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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗
DOE OSTI2023

De novo design of high-affinity binders of bioactive helical peptides

Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity to structured proteins. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Parameterization of Vertical Cloud Distribution from C3M and MERRA Data Using ML Method

Clouds play a key role in regulating the hydrological cycle and the Earth's radiative energy budget. However, global climate models (GCMs) with a horizontal grid spacing on the order of 100 km have limitations in representing sub-grid cloud dynamics with spatial scales on the order of 1 km, leading to potential uncertainties in cloud radiative feedback on the global scale. In our research, we will leverage the capabilities of Deep Machine Learning (DML) methods to construct parameterizations of sub-grid volumetric cloud fraction (VCF), which is the frequency of occurrence on a grid volume accumulated in the horizontal and vertical directions. Our investigation delves into the intricate relationship between VCF obtained from the NASA CALIPSO-CloudSat-CERES-MODIS (CCCM) satellite observation data and 3-D MERRA-2 reanalysis meteorological profiling data (e.g., wind, relative humidity, temperature). Through a comprehensive one-year data training utilizing the Sequence to Sequence DML method, we have successfully disentangled the complicated cloud formation dynamics across diverse meteorological conditions through a day-to-day analysis framework. Preliminary findings reveal promising statistical agreements in geographical and vertical distributions and seasonal variations of volumetric cloud fraction between ML prediction and satellite measurements. These results underscore the aptitude of our DML model to discern underlying cloud physical processes and accurately represent sub-grid cloud formation dynamics. Additionally, we have also employed trained neural network to analyze uncertainties arising from errors in meteorological data, further enhancing the robustness of our VCF parameterization.

Shan Zeng↗
DOE OSTI2024

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Deep Reinforcement Learning for Microgrid Cost Optimization Considering Load Flexibility

This paper proposes a novel Soft-Actor-Critic (SAC) based Deep Reinforcement Learning (DRL) method for optimizing the cost of microgrid operation by leveraging load flexibility. The proposed SAC-DRL method is designed to coordinate the control of distributed energy resources (DERs) and flexible load, addressing practical energy billing formation by power distribution utilities. Key contributions include an innovative reward function to mitigate sparse reward challenges and a mixed control strategy for discrete and continuous variables, ensuring radial network topology and minimizing power loss. We evaluate the proposed method on the model of a real microgrid located in Southern California, U.S.. The SAC-DRL model is tested to demonstrate its efficacy in reducing grid dependence, optimizing resource use, and minimizing costs. The results highlight the potential of DRL in modern energy systems, offering a sustainable and economically efficient solution for energy management in microgrids.

deep reinforcement learning↗
DOE OSTI2022

Neural network reconstruction of the dense matter equation of state from neutron star observables

The Equation of State (EoS) of strongly interacting cold and hot ultra-dense QCD matter remains a major challenge in the field of nuclear astrophysics. With the advancements in measurements of neutron star masses, radii, and tidal deformabilities, from electromagnetic and gravitational wave observations, neutron stars play an important role in constraining the ultra-dense QCD matter EoS. Here, in this work, we present a novel method that exploits deep learning techniques to reconstruct the neutron star EoS from mass-radius (M-R) observations. We employ neural networks (NNs) to represent the EoS in a model-independent way, within the range of ~1-7 times the nuclear saturation density. The unsupervised Automatic Differentiation (AD) framework is implemented to optimize the EoS, so as to yield through TOV equations, an M-R curve that best fits the observations. We demonstrate that this method works by rebuilding the EoS on mock data, i.e., mass-radius pairs derived from a randomly generated polytropic EoS. The reconstructed EoS fits the mock data with reasonable accuracy, using just 11 mock M-R pairs observations, close to the current number of actual observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

Abstract The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Smart Methane Emission Detection System Development (Final Report)

