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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗
DOE OSTI2020

A low-complexity non-intrusive approach to predict the energy demand of buildings over short-term horizons

Reliable, non-intrusive, short-term (of up to 12 hours ahead) prediction of a building's energy demand is a critical component of intelligent energy management applications. A number of such approaches have been proposed over time, utilizing various statistical and, more recently, machine learning techniques, such as decision trees, neural networks and support vector machines. Importantly, all of these works barely outperform simple seasonal auto-regressive integrated moving average models, while their complexity is significantly higher. Here, we propose a novel low-complexity non-intrusive approach that improves the predictive accuracy of the state-of-the-art by up to ~10%. The backbone of our approach is a K-nearest neighbours search method, that exploits the demand pattern of the most similar historical days, and incorporates appropriate time-series pre-processing and easing. In the context of this work, we evaluate our approach against state-of-the-art methods and provide insights on their performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Modeling household-level party composition behavior for multiparty activities: a random parameter nested logit modeling approach

This study presents findings of a household-level party composition model for multiparty activities. It exploits data from a comprehensive Household Travel Survey conducted by Chicago Metropolitan Agency of Planning. The study estimates a random parameter nested logit model to capture households’ unobserved preference heterogeneity and non-proportional substitution patterns in terms of activity party composition for multiparty activities. A wide variety of household demographics, activity attributes and residential neighborhood characteristics are examined in this paper. The magnitude of the impacts of the determinants are tested in this study by analyzing the elasticity of the variables, which suggests that household demographics and attributes of the multiparty activities have significant effects on the household-level activity party composition. Residential neighborhood characteristics, although somewhat less impactful, still play a meaningful role. This model will be implemented within the POLARIS transportation systems simulator to improve the activity generation modeling workflow, and the prediction accuracy of various activity-travel components.

activity party composition↗
DOE OSTI2021

An integrated manifold learning approach for high-dimensional data feature extractions and its applications to online process monitoring of additive manufacturing

As an effective dimension reduction and feature extraction technique, manifold learning has been successfully applied to high-dimensional data analysis. With the rapid development of sensor technology, a large amount of high-dimensional data such as image streams can be easily available. Thus, a promising application of manifold learning is in the field of sensor signal analysis, particular for the applications of online process monitoring and control using high-dimensional data. The objective of this study is to develop a manifold learning-based feature extraction method for process monitoring of Additive Manufacturing (AM) using online sensor data. Due to the non-parametric nature of most existing manifold learning methods, their performance in terms of computational efficiency, as well as noise resistance has yet to be improved. To address this issue, this study proposes an integrated manifold learning approach termed multi-kernel metric learning embedded isometric feature mapping (MKML-ISOMAP) for dimension reduction and feature extraction of online high-dimensional sensor data such as images. Based on the extracted features with the utilization of supervised classification and regression methods, an online process monitoring methodology for AM is implemented to identify the actual process quality status. Finally, in the numerical simulation and real-world case studies, the proposed method demonstrates excellent performance in both prediction accuracy and computational efficiency.

36 MATERIALS SCIENCE↗
DOE OSTI2026

The Sensitivity of Variational Bayesian Neural Network Performance to Hyperparameters

In scientific applications, predictive modeling is often of limited use without accurate uncertainty quantification (UQ) to indicate when a model may be extrapolating or when more data needs to be collected. Bayesian Neural Networks (BNNs) produce predictive uncertainty by propagating uncertainty in neural network (NN) weights and offer the promise of obtaining not only an accurate predictive model but also accurate UQ. However, in practice, obtaining accurate UQ with BNNs is difficult due in part to the approximations used for model training (such as those made in variational inference) and in part to the need to choose a suitable set of hyperparameters; these hyperparameters outnumber those needed for traditional NNs and often have opaque effects on the results. We aim to shed light on the effects of hyperparameter choices for variational BNNs by performing a global sensitivity analysis of variational BNN performance under varying hyperparameter settings. Our results indicate that many of the hyperparameters interact with each other to affect both predictive accuracy and UQ. For improved usage of variational BNNs in real-world applications, we suggest that thorough hyperparameter tuning, including tuning of prior hyperparameters and loss function parameters, is essential for accurate UQ in variational BNNs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Multi-Modal Bayesian Neural Network Surrogates with Conjugate Last-Layer Estimation

