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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗
DOE OSTI2022

Suppressing simulation bias in multi-modal data using transfer learning

Abstract Many problems in science and engineering require making predictions based on few observations. To build a robust predictive model, these sparse data may need to be augmented with simulated data, especially when the design space is multi-dimensional. Simulations, however, often suffer from an inherent bias. Estimation of this bias may be poorly constrained not only because of data sparsity, but also because traditional predictive models fit only one type of observed outputs, such as scalars or images, instead of all available output data modalities, which might have been acquired and simulated at great cost. To break this limitation and open up the path for multi-modal calibration, we propose to combine a novel, transfer learning technique for suppressing the bias with recent developments in deep learning, which allow building predictive models with multi-modal outputs. First, we train an initial neural network model on simulated data to learn important correlations between different output modalities and between simulation inputs and outputs. Then, the model is partially retrained, or transfer learned, to fit the experiments; a method that has never been implemented in this type of architecture. Using fewer than 10 inertial confinement fusion experiments for training, transfer learning systematically improves the simulation predictions while a simple output calibration, which we design as a baseline, makes the predictions worse. We also offer extensive cross-validation with real and carefully designed synthetic data. The method described in this paper can be applied to a wide range of problems that require transferring knowledge from simulations to the domain of experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Temperature-dependent mechanical properties and crystal plasticity parameters for additively manufactured Haynes-214 alloy: Experiments and numerical modeling

Our experimental mechanical testing data demonstrated that the additively manufactured (AM) laser powder bed fusion (L-PBF) Haynes-214 alloy exhibits non-linear mechanical properties as the temperature rises from ambient to 870 °C. Crystal plasticity (CP) simulations provide an effective approach to gaining deeper insights into microstructure-property linkages under thermomechanical loading. This method can reduce the need for costly high-temperature mechanical testing while accounting for the effects of crystallographic texture and grain morphology on the mechanical behavior of AM materials. However, calibrating a CP model is time-consuming because individual simulations are computationally expensive and hundreds (or more) of iterations over parameter sets may be required. To address this issue, we have designed a machine learning-differential evolution (ML-DE) CP framework that can accurately interpolate the tensile properties of AM L-PBF Haynes-214 alloy across a wide temperature range from ambient to 870 °C, with minimal reliance on experimental data. The framework uses electron backscatter diffraction (EBSD) measurements to generate statistically equivalent microstructural volume elements to serve as inputs to the CP modeling framework. Stress–strain curves were generated from 1000 CP simulations, which serve as the training data set for the three ML regression algorithms explored: linear, extra-trees, and multi-layer perceptron. These three regression models were independently evaluated to compare their efficiency and identify the most suitable algorithm for the given problem. Results revealed that the extra-trees ML regressor outperforms the other models in both qualitative and quantitative aspects with an R 2 of 0.98. Subsequently, the differential evolution optimization approach is employed to calibrate the ML-based CP material parameters with experimental results obtained at various temperatures. Finally, temperature-dependent CP material parameters are formulated. The effectiveness and efficiency of the designed framework are validated through comparison with experimental results, demonstrating a high degree of agreement. These calibrated parametric constitutive equations enable further use of the CP model to study the deformation behavior of this alloy under a wide range of thermo-mechanical loading conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Integrating Predictions for Improving Defect Classification Accuracy in NDT-based Assessment of Concrete - 20229

There is an increasing need to create predictive models for defect classification in concrete using the output of non-destructive testing (NDT) techniques. Recent advancement of machine-learning algorithms has offered several techniques for developing classification models for different types of data sets. However, the performance of these algorithms is very uncertain, mainly when applied to small and noisy datasets. For example, when human access is limited (e.g., nuclear facility), robot-based NDT is preferred. But compared to manual tests with humans present on site, the data sets are small, and more noise can exist. Therefore, it is imperative to develop new approaches to ensure a consistently high classification accuracy for inadequate data sets. This study explores the classification performance on NDT dataset using classifiers from different machine-learning algorithms, namely k-Nearest Neighbor (kNN), Decision Tree, Naive Bayes, Logistic Regression, and Support Vector Machine (SVM). The authors further integrated the predictions from these classifiers using proposed methods. The integration strategy combines the output of the classifiers based on two different measures, accuracy, and performance (ACC and PERF), using equations such as sum, average, and square-root-of-sums-of-squares (SRSS). Our results reveal varying classification accuracies across individual classifiers with different misclassifications across the test data set. The integration strategy provided significant improvement in the classification accuracy compared to the individual classifiers. Furthermore, the results indicate minimal variation across the integration methods as compared to the variation across the individual classifiers. To conclude, prediction integration offers a unique approach for combining the output of multiple classifiers to create redundancies with the potential of achieving high classification performance and improved reliability in predictive models for defect detection in concrete. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens

The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will require predictive models that can identify (i) potential zoonoses with a high likelihood of emergence and (ii) environmental or other features that may trigger a shift in host, vector, or pathogen baselines associated with emergence and/or spillover. Artificial intelligence (AI), and particularly its machine learning and deep learning branches, holds enormous potential for detecting shifts in large-scale biodiversity and disease datasets (genomic, ecological, geospatial, etc.). Such algorithms can be trained to identify subtle patterns in large volumes of data to yield insights into complex phenomena for which we have limited knowledge of the true cause(s) or predictor(s), as is the case for emerging infectious diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Comprehensive Review of Latent Space Dynamics Identification Algorithms for Intrusive and Non-Intrusive Reduced-Order-Modeling

Numerical solvers of partial differential equations (PDEs) have been widely employed for simulating physical systems. However, the computational cost remains a major bottleneck in various scientific and engineering applications, which has motivated the development of reduced-order models (ROMs). Recently, machine-learning-based ROMs have gained significant popularity and are promising for addressing some limitations of traditional ROM methods, especially for advection dominated systems. In this chapter, we focus on a particular framework known as Latent Space Dynamics Identification (LaSDI), which transforms the high-fidelity data, governed by a PDE, to simpler and low-dimensional latent-space data, governed by ordinary differential equations (ODEs). These ODEs can be learned and subsequently interpolated to make ROM predictions. Each building block of LaSDI can be easily modulated depending on the application, which makes the LaSDI framework highly flexible. In particular, we present strategies to enforce the laws of thermodynamics into LaSDI models (tLaSDI), enhance robustness in the presence of noise through the weak form (WLaSDI), select high-fidelity training data efficiently through active learning (gLaSDI, GPLaSDI), and quantify the ROM prediction uncertainty through Gaussian processes (GPLaSDI). We demonstrate the performance of different LaSDI approaches on Burgers equation, a non-linear heat conduction problem, and a plasma physics problem, showing that LaSDI algorithms can achieve relative errors of less than a few percent and up to thousands of times speed-ups.

Computational Engineering, Finance, and Science (c↗
DOE OSTI2025

Optimal Transport as a Tool for Scientific Discovery in Radiation Biology

This report summarizes findings from research conducted for the “Exploration of the Poten tial for Artificial Intelligence and Machine Learning to Advance Low-Dose Radiation Biology Re search” (RadBio-AI) program, supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under Awards KP1601011/FWP CC121 and KP1601017/FWP CC121. The research reported here was undertaken in an effort to assess the potential of optimal measure transport methods as components within the larger scope of a com putational framework envisioned to support research in the radiation biology domain. Within this effort, our interest centered on enabling a unified generic framework where probabilistic modeling, inference, and statistical learning can be carried out for a wide range of data distributions. As described next in Section 1 (and in more detail in our original publication), optimal measure transport offers the possibility of such unified approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

CAMELSH: A Large-Sample Hourly Hydrometeorological Dataset and Attributes at Watershed-Scale for CONUS

We present CAMELSH (Catchment Attributes and Hourly HydroMeteorology for Large-Sample Studies), the first large-sample hydrometeorological dataset at the hourly scale for the contiguous United States. CAMELSH intergrates hourly meteorological time series, catchment attributes and boundaries from GAGES-II and HydroATLAS for 9,008 catchments across diverse climatic, hydrological, and anthropogenic conditions. In addition, hourly streamflow time series is provided for 3,166 catchments. The dataset spans 45 years (1980–2024) with 11 meteorological variables from the NLDAS-2 forcing dataset, from which we compute nine climate indices related to precipitation, evapotranspiration, seasonality, and snow fraction. Additionally, CAMELSH includes two sets of catchment attributes: 439 from GAGES-II and 195 derived from HydroATLAS. These attributes include factors related to climate, geology, hydrology, river/stream morphology, landscape, nutrient, soil, topography, and anthropogenic influences. Developed in accordance with FAIR (Findability, Accessibility, Interoperability, and Reusability) principles, CAMELSH is the first large-sample dataset at an hourly timescale, supporting machine learning applications for short-term streamflow (flood) prediction and advancing data-driven hydrological research across multiple timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

AI for Extreme Volcanic Climate Forcing and Feedback Forecasting in the 21st century

Our paradigm-shifting framework will apply machine learning and perform physical analysis of contemporary volcanoes to develop sound forecasts of extreme eruptions in the 21stcentury and their abrupt drying and cooling impacts on the warming climate. We will also bridge climate data driven regression models and earth system model output to trace teleconnections that exacerbate regional impacts such as Arctic amplification and western US droughts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Performance Comparison of Object Detection Networks for Shrapnel Identification in Ultrasound Images

