures is preferred in earthquake engineering for risk evaluations at regional scales, as they make computational studies more feasible. The primary impediment in their gainful use presently is the lack of viable methods for quantifying (and reducing upon) the modeling errors/uncertainties they bear. This study presents a Bayesian calibration method wherein the modeling error is embedded into the parameters of the model. Here, the method is specifically described for coupled shear-flexural beam models here, but it can be applied to any parametric surrogate model. The major benefit the method offers is the ability to consider the modeling uncertainty in the forward prediction of any degree-of-freedom or composite response regardless of the data used in calibration. The method is extensively verified using two synthetic examples. In the first example, the beam model is calibrated to represent a similar beam model but with enforced modeling errors. In the second example, the beam model is used to represent the detailed finite element model of a 52-story building. Both examples show the capability of the proposed solution to provide realistic uncertainty estimation around the mean prediction.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Impact of Lateral Flow on Surface Water and Energy Budgets over the Southern Great Plains – A Modeling Study

As we see the horizontal grid spacing decrease, treatment of hydrologic processes in land surface models, such as the lateral flow of surface and subsurface flow, need to be explicitly represented. Unlike previous studies that mainly focused on the mountainous regions, in this study the offline WRF-Hydro model is employed to study the impact of lateral flow on soil moisture and energy fluxes over the relatively flat southern Great Plains (SGP). The vast amount of measurements over the SGP provide an unique opportunity to assess the model behavior. In addition, newly developed land surface properties and input forcing are ingested into the model, in an attempt to reduce uncertainties associated with the initial and boundary forcing and help to identify model deficiencies. Our results show that the more realistic inputs (parameters, soil types, forcing) lead to larger underestimation of latent heat flux and dry bias, indicating the existence of model structural uncertainty (embedded errors) in WRF-Hydro that need to be characterized to inform future model development efforts. Including lateral flow processes partly mitigates the model deficiencies in representing hydrologic processes and alleviates the dry bias. In particular, both surface and subsurface lateral flow increase soil moisture mainly over the lower elevations, except that subsurface flow also affects soil moisture over steeper terrains. Additional simulations are performed to assess the effect of routing resolution on model results. When LSM resolution is high, noticeable differences in soil moisture are produced between different routing resolutions especially over steep terrain. Whereas when LSM resolution is coarse, differences between routing resolutions become negligible, especially over flat terrain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine learning approaches for integrating multi-omics data to expand microbiome annotation (Final Technical Report)

We fulfilled all original three aims of the proposal. Following the earlier release (during the first phase of the project at Montana) of software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes, we have nearly completed a second gap-filling tool that improves accuracy and explainability. We completed software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we completed a neural embedding model for identifying similarities between protein sequences based on amino-wise latent vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
NASA NTRS1995

Comparison of cloud fields from atmospheric general circulation model, in situ and satellite measurements

This paper focuses on the comparison of cloud amounts derived from an atmospheric general circulation model (AGCM), Satellite-observed clouds, and Ground-based cloud observations. Unlike Earth Radiation Budget Experiment (ERBE)-type comparisons it does not mix potential errors in the cloud amount with those in the radiation code embedded in the model. Long term cloud climatologies were used to compare global cloud amounts and regional seasonal cycles. The AGCM successfully reproduced the signatures of the warm pool and North Pacific seasonal cycle cloudiness but failed in the low stratus region off the coast of South America, a known problem for AGCMs. The data sets also reproduced the anomaly signature associated with El Nino in the warm pool region, but the model amounts were lower. Global results had a similar success rate, with the model generally producing lower total cloud compared to the satellite and in situ measurements. To compare cloud vertical distributions the cloud height may need to be validated using the corresponding radiation fields. Unfortunately there were also some large discrepancies between the two observed cloud data sets. While tremendously improved over the last decade the character of the observed cloud data sets, must be substantially enhanced before they will be useful in validating AGCMs by any but the crudest levels of comparison.