Working with the Department of Energy’s National Energy Technology Laboratory, Southwest Research Institute® (SwRI®) developed a system to identify methane leaks reliably, accurately, and autonomously at critical midstream sections of the natural gas distribution network in real- time for the purpose of mitigating methane emissions using Optical Gas Imaging (OGI) cameras. SwRI’s Smart Leak Detection – Methane (SLED/M) adds a high degree of automation to the process of methane leak detection to minimize sources of human error, minimize response time to a leak event, and maximize midstream visibility. Furthermore, SwRI has been working towards integrating Quantitative OGI (QOGI) capabilities into this existing technology. By leveraging Deep Learning, SwRI now has the capability to estimate fugitive emission leak rates quickly and reliably, which allows operators to detect emissions, quantify leak rate, prioritize repairs, and validate the repairs in a single instrument. The next generation QOGI technology leverages the same cameras used in Leak Detection and Repair (LDAR) programs, with improvements in safety and speed for traditional quantification-based repairs, ultimately leading to less overhead cost for the operators. The goals for this research were to develop two types of models with the following goals: 1. Run in real-time on the edge (≥ 12 Hz) 2. Classification: Achieve less than 5% false positive detection 3. Classification: Achieve ≥ 95% methane plume detection rate 4. Regression: achieve ≤ 10 standard cubic feet per hour (scfh) prediction > 70% of the time In order to achieve these results, multiple infrared (IR) and other sensors were investigated in tandem with the midwave IR (MWIR) OGI to provide additional information to train the underlying models. Information on atmospheric conditions including humidity, temperature, pressure, and solar radiation was provided by a weather station. Several machine learning and deep learning architectures and methods, including looking at quantized classification networks and regressions networks, were explored. As further data was collected, curated, and labeled, it allowed for more refined regressive networks to be adequately trained, leading to better insight into the true flow rates being observed. An important valuable deliverable of this research effort was the development of an advanced network which underwent multiple iterations capable of giving a continuous output. The current network has a predicted mean average percentage error (MAPE) of 12.3% just outside our target goal of 10.00%, but an accuracy of 97.78% at ±50 scfh, well within the overall goal for the Department of Energy (DOE) program. Upon closer inspection, it was observed that more than 10% of datapoints contributing to the MAPE predictions were the result of low flow rate predictions and are beyond the sensitivity of instrument measurement as a result of normal operational variation and noise.

03 NATURAL GAS↗
DOE OSTI2020

Building thermal load prediction through shallow machine learning and deep learning

Building thermal load prediction informs the optimization of cooling plant and thermal energy storage. Physics-based prediction models of building thermal load are constrained by the model and input complexity. In this study, we developed 12 data-driven models (7 shallow learning, 2 deep learning, and 3 heuristic methods) to predict building thermal load and compared shallow machine learning and deep learning. The 12 prediction models were compared with the measured cooling demand. It was found XGBoost (Extreme Gradient Boost) and LSTM (Long Short Term Memory) provided the most accurate load prediction in the shallow and deep learning category, and both outperformed the best baseline model, which uses the previous day's data for prediction. Then, we discussed how the prediction horizon and input uncertainty would influence the load prediction accuracy. Major conclusions are twofold: first, LSTM performs well in short-term prediction (1 h ahead) but not in long term prediction (24 h ahead), because the sequential information becomes less relevant and accordingly not so useful when the prediction horizon is long. Second, the presence of weather forecast uncertainty deteriorates XGBoost's accuracy and favors LSTM, because the sequential information makes the model more robust to input uncertainty. Training the model with the uncertain rather than accurate weather data could enhance the model's robustness. Finally, our findings have two implications for practice. First, LSTM is recommended for short-term load prediction given that weather forecast uncertainty is unavoidable. Second, XGBoost is recommended for long term prediction, and the model should be trained with the presence of input uncertainty.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Methods for rapid identification of anomalous layers in laser powder bed fusion

In situ process monitoring is a key requirement for increased industry acceptance of powder bed Additive Manufacturing. As sensing technologies increase in maturity, attention must also be given to effective data exploration techniques. These data are often high-resolution and multi-modal, with each build consisting of thousands of layers. Here, in this paper, the authors propose two methods enabling users to rapidly identify layers of interest within a build. Both methods leverage results from deep learning based segmentations of in situ powder bed images. The first method is an unsupervised “reverse layer search” algorithm while the second method uses supervised machine learning.

36 MATERIALS SCIENCE↗
DOE OSTI2021

pnnl/mol_dgnn

Molecular dynamics simulations often rely on parameterized atomistic potentials, which can be inaccurate compared to ab initio simulation methods. However, dynamic ab initio simulations come with high computational cost. Deep learning techniques offer a method to obtain both high accuracy and low cost predictions of dynamics. Our method gives a prediction of the structural dynamics of a molecule accounting for the prior dynamics, giving high-accuracy predictions at low computational cost

Ashby, Michael↗
DOE OSTI2021

Smart Methane Emission Detection System Development (Final Report)

