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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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DOE OSTI2025

Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques

Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overdose contributing to the opioid crisis in the United States. Therefore, understanding the structure-activity relationship between MOR and its ligands is essential for predicting MOR binding of chemicals, which could assist in the development of non-addictive or less-addictive opioid analgesics. This study aimed to develop machine learning and deep learning models for predicting MOR binding activity of chemicals. Chemicals with MOR binding activity data were first curated from public databases and the literature. Molecular descriptors of the curated chemicals were calculated using software Mold2. The chemicals were then split into training and external validation datasets. Random forest, k-nearest neighbors, support vector machine, multi-layer perceptron, and long short-term memory models were developed and evaluated using 5-fold cross-validations and external validations, resulting in Matthews correlation coefficients of 0.528–0.654 and 0.408, respectively. Furthermore, prediction confidence and applicability domain analyses highlighted their importance to the models’ applicability. Our results suggest that the developed models could be useful for identifying MOR binders, potentially aiding in the development of non-addictive or less-addictive drugs targeting MOR.

Research & Experimental Medicine↗

DOE OSTI2025

Denoising Seismograms in the Time Domain Using a Deep Learning Model

Deep learning has emerged as a transformative tool for enhancing the extraction of reliable information from seismograms, addressing the increasing demand for precise and efficient seismic data analysis. We introduce an innovative encoder–decoder deep learning model, named WaveDenoiser, designed for noise reduction in the time domain, thereby eliminating the need for spectrogram computations that have been used for existing deep learning tools and significantly improving processing speed. Utilizing the benchmark dataset that is Stanford Earthquake Dataset, we developed three models of varying sizes: base, medium, and large. Notably, the large (referred to as WaveDenoiser) model demonstrated superior performance, achieving a median signal‐to‐noise ratio improvement of 8.8 dB on in‐distribution unseen data (in the same geographic region) and 7.7 dB on out‐distribution unseen data (in a new geographic region), outpacing both the base and medium models. Further evaluation of the WaveDenoiser model revealed a reduction in median arrival‐time errors by 0.02 s for P waves and 0.01 s for S waves when processing waveforms prior to phase picking using PhaseNet on in‐distribution unseen data. When tested on out‐distribution unseen data, the model also effectively reduced the P‐wave median arrival‐time error by 0.02 and 0.01 s in median arrival‐time error for S waves. Importantly, the application of WaveDenoiser resulted in a significant reduction of phase picking outliers by 1.1% to 3.6% for both P and S waves. In addition, we achieved over five times acceleration in processing speed compared with the seisBench implementation of DeepDenoiser. Our findings underscore the potential of WaveDenoiser as a powerful tool for improving seismic data analysis and processing efficiency.

P-waves↗

DOE OSTI2026

Data for FUN-PROSE: A Deep Learning Approach to Predict Condition-Specific Gene Expression in Fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Genomics↗

DOE OSTI2025

Applying Deep Learning for Wildfire Identification: Economical and Accessible Solutions Leveraging Small Datasets

Wildfires significantly impact human health, air quality, visibility, weather, and climate change and cause substantial economic losses. While state and county-operated air quality monitors provide critical insights during wildfires, they are not available in all regions. This highlights the need for affordable, accessible tools that allow the general public to assess air quality impacts. In this study, we apply machine learning with deep neural networks to diagnose air quality rapidly from sky images taken at the Pacific Northwest National Laboratory in Richland, WA, USA. Using a convolutional neural network (CNN) framework, we trained a deep learning model to classify air quality indices based on sky images. By leveraging transfer learning, our approach fine-tunes a pre-trained model on a small dataset of sky images, significantly reducing training time while maintaining high accuracy. Our results demonstrate the potential of deep learning to provide rapid air quality diagnostics during wildfire episodes, offering early warnings to the public and enabling timely mitigation strategies, particularly for vulnerable populations. Additionally, we show that lower respiratory infections pose the highest health risk during acute smoke exposures. Reactive oxygen species (ROS) from wildfire particles further exacerbate health risks by triggering inflammation and other adverse effects.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models

Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they enable researchers to create accurate models with minimal effort and computational resources. Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. We argue that these models are the equivalent of foundation models in natural language processing in their utility, as they encode within them chromatin state in its different aspects, providing useful representations that allow quick deployment of accurate models of gene regulation. We demonstrate this premise by leveraging the recently created Sei model to develop simple, interpretable models of intron retention, and demonstrate their advantage over models based on the DNA language model DNABERT-2. Our work also demonstrates the impact of chromatin state on the regulation of intron retention. Using representations learned by Sei, our model is able to discover the involvement of transcription factors and chromatin marks in regulating intron retention, providing better accuracy than a recently published custom model developed for this purpose.