Ultrasound imaging is a critical tool for triaging and diagnosing subjects but only if images can be properly interpreted. Unfortunately, in remote or military medicine situations, the expertise to interpret images can be lacking. Machine-learning image interpretation models that are explainable to the end user and deployable in real time with ultrasound equipment have the potential to solve this problem. We have previously shown how a YOLOv3 (You Only Look Once) object detection algorithm can be used for tracking shrapnel, artery, vein, and nerve fiber bundle features in a tissue phantom. However, real-time implementation of an object detection model requires optimizing model inference time. Here, we compare the performance of five different object detection deep-learning models with varying architectures and trainable parameters to determine which model is most suitable for this shrapnel-tracking ultrasound image application. We used a dataset of more than 16,000 ultrasound images from gelatin tissue phantoms containing artery, vein, nerve fiber, and shrapnel features for training and evaluating each model. Every object detection model surpassed 0.85 mean average precision except for the detection transformer model. Overall, the YOLOv7tiny model had the higher mean average precision and quickest inference time, making it the obvious model choice for this ultrasound imaging application. Other object detection models were overfitting the data as was determined by lower testing performance compared with higher training performance. In summary, the YOLOv7tiny object detection model had the best mean average precision and inference time and was selected as optimal for this application. Next steps will implement this object detection algorithm for real-time applications, an important next step in translating AI models for emergency and military medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Learning curves for drug response prediction in cancer cell lines

Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensitivity studies continue generating drug response data, a common question is whether the generalization performance of existing prediction models can be further improved with more training data. We utilize empirical learning curves for evaluating and comparing the data scaling properties of two neural networks (NNs) and two gradient boosting decision tree (GBDT) models trained on four cell line drug screening datasets. The learning curves are accurately fitted to a power law model, providing a framework for assessing the data scaling behavior of these models. The curves demonstrate that no single model dominates in terms of prediction performance across all datasets and training sizes, thus suggesting that the actual shape of these curves depends on the unique pair of an ML model and a dataset. The multi-input NN (mNN), in which gene expressions of cancer cells and molecular drug descriptors are input into separate subnetworks, outperforms a single-input NN (sNN), where the cell and drug features are concatenated for the input layer. In contrast, a GBDT with hyperparameter tuning exhibits superior performance as compared with both NNs at the lower range of training set sizes for two of the tested datasets, whereas the mNN consistently performs better at the higher range of training sizes. Moreover, the trajectory of the curves suggests that increasing the sample size is expected to further improve prediction scores of both NNs. These observations demonstrate the benefit of using learning curves to evaluate prediction models, providing a broader perspective on the overall data scaling characteristics. A fitted power law learning curve provides a forward-looking metric for analyzing prediction performance and can serve as a co-design tool to guide experimental biologists and computational scientists in the design of future experiments in prospective research studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

The rapid increase in computing power, especially with the integration of graphics processing units, has dramatically increased the capabilities of molecular dynamics simulations. To date, these capabilities extend from running very long simulations (tens to hundreds of microseconds) to thousands of short simulations. However, the expansive data generated in these simulations must be made interpretable not only by the investigator who performs them but also by others as well. Here, we demonstrate how integrating learning techniques, such as artificial intelligence, machine learning, and neural networks, into analysis pipelines can reveal the kinetics of Alzheimer's disease (AD) protein aggregation. Finally, we review select AD targets, describe current simulation methods, and introduce learning concepts and their application in AD, highlighting limitations and potential solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A machine-learning inverse model framework for rapid forecasting and history matching in unconventional reservoirs

Model-based optimization for real-time forecasting in unconventional reser-voirs requires novel methods and work?ows since the strategies and work?ows used in conventional reservoirs are either inapplicable, or prohibitively expen-sive and time-consuming. Insu?cient site data and computational expense of high-?delity simulations mean that work?ows with high-?delity simulations are not ideal for usage in comprehensive uncertainty quanti?cation stud-ies that require 1000s of forward model runs. We present an alternative, novel work?ow for unconventional reservoirs, based on the interplay between reduced-order models and machine-learning. Our physics-informed machine-learning (PIML) work?ow addresses the challenges to real-time reservoir management in uncoventionals, namely lack of data (the time-frame for which the wells have been producing), and computational expense of high-?delity modeling. We use the machine-learning paradigm of transfer-learning to bind together fast but less accurate reduced-order models with slow, but accurate high-?delity models and circumvent the di?culties inherent in the current state-of-the-art for unconventionals. Such a PIML work?ow, grounded in physics, is a viable candidate for real-time history matching and production forecasting in a fractured shale gas reservoir. The signi?cance of our approach is that while it is developed for a particu-lar well and site in the Marcelus Shale gas reservoir of the Appalachian basin (MSEEL), it is not wedded to it. We expect the same work?ow can be ap-plied to other shale formations (e.g., Woodford, Barnett, Utica, EagleFord) should site-data become available, using the same set of machine-learning techniques from transfer learning. Some ?ne-tuning (or minimal retraining of the neural networks) will be required to transfer knowledge across shale gas sites/formations but it is a clearly superior alternative to developing a new machine-learning model altogether when considering a di?erent site.

