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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 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Empirically-calibrated H100 node power models for accurate AI training energy estimation

Accurately quantifying the energy use of artificial intelligence (AI) training is critical for infrastructure planning, carbon accounting, and sustainable data center operation, but few studies have directly measured the power consumption of production workloads on contemporary hardware. By combining empirical measurements from Brookhaven National Laboratory during AI training on 8-graphics-processing-unit H100 systems with open-source benchmarking data, we develop statistical models relating computational intensity to node-level power consumption. We measure the gap between manufacturer-rated thermal design power (TDP) and actual power demand during AI training. Our analysis reveals that even computationally intensive workloads operate at only 76% of the 10.2 kW TDP rating. Our architecture-specific model, calibrated to floating-point operations, predicts energy consumption with 11.4% mean absolute percentage error, significantly outperforming TDP-based approaches (27%–37% error). We identified distinct power signatures between transformer and convolutional neural network architectures, with transformers showing characteristic fluctuations that may impact grid stability. These results provide a measurement-grounded basis for improving AI training energy estimates, enabling more reliable infrastructure sizing, cost projections, and environmental impact assessments.

Newkirk, Alex C↗
DOE OSTI2024

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Ludwig, David W↗
DOE OSTI2025

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Summary Protein property prediction via machine learning with and without labeled data is becoming increasingly powerful, yet methods are disparate and capabilities vary widely over applications. The software presented here, “Artificial Intelligence Driven protein Estimation (AIDE)”, enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods for variants and variable length homologs in a single, reproducible notebook or script by defining a modular, standardized application programming interface (API), i.e. drop-in compatible with scikit-learn transformers and pipelines. Availability and implementation AIDE is an installable, importable python package inheriting from scikit-learn classes and API and is installable on Windows, Mac, and Linux. Many of the wrapped models internal to AIDE will be effectively inaccessible without a GPU, and some assume CUDA. The newest stable, tested version can be found at https://github.com/beckham-lab/aide_predict and a full user guide and API reference can be found at https://beckham-lab.github.io/aide_predict/. Static versions of both at the time of writing can be found on Zenodo.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning

Abstract Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.

Plant Sciences↗
DOE OSTI2024

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗
DOE OSTI2023

Towards an astronomical foundation model for stars with a transformer-based model

ABSTRACT Rapid strides are currently being made in the field of artificial intelligence using transformer-based models like Large Language Models (LLMs). The potential of these methods for creating a single, large, versatile model in astronomy has not yet been explored. In this work, we propose a framework for data-driven astronomy that uses the same core techniques and architecture as used by LLMs. Using a variety of observations and labels of stars as an example, we build a transformer-based model and train it in a self-supervised manner with cross-survey data sets to perform a variety of inference tasks. In particular, we demonstrate that a single model can perform both discriminative and generative tasks even if the model was not trained or fine-tuned to do any specific task. For example, on the discriminative task of deriving stellar parameters from Gaia XP spectra, we achieve an accuracy of 47 K in Teff, 0.11 dex in log g, and 0.07 dex in [M/H], outperforming an expert XGBoost model in the same setting. But the same model can also generate XP spectra from stellar parameters, inpaint unobserved spectral regions, extract empirical stellar loci, and even determine the interstellar extinction curve. Our framework demonstrates that building and training a single foundation model without fine-tuning using data and parameters from multiple surveys to predict unmeasured observations and parameters is well within reach. Such ‘Large Astronomy Models’ trained on large quantities of observational data will play a large role in the analysis of current and future large surveys.

Leung, Henry W. (ORCID:0000000200362752)↗
DOE OSTI2023

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗
DOE OSTI2026

Conditional deep generative models for simultaneous simulation and reconstruction of entire events

We extend the particle-flow neural assisted simulations (arnassus) framework of fast simulation and reconstruction to entire collider events. In particular, we use two generative artificial intelligence tools, continuous normalizing flows and diffusion models, to create a set of reconstructed particle-flow objects conditioned on truth-level particles from CMS Open Simulations. While previous work focused on jets, our updated methods now can accommodate all particle-flow objects in an event along with particle-level attributes like particle type and production vertex coordinates. This approach is fully automated, entirely written in Python, and GPU-compatible. Using a variety of physics processes at the LHC, we show that the extended arnassus is able to generalize beyond the training dataset and outperforms the standard, public tool elphes.