Biochemistry & Molecular Biology↗

DOE OSTI2025

S AP F LOWER : an automated tool for sap flow data preprocessing, gap-filling, and analysis using deep learning

Sap flow, a critical process in plant water use and ecosystem water cycles, is often measured using thermal dissipation probes (TDP) due to their ease of installation and continuous data collection. However, sap flow data frequently include noise, outliers, and gaps, creating challenges for analysis and requiring substantial manual processing. We developed S AP F LOWER , a tool that automates data preprocessing, model training, gap-filling, sapwood area scaling and modeling, and water use analysis. It integrates autocleaning, machine learning and deep learning models (e.g. random forest, Gaussian process regression, long short-term memory (LSTM), bidirectional LSTM (BiLSTM)), and efficient workflows to process sap flow data. S AP F LOWER can remove over 90% of noisy data while preserving legitimate variations and achieve high accuracy in gap-filling based on user-determined parameters. Random forest, LSTM, and BiLSTM models reduced root mean square error to 10% or less for long-term gaps. Model training and prediction can be performed efficiently within seconds. S AP F LOWER significantly enhances the efficiency and accessibility of TDP data analysis by automating complex tasks, enabling researchers without programming expertise to employ advanced techniques. Future improvements will focus on species-specific corrections for TDP and support for additional measurement methods. S AP F LOWER is openly available on GitHub (https://github.com/JiaxinWang123/SapFlower) and Zenodo (doi: 10.5281/zenodo.13665919).

ecosystem water balance↗

DOE OSTI2025

Kinetic Deep Learning v0.1

Here, we present a method that uses protein levels to predict times series of metabolite concentrations. Understanding this type of pathway dynamics is important in order to predict the behavior of the pathway and, more pragmatically, to be able to design biological systems (such as strains bioengineered to produce chemical products) reliably. Typically, for this purpose, kinetic models consisting of differential equations based on the Michaelis-Menten dynamics have been used in the past. However, these methods can rarely produce good fits to measured data time series. Possibly, this happens because the kinetic constants are unknown or are different from the ones measured in vivo, or perhaps because Michaelis-Menten dynamics is not a satisfactory description. In order to improve the predictive nature of these kinetic models we have eliminated the Michaelis-Menten description of pathway dynamics and we have substituted it by algorithms that automatically learn these dynamics from previously obtained metabolomics and proteomics data using machine learning approaches. Specifically, kinetic deep learning uses deep learning to map proteomics time series to metabolite concentration time series, instead of learning the first metabolite derivative and integrating in (as in the first version of kinetic learning). This approach is shown to provide good to excellent results with a data set specifically collected for this purpose.

Garcia Martin, Hector [Joint BioEnergy Institute (↗

DOE OSTI2025

Embracing the unknown: Why uncertainty matters in deep learning

Most cutting-edge deep learning models are focused on only one thing: improving prediction accuracy. But in the real world, especially in high-stakes domains like science, medicine, and safety (e.g. self-driving cars), knowing what your model doesn't know can be just as important. My goal for this talk is to convince you that uncertainty quantification (UQ) is essential in deep learning. We’ll explore how existing UQ methods work, what they still get wrong, and how ideas from disciplines like astrophysics and environmental science are key to driving the development of better (more trustworthy) deep learning methods.

Nevin, Becky [Fermilab]↗

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 OSTI2025

Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry

Graph deep learning models, which incorporate a natural inductive bias for atomic structures, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, MatGL is designed to be an extensible “batteries-included” library for developing advanced model architectures for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also provides several pre-trained foundation potentials (FPs) with coverage of the entire periodic table, and property prediction models for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL integrates with PyTorch Lightning to enable efficient model training.

chemistry↗

DOE OSTI2025

Deciphering the small-angle scattering of polydisperse hard spheres using deep learning

We introduce a deep learning approach for analyzing the scattering function of the polydisperse hard sphere system. We use a variational autoencoder-based neural network to learn the bidirectional mapping between the scattering function and the system parameters, including the volume fraction and polydispersity. Such that the trained model serves both as a generator that produces a scattering function from the system parameters and an inferrer that extracts system parameters from the scattering function. We first generate a scattering dataset by carrying out molecular dynamics simulations of the polydisperse hard spheres modeled by the truncated-shifted Lennard-Jones model, then analyze the scattering function dataset using singular value decomposition to confirm the feasibility of dimensional compression. Then, we split the dataset into training and testing sets and train our neural network on the training set only. Our generator model produces a scattering function with significantly higher accuracy compared to the traditional Percus–Yevick approximation and β correction, and the inferrer model can extract the volume fraction and polydispersity with much higher accuracy than traditional model functions.