Working with the Department of Energy's National Energy Technology Laboratory, Southwest Research Institute® (SwRI®) developed a system to identify methane leaks reliably, accurately, and autonomously at critical midstream sections of the natural gas distribution network in real-time for the purpose of mitigating methane emissions using Optical Gas Imaging (OGI) cameras. SwRI's Smart Leak Detection – Methane (SLED/M) adds a high degree of automation to the process of methane leak detection to minimize sources of human error, minimize response time to a leak event, and maximize midstream visibility. Furthermore, SwRI has been working towards integrating Quantitative OGI (QOGI) capabilities into this existing technology. By leveraging Deep Learning, SwRI now has the capability to estimate fugitive emission leak rates quickly and reliably, which allows operators to detect emissions, quantify leak rate, prioritize repairs, and validate the repairs in a single instrument. The next generation QOGI technology leverages the same cameras used in Leak Detection and Repair (LDAR) programs, with improvements in safety and speed for traditional quantification-based repairs, ultimately leading to less overhead cost for the operators. The goals for this research were to develop two types of models with the following goals: Run in real-time on the edge (≥ 12 Hz), Classification: Achieve less than 5% false positive detection, Classification: Achieve ≥ 95% methane plume detection rate, Regression: achieve ≤ 10 standard cubic feet per hour (scfh) prediction > 70% of the time. In order to achieve these results, multiple infrared (IR) and other sensors were investigated in tandem with the midwave IR (MWIR) OGI to provide additional information to train the underlying models. Information on atmospheric conditions including humidity, temperature, pressure, and solar radiation was provided by a weather station. Several machine learning and deep learning architectures and methods, including looking at quantized classification networks and regressions networks, were explored. As further data was collected, curated, and labeled, it allowed for more refined regressive networks to be adequately trained, leading to better insight into the true flow rates being observed. An important valuable deliverable of this research effort was the development of an advanced network which underwent multiple iterations capable of giving a continuous output. The current network has a predicted mean average percentage error (MAPE) of 12.3% just outside our target goal of 10.00%, but an accuracy of 97.78% at ±50 scfh, well within the overall goal for the Department of Energy (DOE) program. Upon closer inspection, it was observed that more than 10% of datapoints contributing to the MAPE predictions were the result of low flow rate predictions and are beyond the sensitivity of instrument measurement as a result of normal operational variation and noise.

03 NATURAL GAS↗
DOE OSTI2022

Sparse Data Machine Learning Integration with Theory, Experiment and Uncertainty Quantification: Process-Structure-Property-Performance of Friction Deformation Processing

Computer vision and deep learning tools that advance the ability to establish processing-structure-property-performance (PSPP) relations are presented. The Bayesian binning method for image segmentation enables quantitative analysis of microstructural features in an automated way, while the analysis of shapes and relative orientation of these features reveals local deformation maps indicative of both, material flow and residual stresses due to materials processing. The deep learning method leads to the previous knowledge agnostic mapping of empirically observed microstructural zones in friction stir welding (FSW) process and synthetic microstructure generation capability that is statistically equivalent to experimentally collected data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. In this paper a comprehensive method for accurate 3D instance segmentation of cells in the brain tissue is introduced. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with current deep learning-based 3D instance segmentation methods.

3D instance segmentation↗
DOE OSTI2023

Integrated path planning and control through proximal policy optimization for a marine current turbine

This paper presents an integrated path planning and tracking control framework for a marine current turbine (MCT), where the MCT is treated as an energy-harvesting autonomous underwater vehicle (AUV). Considering the ocean (space of action) is continuous, the proposed framework employs two modules to address path planning and path tracking enabled by the proximal policy optimization (PPO) algorithm, which is a policy gradient deep reinforcement learning (RL) method. Further, to enable fully autonomous operation in a stochastic oceanic environment, the proposed path planning seeks a primary objective of maximizing the harvested energy; then, the path tracking module is designed to minimize the tracking error and avoid collisions with static and dynamic obstacles. Using field-collected acoustic Doppler current profiler (ADCP) data, the performance of the proposed framework is evaluated. Comparative studies with baseline algorithms in three different scenarios of path planning, path tracking without an obstacle, and path tracking with collision avoidance verify the effectiveness of our proposed approach.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Subject-specific modeling framework for particle deposition using computational fluid dynamics