Dreyer, Etienne [Weizmann Institute of Science, Re↗
DOE OSTI2026

Realizing the scientific program with polarized ion beams at the future BNL Electron Ion Collider

Polarized ion beams at the Electron Ion Collider (EIC) are essential to address some of the most important open questions at the twenty-first century frontiers of understanding of the fundamental structure of matter. Here, in this work, we summarize the science case and identify polarized 2 H, 3 He, 6 Li, and 7 Li ion beams as critical technology that will enable experiments which address the most important science. Furthermore, we discuss the required ion polarimetry and spin manipulation at the EIC. The current EIC accelerator design is presented. We identify a significant research and development effort across national and international laboratories and universities that is required over about a decade to realize the polarized ion beams and estimate (based on previous experience) that it will require about 20 full-time equivalent (FTE) over 10 years (or a total of about 200 FTE-years) of personnel, including graduate students, postdoctoral researchers, technicians, and engineers. Attracting, educating, and training a new generation of physicists in experimental spin techniques will be essential for the successful realization. Artificial intelligence and machine learning are seen as having significant potential for both acceleration of research and development and amplification of discovery in the optimal realization of this unique quantum technology on a cutting-edge collider. The research and development effort is synergistic with research in atomic physics and fusion energy science.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Designing and Utilizing Material Acceleration Platforms: Need for Workforce Development

In the quest to accelerate scientific discovery, the materials science field is rapidly moving toward the implementation of robotics and artificial intelligence driven workflows. Our recent summer school “Future Labs: Robotic Synthesis Coupled with Machine Learning for Energy Materials” provided learning opportunities for students, researchers, and educators in the materials science community. We describe this experience and provide our perspective on which new directions could be pursued to enable the future workforce to acquire cross-disciplinary skills.

Educational policy↗
DOE OSTI2025

AI-assisted transport of radioactive ion beams

Beams of radioactive heavy ions allow researchers to study rare and unstable atomic nuclei, shedding light into the internal structure of exotic nuclei and on how chemical elements are formed in stars. However, the extraction and transport of radioactive beams rely on time-consuming expert-driven tuning methods, where hundreds of parameters are manually optimized. Here, in this study, we introduce a system that employs Artificial Intelligence (AI), specifically utilizing Bayesian Optimization, to assist in the transport process of radioactive beams. We apply our methodology to real-life scenarios showing advantages when compared with standard tuning methods. This AI-assisted approach can be extended to other radioactive beam facilities around the world to improve operational efficiency and enhance scientific output.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Fundamental limit of jet tagging

Identifying the origin of high-energy hadronic jets (jet tagging) has been a critical benchmark problem for machine learning in particle physics. Jets are ubiquitous at colliders and are complex objects that serve as prototypical examples of collections of particles to be categorized. Over the last decade, machine learning-based classifiers have replaced classical observables as the state of the art in jet tagging. Increasingly complex machine learning models are leading to increasingly more effective tagger performance. Our goal is to address the question of convergence—are we getting close to the fundamental limit on jet tagging or is there still potential for computational, statistical, and physical insights for further improvements? We address this question using state-of-the-art generative models to create a realistic, synthetic dataset with a known jet tagging optimum. Various state-of-the-art taggers are deployed on this dataset, showing that there is a significant gap between their performance and the optimum. Our dataset and software are made public to provide a benchmark task for future developments in jet tagging and other areas of particle physics.

Artificial intelligence↗
DOE OSTI2024

Effectiveness of denoising diffusion probabilistic models for fast and high-fidelity whole-event simulation in high-energy heavy-ion experiments

Artificial intelligence (AI) generative models, such as generative adversarial networks (GANs), variational autoencoders, and normalizing flows, have been widely used and studied as efficient alternatives for traditional scientific simulations. However, they have several drawbacks, including training instability and inability to cover the entire data distribution, especially for regions where data are rare. This is particularly challenging for whole-event, full-detector simulations in high-energy heavy-ion experiments, such as sPHENIX at the Relativistic Heavy Ion Collider and Large Hadron Collider experiments, where thousands of particles are produced per event and interact with the detector. This work investigates the effectiveness of denoising diffusion probabilistic models (DDPMs) as an AI-based generative surrogate model for the sPHENIX experiment that includes the heavy-ion event generation and response of the entire calorimeter stack. DDPM performance in sPHENIX simulation data is compared with a popular rival, GANs. Results show that both DDPMs and GANs can reproduce the data distribution where the examples are abundant (low-to-medium calorimeter energies). Nonetheless, DDPMs significantly outperform GANs, especially in high-energy regions where data are rare. Additionally, DDPMs exhibit superior stability compared to GANs. The results are consistent between both central and peripheral centrality heavy-ion collision events. Moreover, DDPMs offer a substantial speedup of approximately a factor of 100 compared to the traditional Geant4 simulation method.

42 ENGINEERING↗
DOE OSTI2023

Gluon helicity in the nucleon from lattice QCD and machine learning

We present the first lattice QCD determination of the light cone gluon helicity correlation parton distribution function (PDF) with numerical evidence toward disfavoring negative gluon polarization in the nucleon. We present a solution for eliminating an inevitable contamination term that dominates the Euclidean correlations and makes determining gluon helicity PDF unfeasible. The proposed synergy between lattice QCD and artificial intelligence offers a superior platform to alleviate the defining challenge of extracting quark and gluon PDFs from the lattice data that are available in a limited domain due to a finite range of accessible hadron momenta. We suggest a systematically improvable method to extract PDFs from the lattice data, independent of inadequate parametrizations. The result of the gluon helicity will improve our understanding of the role of spin in the strong interaction and the nucleon-spin structure.

Lattice QCD↗