As data collection and simulation capabilities advance, multi-modal learning, the task of learning from multiple modalities and sources of data, is becoming an increasingly important area of research. Surrogate models that learn from data of multiple auxiliary modalities to support the modeling of a highly expensive quantity of interest have the potential to aid outer loop applications such as optimization, inverse problems, or sensitivity analyses when multi-modal data are available. We develop two multi-modal Bayesian neural network surrogate models and leverage conditionally conjugate distributions in the last layer to estimate model parameters using stochastic variational inference (SVI). We provide a method to perform this conjugate SVI estimation in the presence of partially missing observations. Here, we demonstrate improved prediction accuracy and uncertainty quantification compared to unimodal surrogate models for both scalar and time series data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Active learning of a crystal plasticity flow rule from discrete dislocation dynamics simulations

Continuum-scale material deformation models, such as crystal plasticity (CP), can significantly enhance their predictive accuracy by incorporating input from lower-scale (i.e. mesoscale) models. The procedure to generate and extract the relevant information is however typically complex and ad hoc, involving decision and intervention by domain experts, leading to long development times. In this study, we develop a principled approach for calibration of continuum-scale models using lower scale information by representing a CP flow rule as a Gaussian process model. This representation allows for efficient parameter space exploration, guided by the uncertainty embedded in the model through a process known as Bayesian optimization (BO). We demonstrate a semi-autonomous BO loop which instantiates discrete dislocation dynamics simulations whose initial conditions are automatically chosen to optimize the uncertainty of a model CP flow rule. Our self-guided computational pipeline efficiently generated a dataset and corresponding model whose error, uncertainty, and physical feature sensitivities were validated with comparison to an independent dataset four times larger, demonstrating a valuable and efficient active learning implementation readily transferable to similar material systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Advances in prediction of tokamak experiments with theory-based models

The successful validation of theory-based models of transport, MHD stability, heating and current drive, with tokamak measurements over the last 20 years, has laid the foundation for a new era where these models can be routinely used in a "predict first" approach to design and predict the outcomes of experiments on tokamaks today. The capability to predict the plasma confinement and core profiles with a quantified uncertainty, based on a multi-machine, international, database of experience, will provide confidence that a proposed discharge will remain within the operational limits of the tokamak. Developing this predictive capability for the first generation of burning plasma devices, beginning with ITER, and progressing to tokamak demonstration reactors, is a critical mission of fusion energy research. Major advances have been made implementing this predict first methodology on today's tokamaks. In this work, an overview of several of these recent advances will be presented, providing the integrated modeling foundations of the experimental successes. The first steps to include boundary plasmas, and tokamak control systems, have been made. A commitment to predicting experiments as part of the planning process is needed in order to collect predictive accuracy data and evolve the models and software into a robust whole discharge pulse design simulator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Artificial intelligence-based predictive modeling for imaging neutral particle analyzers on the DIII-D tokamak

The Imaging Neutral Particle Analyzer (INPA) at DIII-D is a diagnostic system used to accurately resolve the energy and spatial distributions of fast ions in fusion plasmas. A novel artificial intelligence (AI) technique named INPA-net is based on Reservoir Computing Networks and developed here to predict active and passive signals produced by charge-exchange reactions from injected and edge-cold neutrals, respectively, in magnetically confined fusion plasmas. This model is trained using a set of 21 time domain signals between 0 s to 3.35 s that includes injected beam and thermal plasma information, and 6444 real 2D experimental images of the INPA in 12 plasma discharges at DIII-D. The trained neural network is able to forecast experimental images in real-time. The model achieves an R-squared value of 0.91, which is higher than the 0.83 value achieved by a simple linear regression model. This improvement highlights the model's enhanced predictive accuracy for measured images from the validation set. This AI approach is valuable due to its rapid response times and potential for integration into real-time plasma control systems. A version of this model capable of generating syntehic images would be useful for the real-time monitoring of fast-ion transport. A comprehensive sensitivity study reveals that INPA-net maintains high performance even with variations in the input parameters, indicating the model's robustness and reliability. While developed for the INPA, the underlying architecture is adaptable and may be applied to various 2D imaging diagnostics in fusion research.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