Quantifying particle deposition and dose in the respiratory tract requires a physiologically realistic representation and reproducible computational workflows. However, existing modeling frameworks, such as the International Commission on Radiological Protection (ICRP) compartmental models and the Multiple Path Particle Dosimetry (MPPD) tool, lack detailed deposition profiles and subject-specific capabilities. The combination of advances in computer vision algorithms applied to the respiratory tract and Computational Fluid and Particle Dynamics (CFPD) allows high-fidelity simulations of particle behavior in anatomically accurate geometries derived from individual CT scans. The segmentation, preprocessing, and file preparation task for a CFPD simulation was often time-consuming, and no prior studies to-date have yet presented a fully automated framework. This work presents a fully automated workflow to obtain individualized particle deposition profiles in the human respiratory tract. The pipeline starts with segmenting upper and lower airway geometries using morphological and deep learning-based methods, generating three-dimensional (3D) models from CT imaging data. Next, a series of algorithms are presented to quality check and prepare the 3D geometry for a CFD or CFPD simulation. The preprocessing step includes correcting geometric artifacts, enforcing a physically consistent mesh, and automatically identifying and capping multiple outlets, which is required for CFD/CFPD simulations. These processed models are then input into open-source (OpenFOAM) or commercial (StarCCM+) CFD solvers, where flow and transient particle transport equations — including turbulence and particle–wall interactions are solved under realistic breathing conditions. Finally, the resulting particle deposition profiles can be integrated with Monte Carlo radiation transport codes and state-of-the-art computational phantoms to assess organ-specific absorbed doses in scenarios of radioactive aerosol inhalation. The presented work streamlines respiratory tract segmentation, preprocessing for CFD/CFPD simulations, and integration with dose assessment workflows, reducing manual intervention and improving access to high-fidelity, subject-specific modeling. The high precision in predicted particle deposition and dose distributions can improve personalized treatment strategies in respiratory medicine and refine dose estimates for radiation protection.

AI↗
DOE OSTI2026

scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation

Accurate cell type annotation remains a major bottleneck in plant single-cell RNA sequencing (scRNA-seq), where existing tools are often adapted from animal studies and perform sub-optimally on plant data. The lack of plant-specific computational frameworks limits the construction of plant cell atlases and downstream biological discovery. We develop and evaluate scPlantAnnotate, a Transformer-based reference annotation framework tailored for plant scRNA-seq data, and benchmark it against state-of-the-art deep learning and conventional methods across multiple plant species. Species-specific scPlantAnnotate models were trained using curated datasets from Arabidopsis thaliana, Zea mays, Oryza sativa, and Glycine max. We compared scPlantAnnotate with leading baselines under both standard random-split evaluation and a more stringent leave-one-dataset-out setting, which tests robustness to completely unseen datasets and tissue types. scPlantAnnotate consistently outperforms existing approaches across all four species under random-split evaluation. In the leave-one-dataset-out setting for A. thaliana, where performance drops markedly for all methods due to strong batch effects and dataset heterogeneity, scPlantAnnotate nonetheless achieves the highest Accuracy, Macro-F1, Balanced Accuracy, and Macro-AUROC on average and ranks first on most held-out datasets. These results demonstrate improved robustness to dataset shifts, a critical yet underexplored challenge in plant scRNA-seq analysis. A freely accessible web server enables users to annotate their own datasets using pretrained models. scPlantAnnotate provides a plant-specific, Transformer-based framework for single-cell annotation that delivers state-of-the-art performance and enhanced robustness to unseen datasets. By addressing limitations of existing tools and enabling scalable reference-based annotation, scPlantAnnotate supports the development of comprehensive plant cell atlases and facilitates broader use of single-cell genomics in plant biology.

Bioinformatics↗
DOE OSTI2022

Machine Learning-Guided Discovery of Ternary Compounds Containing La, P, and Group 14 Elements

In this work, we integrate a deep machine learning (ML) method with first-principles calculations to efficiently search for the energetically favorable ternary compounds. Using La–Si–P as a prototype system, we demonstrate that ML-guided first-principles calculations can efficiently explore crystal structures and their relative energetic stabilities, thus greatly accelerate the pace of material discovery. A number of new La–Si–P ternary compounds with formation energies less than 30 meV/atom above the known ternary convex hull are discovered. Among them, the formation energies of La 5 SiP 3 and La 2 SiP phases are only 2 and 10 meV/atom, respectively, above the convex hull. These two compounds are dynamically stable with no imaginary phonon modes. Moreover, by replacing Si with heavier-group 14 elements in the eight lowest-energy La–Si–P structures from our ML-guided predictions, a number of low-energy La–X–P phases (X = Ge, Sn, Pb) are predicted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