Srinivasan, Shriram↗
DOE OSTI2023

Towards the extraction of the crystal cell parameters from pair distribution function profiles

The approach based on atomic pair distribution function (PDF) has revolutionized structural investigations by X-ray/electron diffraction of nano or quasi-amorphous materials, opening up the possibility of exploring short-range order. However, the ab initio crystal structural solution by the PDF is far from being achieved due to the difficulty in determining the crystallographic properties of the unit cell. A method for estimating the crystal cell parameters directly from a PDF profile is presented, which is composed of two steps: first, the type of crystal cell is inferred using machine-learning approaches applied to the PDF profile; second, the crystal cell parameters are extracted by means of multivariate analysis combined with vector superposition techniques. The procedure has been validated on a large number of PDF profiles calculated from known crystal structures and on a small number of measured PDF profiles. The lattice determination step has been benchmarked by a comprehensive exploration of different classifiers and different input data. The highest performance is obtained using the k -nearest neighbours classifier applied to whole PDF profiles. Descriptors calculated from the PDF profiles by recurrence quantitative analysis produce results that can be interpreted in terms of PDF properties, and the significance of each descriptor in determining the prediction is evaluated. The cell parameter extraction step depends on the cell metric rather than its type. Monometric, dimetric and trimetric cells have top-1 estimates that are correct 40, 20 and 5% of the time, respectively. Promising results were obtained when analysing real nanocrystals, where unit cells close to the true ones are found within the top-1 ranked solution in the case of monometric cells and within the top-6 ranked solutions in the case of dimetric cells, even in the presence of a crystalline impurity with a weight fraction up to 40%.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A kinetic-based regularization method for data science applications

We propose a physics-based regularization technique for function learning, inspired by statistical mechanics. By drawing an analogy between optimizing the parameters of an interpolator and minimizing the energy of a system, we introduce corrections that impose constraints on the lower-order moments of the data distribution. This minimizes the discrepancy between the discrete and continuum representations of the data, in turn allowing to access more favorable energy landscapes, thus improving the accuracy of the interpolator. Our approach improves performance in both interpolation and regression tasks, even in high-dimensional spaces. Unlike traditional methods, it does not require empirical parameter tuning, making it particularly effective for handling noisy data. We also show that thanks to its local nature, the method offers computational and memory efficiency advantages over Radial Basis Function interpolators, especially for large datasets.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

Automated classification of scientific publications linked to GES DISC datasets

The data collections archived and distributedby the GES DISC NASA data center arewidely utilized for various Earth Science studies.As these collections are created, many researchworks are published regarding the collections, algorithms,validations and applications. SinceGES DISC collects these publications and providestheir citations for the users, it is helpful tocategorize them based on how they relate to the datasetsthey are associated with. Specifically,whether the publication that is linked to GES DISCdataset is using it for applicational research,or if it describes the algorithm for dataset creation,or the validation of the dataset, or providesthe general overview of the data collection. Currently,this process requires simple manuallabelling, and as such, may be possible to solve viaautomation. To approach this problem, wedeveloped machine learning classifiers to predictthe category a publication belongs to. We usedmanually labeled publications as training data forsupervised machine learning algorithms:Random Forest and Naive Bayes. We achieved classificationaccuracy that is substantially betterthan the baseline accuracy, thus greatly improvingthe efficiency of the publication internalanalysis.

Rohan Dayal↗
DOE OSTI2022

Development of a Multi-Sensor Data Science System Used for Signature Development on Solvent Extraction Processes in support of safeguards- an overview

A new nuclear fuel cycle test bed is being built at Idaho National Laboratory to support the purification of special nuclear material recovered from used fuel. The test bed provides an opportunity to research process flow and the application of computational tools in solvent extraction processes. A deeper understanding of process and equipment behavior coupled with real time data collection can indicate whether a process failure is accidental or purposeful. The goal of this project is to develop a system that utilizes non-traditional measurement sources such as vibration, acoustics, current, light, flow, and temperature in conjunction with data-based, machine learning techniques that will allow for signal discovery. This multi-sensor data can support the development of safeguards by design and security by design measures for such a facility. Additionally, it can aid in early detection and identification of removed materials indicating diversion, which is essential for initiating material recovery and actor identification. This overview encompasses the current research and testing of sensors to develop a spectrum of process signatures. To be followed by planned experiments aimed to characterize said signatures and study potential feature extraction techniques to identify a fault in the system (i.e. flow diversion).

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