Ding, Lijie [ORNL] (ORCID:0000000227454606)↗

DOE OSTI2026

FitCache: A Transparent Drop-In Framework for Multi-Tier Caching to Accelerate Distributed Deep Learning Workloads

Training in Deep learning (DL) remains highly compute- and data-intensive, with I/O becoming a critical bottleneck as models and datasets scale. Recent studies report that data loading can dominate training time, especially on large-scale HPC systems with shared parallel file systems (PFS). Existing caching approaches either rely on single-tier designs or require intrusive modifications to training pipelines, limiting their portability and effectiveness. In this work, we present FitCache, a transparent drop-in framework for multi-tier caching to accelerate distributed DL training by coordinating fast local memory (e.g., DRAM, Persistent Memory (PMem)) and NVMe as hierarchical caches atop PFS. Our design adapts to hardware diversity, i.e., if NVMe is missing, memory transparently acts as a caching tier, ensuring stable performance. FitCache transparently intercepts I/O requests and issues concurrent fetches across all tiers, returning data from the fastest responder without centralized metadata or static redirection paths. FitCache adapts to dynamic workloads and heterogeneous clusters while maintaining POSIX compatibility. Experiments on Frontier (2048 GPUs) and smaller research clusters show that FitCache reduces training time by up to 40% and per-batch I/O latency by up to 71.6% compared to Lustre Orion PFS, offering a drop-in solution for scalable DL training.

Hu, Guangxing [ORNL] (ORCID:0009000283203614)↗

DOE OSTI2025

hls4ml: A Flexible, Open-Source Platform for Deep Learning Acceleration on Reconfigurable Hardware

We present hls4ml, a free and open-source platform that translates machine learning (ML) models from modern deep learning frameworks into high-level synthesis (HLS) code that can be integrated into full designs for field-programmable gate arrays (FPGAs) or application-specific integrated circuits (ASICs). With its flexible and modular design, hls4ml supports a large number of deep learning frameworks and can target HLS compilers from several vendors, including Vitis HLS, Intel oneAPI and Catapult HLS. Together with a wider eco-system for software-hardware co-design, hls4ml has enabled the acceleration of ML inference in a wide range of commercial and scientific applications where low latency, resource usage, and power consumption are critical. In this paper, we describe the structure and functionality of the hls4ml platform. The overarching design considerations for the generated HLS code are discussed, together with selected performance results.

FOS: Computer and information sciences↗

DOE OSTI2025

hls4ml: A Flexible, Open-Source Platform for Deep Learning Acceleration on Reconfigurable Hardware

Schulte, Jan-Frederik [Purdue U.] (ORCID:000000034↗

DOE OSTI2025

Scaling deep learning for material imaging with a pseudo 3D model for domain transfer

The recent introduction of deep learning methods for image processing has greatly advanced the characterization of materials using three-dimensional (3D) X-ray imaging techniques. However, deep learning models often have difficulty performing consistently across images owing to unavoidable variations in imaging conditions, which create inconsistencies even for the same material. As a result, networks must frequently be retrained for new datasets, limiting their applicability and generalization. Thus, it is critical to reduce the variations between images to enable a single model to process multiple datasets. Herein, we introduce P3T-Net, a pseudo-3D domain transfer network that transfers diverse 3D images into a uniform domain before processing using deep learning models. Remarkably, P3T-Net enables the reuse of previously trained networks for processing new images and considerably reduces the computational cost of transferring 3D images across domains. These unique capabilities were demonstrated in the following scenarios: (i) image enhancement of fast scans for geological rock and hydrogen fuel cells, (ii) enhancement of images to match the quality of multi-source imaging for lithium-ion batteries, (iii) accurate segmentation of images captured under different conditions, and (iv) tera-scale 3D transfer (10 11 voxels) on a single GPU. Overall, the proposed approach addresses cross-domain inconsistencies across various materials and conditions, thereby enabling more robust and generalizable deep learning solutions for a wide range of material imaging tasks.