Abstract Motivation Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. Results We developed TransFun—a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating that the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. Availability and implementation The source code of TransFun is available at https://github.com/jianlin-cheng/TransFun.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Emulation of seismic-phase traveltimes with machine learning

SUMMARY We present a machine learning (ML) method for emulating seismic-phase traveltimes that are computed using a global-scale 3-D earth model and physics-based ray tracing. Accurate traveltime predictions based on 3-D earth models are known to reduce the bias of event location estimates, increase our ability to assign phase labels to seismic detections and associate detections to events. However, practical use of 3-D models is challenged by slow computational speed and the unwieldiness of pre-computed lookup tables that are often large and have prescribed computational grids. In this work, we train a ML emulator using pre-computed traveltimes, resulting in a compact and computationally fast way to approximate traveltimes that are based on a 3-D earth model. Our model is trained using approximately 850 million P-wave traveltimes that are based on the global LLNL-G3D-JPS model, which was developed for more accurate event location. The training-set consists of traveltimes between 10 393 global seismic stations and randomly sampled event locations that provide a prescribed, distance-dependent geographic sample density for each station. Prediction accuracy is dependent on event-station distance and whether the station was included in the training set. For stations included in the training set the mean absolute deviation (MAD) of the difference between traveltimes computed using ray tracing through the 3-D model and the ML emulator for local, regional, and teleseismic distances are 0.090, 0.125 and 0.121 s, respectively. For tested station locations not included in the training set, MAD values for the three distance ranges increase to 0.173, 0.219 and 0.210 s, respectively. Empirical traveltime residuals for a global reference data are indistinguishable when ML emulation or the 3-D model is used to compute traveltimes. This result holds regardless of whether the recording station is used in ML training or not.

58 GEOSCIENCES↗
DOE OSTI2025

Evaluating algorithmic bias on biomarker classification of breast cancer pathology reports

Objectives: This work evaluated algorithmic bias in biomarkers classification using electronic pathology reports from female breast cancer cases. Bias was assessed across 5 subgroups: cancer registry, race, Hispanic ethnicity, age at diagnosis, and socioeconomic status. Materials and Methods: We utilized 594 875 electronic pathology reports from 178 121 tumors diagnosed in Kentucky, Louisiana, New Jersey, New Mexico, Seattle, and Utah to train 2 deep-learning algorithms to classify breast cancer patients using their biomarkers test results. We used balanced error rate (BER), demographic parity (DP), equalized odds (EOD), and equal opportunity (EOP) to assess bias. Results: We found differences in predictive accuracy between registries, with the highest accuracy in the registry that contributed the most data (Seattle Registry, BER ratios for all registries >1.25). BER showed no significant algorithmic bias in extracting biomarkers (estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2) for race, Hispanic ethnicity, age at diagnosis, or socioeconomic subgroups (BER ratio <1.25). DP, EOD, and EOP all showed insignificant results. Discussion: We observed significant differences in BER by registry, but no significant bias using the DP, EOD, and EOP metrics for socio-demographic or racial categories. This highlights the importance of employing a diverse set of metrics for a comprehensive evaluation of model fairness. Conclusion: A thorough evaluation of algorithmic biases that may affect equality in clinical care is a critical step before deploying algorithms in the real world. We found little evidence of algorithmic bias in our biomarker classification tool. Artificial intelligence tools to expedite information extraction from clinical records could accelerate clinical trial matching and improve care.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Photometric redshifts from SDSS images with an interpretable deep capsule network