Haskins, Robert D.↗
NASA NTRS2011

NASA Tech Briefs, May 2011

Topics covered include: 1) Method to Estimate the Dissolved Air Content in Hydraulic Fluid; 2) Method for Measuring Collimator-Pointing Sensitivity to Temperature Changes; 3) High-Temperature Thermometer Using Cr-Doped GdAlO3 Broadband Luminescence; 4)Metrology Arrangement for Measuring the Positions of Mirrors of a Submillimeter Telescope; 5) On-Wafer S-Parameter Measurements in the 325-508-GHz Band; 6) Reconfigurable Microwave Phase Delay Element for Frequency Reference and Phase-Shifter Applications; 7) High-Speed Isolation Board for Flight Hardware Testing; 8) High-Throughput, Adaptive FFT Architecture for FPGA-Based Spaceborne Data Processors; 9) 3D Orbit Visualization for Earth-Observing Missions; 10) MaROS: Web Visualization of Mars Orbiting and Landed Assets; 11) RAPID: Collaborative Commanding and Monitoring of Lunar Assets; 12) Image Segmentation, Registration, Compression, and Matching; 13) Image Calibration; 14) Rapid ISS Power Availability Simulator; 15) A Method of Strengthening Composite/Metal Joints; 16) Pre-Finishing of SiC for Optical Applications; 17) Optimization of Indium Bump Morphology for Improved Flip Chip Devices; 18) Measuring Moisture Levels in Graphite Epoxy Composite Sandwich Structures; 19) Marshall Convergent Spray Formulation Improvement for High Temperatures; 20) Real-Time Deposition Monitor for Ultrathin Conductive Films; 21) Optimized Li-Ion Electrolytes Containing Triphenyl Phosphate as a Flame-Retardant Additive; 22) Radiation-Resistant Hybrid Lotus Effect for Achieving Photoelectrocatalytic Self-Cleaning Anticontamination Coatings; 23) Improved, Low-Stress Economical Submerged Pipeline; 24) Optical Fiber Array Assemblies for Space Flight on the Lunar Reconnaissance Orbiter; 25) Local Leak Detection and Health Monitoring of Pressurized Tanks; 26) Dielectric Covered Planar Antennas at Submillimeter Wavelengths for Terahertz Imaging; 27) Automated Cryocooler Monitor and Control System; 28) Broadband Achromatic Phase Shifter for a Nulling Interferometer; 29) Super Dwarf Wheat for Growth in Confined Spaces; 30) Fine Guidance Sensing for Coronagraphic Observatories; 31) Single-Antenna Temperature- and Humidity-Sounding Microwave Receiver; 32) Multi-Wavelength, Multi-Beam, and Polarization-Sensitive Laser Transmitter for Surface Mapping; 33) Optical Communications Link to Airborne Transceiver; 34) Ascent Heating Thermal Analysis on Spacecraft Adaptor Fairings; 35) Entanglement in Self-Supervised Dynamics; 36) Prioritized LT Codes; 37) Fast Image Texture Classification Using Decision Trees; 38) Constraint Embedding Technique for Multibody System Dynamics; 39) Improved Systematic Pointing Error Model for the DSN Antennas; 40) Observability and Estimation of Distributed Space Systems via Local Information-Exchange Networks; 41) More-Accurate Model of Flows in Rocket Injectors; 42) In-Orbit Instrument-Pointing Calibration Using the Moon as a Target; 43) Reliability of Ceramic Column Grid Array Interconnect Packages Under Extreme Temperatures; 44) Six Degrees-of-Freedom Ascent Control for Small-Body Touch and Go; and 45) Optical-Path-Difference Linear Mechanism for the Panchromatic Fourier Transform Spectrometer.

Source record↗
DOE OSTI2024

Machine learning approaches for integrating multi-omics data to expand microbiome annotation

Preliminary: This final report corresponds to a grant (DE-SC0021216) that was awarded to the University of Montana. Mid-way through the grant period, I relocated from the University of Montana to the University of Arizona. The grant was ended at University of Montana in late 2022, with all efforts concluding on 08/26/22; the remaining funds supporting the project were relinquished by University of Montana, and were later awarded to University of Arizona under a new grant, with start date 04/01/23. This report focuses on results of research efforts at UMontana through 08/26/22. Results: We made progress in each of the three aims of the proposal. We released software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes. We made substantial progress in developing software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we made notable progress in developing AI methods (specifically: a neural embedding model) for identifying similarities between protein sequences based on amino-wise latent vectors. These efforts were supplemented by development of methods for protein modeling in support of predicting protein-drug binding activity, and by my leadership of a team in the NIH/DOE 2021 Petabyte-Scale Sequence Search hack-a-thon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multiscale analysis in solids with unseparated scales: fine-scale recovery, error estimation, and coarse-scale adaptivity

There are several engineering applications in which the assumptions of homogenization and scale separation may be violated, in particular, for metallic structures constructed through additive manufacturing. Instead of resorting to direct numerical simulation of the macroscale system with an embedded fine scale, an alternative approach is to use an approximate macroscale constitutive model, but then estimate the model-form error using a posteriori error estimation techniques and subsequently adapt the macroscale model to reduce the error for a given boundary value problem and quantity of interest. Here, we investigate this approach to multiscale analysis in solids with unseparated scales using the example of an additively manufactured metallic structure consisting of a polycrystalline microstructure that is neither periodic nor statistically homogeneous. As a first step to the general nonlinear case, we focus here on linear elasticity in which each grain within the polycrystal is linear elastic but anisotropic.