25 ENERGY STORAGE↗

DOE OSTI2025

Development and Evaluation of a General Drag Model for Gas-Solid Flows via Deep Learning

This project presents the development and evaluation of a general drag model for gas–solid multiphase flows using deep learning techniques. A comprehensive database of more than 4,000 experimental and numerical data points for spherical and non spherical particles was compiled, incorporating geometric features such as sphericity, aspect ratio, and orientation. Several predictive approaches—including traditional em pirical correlations, machine learning, and deep neural networks—were benchmarked, with the proposed Drag Coefficient Correlation-aided Deep Neural Network (DCC DNN) demonstrating superior accuracy. To account for particle–particle interactions, additional drag data were generated using CFD-based simulations of packed and flu idized beds, leading to the development of a retrained model capable of incorporat ing volume fraction effects. Integration of the trained model with the MFiX CFD solver was achieved using FTorch, enabling drag predictions during discrete element method (DEM) simulations. Validation against experimental data for single particles and fluidized beds confirmed the model’s improved predictive ability, particularly for non-spherical geometries. While the model performed strongly under fluidized con ditions, limitations remained in unfluidized regimes, suggesting a need for expanded datasets. Overall, this study demonstrates the feasibility of combining deep learning with physics-informed CFD to improve drag modeling for gas–solid flows, with promis ing implications for scaling multiphase simulations in industrial applications.

42 ENGINEERING↗

DOE OSTI2026

Multi‐Scale Model‐Informed Deep Learning for Plasma‐Nanoparticle Interaction

The Overarching Goal of this proposed research is to understand and quantitively determine the interactions between non-thermal plasma (hot electrons, reactive radicals, vibrationally excited species) and surface reactions on influencing the activity and selectivity of the desired reactions via developing multi-scale model informed deep learning algorithm. Investigating non-thermal plasma-surface interaction is feasible due to the low bulk temperature in the discharge region. To investigate the role of plasma-nanoparticle interaction on enhancing the reaction kinetics, we will focus on ammonia cracking to generate clean hydrogen over earth-abundant, non-critical metallic nanoparticles, which is of great significance for decarbonization. We hypothesize that (1) reactive radicals interacting with surface reaction species via Eley–Rideal mechanism will significantly lower the energetics of the potential rate-limiting step of nitrogen formation; (2) the surface will be charged heterogeneously under non-thermal plasma conditions and the charged site will lower the energetics of ammonia cracking through Langmuir– Hinshelwood mechanism; (3) vibrationally excited ammonia will further promote the initial N-H bond cleavage. To access the hypothesis, we will (1) reveal the surface charge effects on tunning the reaction energetics via interpretable, physics-informed deep learning accelerated density functional theory (DFT) calculations; (2) determine the reactive radicals interacting with surface reaction species on tuning the reaction energetics via DFT; (3) reveal the surface charge effects on tunning the reaction energetics via DFT and deep learning models, (4) quantify how vibrationally excited species, reactive radicals, and surface charging effects on enhancing the catalysis via developing DFT-based microkinetic modeling (MKM) and active learning. Deep and active learning of plasma-nanoparticle interactions effects on enhancing ammonia cracking to generate hydrogen represents a new paradigm for designing high performance plasma materials. The fundamental science of how plasma-nanoparticle interactions will change the plasma kinetics and will improve the energy efficiency for decarbonization and sustainability. The interpretable and physics-informed machine learning model will accelerate low temperature plasma chemistry and material discovery with physics rules and model interpretation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Evaluating Probabilistic Deep Learning Methods for Uncertainty Quantification of Precipitation Bias Correction

Climate models often exhibit biases in their precipitation predictions, particularly underestimating high-intensity events and overestimating low precipitation. Deep learning approaches offer promising solutions, but their epistemic uncertainty associated with a deep learning–based bias correction method has not previously been quantified for reliable downstream climate impact studies. While methods for capturing the epistemic uncertainty in deep learning frameworks exist, there is currently no consensus on the best method. In this work, we compare three uncertainty quantification (UQ) methods—Deep Ensembles (DEns), Monte Carlo Dropout (MCD), and Flipout—by assessing the reliability of their uncertainty estimates using standard measures such as sharpness and calibration. These UQ methods are applied to an existing deep learning precipitation bias correction model known as UFNet: a coupled U-Net and fully connected neural network. The methods utilized to assess the models’ uncertainties are 1) calibration, which ensures that the expected probabilities of the model align with reality and 2) sharpness, which is a measure of the precision of the model’s probabilistic predictions. Of the three UQ methods evaluated, the DEns and MCD methods demonstrated the best-calibrated performance (expected calibration error of 0.36 and 0.35, respectively), compared to Flipout (0.58). In contrast, Flipout had the sharpest predictions and the highest metric performance in bias correcting precipitation—especially for higher-order moments such as kurtosis with a spatial correlation of 72% compared to 32% and 55% spatial correlation for DEns and MCD, respectively. Of the three UQ methods, MCD was found to be the most suitable method for UQ purposes based on its calibration, sharpness, and computational requirements.

Bayesian methods↗