ABSTRACT Studies of cosmology, galaxy evolution, and astronomical transients with current and next-generation wide-field imaging surveys like the Rubin Observatory Legacy Survey of Space and Time are all critically dependent on estimates of photometric redshifts. Capsule networks are a new type of neural network architecture that is better suited for identifying morphological features of the input images than traditional convolutional neural networks. We use a deep capsule network trained on ugriz images, spectroscopic redshifts, and Galaxy Zoo spiral/elliptical classifications of ∼400 000 Sloan Digital Sky Survey galaxies to do photometric redshift estimation. We achieve a photometric redshift prediction accuracy and a fraction of catastrophic outliers that are comparable to or better than current methods for SDSS main galaxy sample-like data sets (r ≤ 17.8 and zspec ≤ 0.4) while requiring less data and fewer trainable parameters. Furthermore, the decision-making of our capsule network is much more easily interpretable as capsules act as a low-dimensional encoding of the image. When the capsules are projected on a two-dimensional manifold, they form a single redshift sequence with the fraction of spirals in a region exhibiting a gradient roughly perpendicular to the redshift sequence. We perturb encodings of real galaxy images in this low-dimensional space to create synthetic galaxy images that demonstrate the image properties (e.g. size, orientation, and surface brightness) encoded by each dimension. We also measure correlations between galaxy properties (e.g. magnitudes, colours, and stellar mass) and each capsule dimension. We publicly release our code, estimated redshifts, and additional catalogues at https://biprateep.github.io/encapZulate-1.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Sparse expansions of multicomponent oxide configuration energy using coherency and redundancy

We report that compressed sensing has become a widely accepted paradigm to construct high dimensional cluster expansion models used for statistical mechanical studies of atomic configuration in complex multicomponent crystalline materials. However, strict sampling requirements necessary to obtain minimal coherence measurements for compressed sensing to guarantee accurate estimation of model parameters are difficult and in some cases impossible to satisfy due to the inability of physical systems to access certain configurations. Nevertheless, the dependence of energy on atomic configuration can still be adequately learned without these strict requirements by using compressed sensing by way of coherent measurements using redundant function sets known as frames. We develop a particular frame constructed from the union of all occupancy-based cluster expansion basis sets. We illustrate how using this highly redundant frame yields sparse expansions of the configuration energy of complex oxide materials that are competitive and often surpass the prediction accuracy and sparsity of models obtained from standard cluster expansions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Ab initio calculation of carrier mobility in semiconductors including ionized-impurity scattering

The past decade has seen the emergence of ab initio computational methods for calculating phonon-limited carrier mobilities in semiconductors with predictive accuracy. More realistic calculations ought to take into account additional scattering mechanisms such as, for example, impurity and grain-boundary scattering. Here, in this paper, we investigate the effect of ionized-impurity scattering on the carrier mobility. We model the analytical impurity potential parameterized from first principles by a collection of randomly distributed Coulomb scattering centers, and we include this relaxation channel into the ab initio Boltzmann transport equation, as implemented in the EPW code. We demonstrate this methodology by considering silicon, silicon carbide, and gallium phosphide, for which detailed experimental data are available. Our calculations agree well with experiments over a broad range of temperatures and impurity concentrations. For each compound investigated here, we compare the relative importance of electron-phonon scattering and ionized-impurity scattering, and we critically assess the reliability of Matthiessen's rule. We also show that an accurate description of dielectric screening and carrier effective masses can improve quantitative agreement with experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Model orthogonalization and Bayesian forecast mixing via principal component analysis

One can improve predictability in the unknown domain by combining forecasts of imperfect complex computational models using a Bayesian statistical machine learning framework. In many cases, however, the models used in the mixing process are similar. In addition to contaminating the model space, the existence of such similar, or even redundant, models during the multimodeling process can result in misinterpretation of results and deterioration of predictive performance. In this paper we describe a method based on the principal component analysis that eliminates model redundancy. We show that by adding model orthogonalization to the proposed Bayesian model combination framework, one can arrive at better prediction accuracy and reach excellent uncertainty quantification performance.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