42 ENGINEERING↗
NASA NTRS2013

Investigating System Dependability Modeling Using AADL

This report describes Architecture Analysis & Design Language (AADL) models for a diverse set of fault-tolerant, embedded data networks and describes the methods and tools used to created these models. It also includes error models per the AADL Error Annex. Some networks were modeled using Error Detection Isolation Containment Types (EDICT). This report gives a brief description for each of the networks, a description of its modeling, the model itself, and evaluations of the tools used for creating the models. The methodology includes a naming convention that supports a systematic way to enumerate all of the potential failure modes.

Hall, Brendan↗
DOE OSTI2020

Evaluation of a New Chemical Mechanism for 2-Amino-2-methyl-1-propanol in a Reactive Environment from CSIRO Smog Chamber Experiments

Amines are considered as an emerging class of atmospheric pollutants that are of great importance to atmospheric chemistry and new particle formation. As a typical amine, 2-amino-2-methyl-1-propanol (AMP) is one of the proposed solvents for capturing CO 2 from flue gas streams in amine-based post-combustion CO 2 capture plants, and it is expected to result in AMP emission and secondary products formation in the atmosphere. However, the current knowledge of its atmospheric chemistry and kinetics is poorly understood, particularly in a reactive environment. As such, in this work we used the CSIRO smog chamber to study the photo-oxidation of AMP in the presence of VOCs–NOx surrogate mixtures over a range of initial amine concentrations. O 3 formation was significantly inhibited when AMP was added to the surrogate VOCs–NOx mixtures, implying that AMP could alter known atmospheric chemical reaction pathways and the prevailing reactivity. Simultaneously, a large amount of AMP-derived secondary aerosol was formed, with a considerably high aerosol mass yield (i.e. ratio of aerosol formed to reacted AMP) of 1.06±0.20. Based on updated knowledge of its kinetics, oxidation pathways and product yields, we have developed a new mechanism (designated as CSIAMP-19) and integrated into the Carbon Bond 6 (CB6) chemical mechanism, and evaluated it against available smog chamber data. Compared with the existing AMP mechanism (designated as CarterAMP-08), the modified CB6 with CSIAMP-19 mechanism improves prediction against AMP–VOCs–NOx experiments across a range of initial AMP concentrations, within ±10% model error for gross ozone production. Our results contribute to scientific understanding of AMP photochemistry and to the development of the chemical mechanism of other amines. The updated AMP chemical reactions scheme can be further embedded into the chemical transport model for regional modelling scenarios where AMP-related emissions are of concern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

Logic flowgraph methodology - A tool for modeling embedded systems

The logic flowgraph methodology (LFM), a method for modeling hardware in terms of its process parameters, has been extended to form an analytical tool for the analysis of integrated (hardware/software) embedded systems. In the software part of a given embedded system model, timing and the control flow among different software components are modeled by augmenting LFM with modified Petrinet structures. The objective of the use of such an augmented LFM model is to uncover possible errors and the potential for unanticipated software/hardware interactions. This is done by backtracking through the augmented LFM mode according to established procedures which allow the semiautomated construction of fault trees for any chosen state of the embedded system (top event). These fault trees, in turn, produce the possible combinations of lower-level states (events) that may lead to the top event.

Muthukumar, C. T.↗
DOE OSTI2024

HAPPA: A Modular Platform for HPC Application Resilience Analysis with LLMs Embedded

High-performance computing (HPC) systems are increasingly vulnerable to soft errors, which pose significant challenges in maintaining computational accuracy and reliability. Predicting the resilience of HPC applications to these errors is crucial for robust code protection and detailed resilience analysis. In this study, we present HAppA, a modular platform designed for HPC Application Resilience Analysis. Embedding Large Language Models (LLMs), HAppA addresses understanding the context information of long code sequences typical in HPC applications. HAppA implements a novel code representation module that chunks the code into fixed-size segments and aggregates the embeddings of these segments. Three aggregation methods have been explored: MeanPooling, MaxPooling, and LSTM-based techniques. We built a DAtaset for REsilience analysis using Fault Injection (FI), named DARE. Using our DARE dataset, HAppA is trained for regression prediction tasks. Our evaluation results demonstrate the predictive accuracy of HAppA compared to other models, particularly noting that the LSTM-based aggregation method -- HAppA-LSTM -- achieves a mean squared error (MSE) of 0.078 for SDC prediction, surpassing the existing state-of-the-art PARIS model, which recorded an MSE of 0.1172. Additionally, HAppA with the KeyBERT model extracts a list of keywords representing the source code. A comprehensive importance analysis of these keywords further elucidates the code patterns contributing to the error rate. These findings highlight the effectiveness of HAppA in analyzing the resilience of HPC applications and establish a new benchmark for predictive accuracy in resilience.

Jiang, Hailong [Kent State University]↗
DOE OSTI2021

Revisiting Understanding of Electrochemical CO 2 Reduction on Cu(111): Competing Proton-Coupled Electron Transfer Reaction Mechanisms Revealed by Embedded Correlated Wavefunction Theory

Copper (Cu) electrodes, as the most efficacious of CO 2 reduction reaction (CO 2 RR) electrocatalysts, serve as prototypes for determining and validating reaction mechanisms associated with electrochemical CO 2 reduction to hydrocarbons. As in situ electrochemical mechanism determination by experiments is still out of reach, such mechanistic analysis typically is conducted using density functional theory (DFT). The semilocal exchange-correlation (XC) approximations most often used to model such catalysis unfortunately engender a basic error: predicting the wrong adsorption site for CO (a key CO 2 RR intermediate) on the most ubiquitous facet of Cu, namely, Cu(111). This longstanding inconsistency casts lingering doubt on previous DFT predictions of the attendant CO 2 RR kinetics. Here, we apply embedded correlated wavefunction (ECW) theory, which corrects XC functional error, to study the CO 2 RR on Cu(111) via both surface hydride (*H) transfer and proton-coupled electron transfer (PCET). We predict that adsorbed CO (*CO) reduces almost equally to two intermediates, namely, hydroxymethylidyne (*COH) and formyl (*CHO) at –0.9 V vs the RHE. In contrast, semilocal DFT approximations predict a strong preference for *COH. With increasing applied potential, the dominance of *COH (formed via potential-independent surface *H transfer) diminishes, switching to the competitive formation of both *CHO and *COH (both formed via potential-dependent PCET). Furthermore, our results also demonstrate the importance of including explicitly modeled solvent molecules in predicting electron-transfer barriers and reveal the pitfalls of overreliance on simple surface *H transfer models of reduction reactions.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2021

Sentiment Analysis based Error Detection for Large-Scale Systems

Today's large-scale systems such as High Performance Computing (HPC) Systems are designed/utilized towards exascale computing, inevitably decreasing its reliability due to the increasing design complexity. HPC systems conduct extensive logging of their execution behaviour. In this paper, we leverage the inherent meaning behind the log messages and propose a novel sentiment analysis-based approach for the error detection in large-scale systems, by automatically mining the sentiments in the log messages. Our contributions are four-fold. (1) We develop a machine learning (ML) based approach to automatically build a sentiment lexicon, based on the system log message templates. (2) Using the sentiment lexicon, we develop an algorithm to detect system errors. (3) We develop an algorithm to identify the nodes and components with erroneous behaviors, based on sentiment polarity scores. (4) We evaluate our solution vs. other state-of-the-art machine/deep learning algorithms based on three representative supercomputers' system logs. Experiments show that our error detection algorithm can identify error messages with an average MCC score and f -score of 91% and 96% respectively, while state of the art ML/deep learning model (LSTM) obtains only 67% and 84%. To the best of our knowledge, this is the first work leveraging the sentiments embedded in log entries of large-scale systems for system health analysis.

error detection↗
DOE OSTI2023

Solvent Dynamics Are Critical to Understanding Carbon Dioxide Dissolution and Hydration in Water

Simulations of carbon dioxide (CO 2 ) in water may aid in understanding the impact of its accumulation in aquatic environments and help advance technologies for carbon capture and utilization (via, e.g., mineralization). Quantum mechanical (QM) simulations based on static molecular models with polarizable continuum solvation poorly reproduce the energetics of CO 2 hydration to form carbonic acid in water, independent of the level of QM theory employed. Only with density-functional-theory-based molecular dynamics and rare-event sampling, followed by energy corrections based on embedded correlated wavefunction theory (in conjunction with density functional embedding theory), can a close agreement between theory and experiment be achieved. Such multilevel simulations can serve as benchmarks for simpler, less costly models, giving insight into potential errors of the latter. The strong influence of sampling/averaging over dynamical solvent configurations on the energetics stems from the difference in polarity of both the transition state and product (both polar) versus the reactant (nonpolar). When a solute undergoes a change in polarity during reaction, affecting its interaction with the solvent, careful assessment of the energetic contribution of the solvent response to this change is critical. Here, we show that static models (without structural sampling) that incorporate three explicit water molecules can yield far superior results than models with more explicit water molecules because fewer water molecules yield less configurational artifacts. Static models intelligently incorporating both explicit (molecules directly participating in the reaction) and implicit solvation, along with a proper QM theory, e.g., CCSD(T) for closed-shell systems, can close the accuracy gap between static and dynamic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