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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

This review article describes the co-evolution of structural biology as a discipline and the Protein Data Bank (PDB), established in 1971 as the first open-access data resource in biology by like-minded structural scientists. As the PDB archive grew in size and scope to encompass macromolecular crystallography, NMR spectroscopy, and cryo-electron microscopy, new technologies were developed to ingest, validate, curate, store, and distribute the information. Community engagement ensured that the needs of structural biologists (data depositors) and data consumers were met. Today, the archive houses more than 230,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexes with one another and small-molecule ligands. Aggregate costs of PDB data preservation are ~1% of the cost of structure determination. The enormous impact of PDB data on basic and applied research and education across the natural and medical sciences is presented and highlighted with illustrative examples. Enablement of de novo protein structure prediction (AlphaFold2, RoseTTAfold, OpenFold, etc.) is the most widely appreciated benefit of having a corpus of rigorously validated, expertly curated 3D biostructure data.

bioinformatics↗
DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗
DOE OSTI2024

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

A Curated Experimental Compilation Analyzed by Theory Is More than a Review

Macromolecules is an exceptional resource in the field of polymer science and now publishes more than 1000 original articles a year that set the standard for scientific rigor and creative insights. Over the years, these individual contributions have combined to build the foundation of polymer science, broadly and inclusively defined. In addition to the individual articles, many of which are being celebrated in this series of editorials, Macromolecules has published invaluable reviews and perspectives. These scholarly contributions integrate the insights and results from numerous sources into a unified whole and often recommend future directions for the field. Novices and experts alike benefit from these works that capture topics from emerging discoveries to long-pondered topics and everything in between. To explore the importance of Macromolecules’ reviews and perspectives, we considered their influence on the field and found the 1994 review by Fetters et al. entitled “Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties”1 to be a singularity. This review expertly curates and compiles a trove of data to build robust correlations between molecular characteristics and macroscopic viscoelastic properties of polymer melts, in the context of the tube model of entanglements.

36 MATERIALS SCIENCE↗
DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Benchmarking the performance of uncertainty quantification methods for neural network-based interatomic potentials

Machine-learned interatomic potentials (ML-IAPs) continue to gain popularity as accurate, computationally efficient replacements for traditional, physics-based interatomic potentials and expensive ab initio methods. Uncertainty quantification (UQ) of ML-IAPs is a growing area of research as UQ is critical in many applications of IAPs, such as developing curated datasets, active learning-based data augmentation, self-improving models, and estimating the uncertainty of molecular dynamics simulations. In this paper, we construct and benchmark a series of different neural network potentials (NNPs) with varying network architectures to determine the performance of these models with respect to both the mean and uncertainty calibration error. Each NNP method is specifically designed to predict either epistemic or aleatoric uncertainty with particular focus on the differences in behavior between the epistemic and aleatoric uncertainty estimates. We benchmark these methods using multiple datasets common in the ML-IAP literature. The results show that the aleatoric uncertainty from single-shot model architectures is a competitive alternative to ensemble-based epistemic uncertainty predictions in regions of sufficient data-density. However, in regions where the representative data is sparse, aleatoric uncertainty models tend to overpredict and epistemic methods tend to underpredict the actual model error. We conclude that the type of UQ is crucial when discussing performance of probabilistic model results as different methods have different performance characteristics depending on the regime in which they are evaluated. Therefore, the type of UQ method should be carefully evaluated against both the data characteristics and requirements for the intended application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Toward Urban Water Security: Broadening the Use of Machine Learning Methods for Mitigating Urban Water Hazards

Due to the complex interactions of human activity and the hydrological cycle, achieving urban water security requires comprehensive planning processes that address urban water hazards using a holistic approach. However, the effective implementation of such an approach requires the collection and curation of large amounts of disparate data, and reliable methods for modeling processes that may be co-evolutionary yet traditionally represented in non-integrable ways. In recent decades, many hydrological studies have utilized advanced machine learning and information technologies to approximate and predict physical processes, yet none have synthesized these methods into a comprehensive urban water security plan. In this paper, we review ways in which advanced machine learning techniques have been applied to specific aspects of the hydrological cycle and discuss their potential applications for addressing challenges in mitigating multiple water hazards over urban areas. We also describe a vision that integrates these machine learning applications into a comprehensive watershed-to-community planning workflow for smart-cities management of urban water resources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

From RNNs to Foundation Models: An Empirical Study on Commercial Building Energy Consumption

Accurate short-term energy consumption forecasting for commercial buildings is crucial for smart grid operations. While smart meters and deep learning models enable forecasting using past data from multiple buildings, data heterogeneity from diverse buildings can reduce model performance. The impact of increasing dataset heterogeneity in time series forecasting, while keeping size and model constant, is understudied. We tackle this issue using the ComStock dataset, which provides synthetic energy consumption data for U.S. commercial buildings. Two curated subsets, identical in size and region but differing in building type diversity, are used to assess the performance of various time series forecasting models, including finetuned open-source foundation models (FMs). The results show that dataset heterogeneity and model architecture have a greater impact on post-training forecasting performance than the parameter count. Moreover, despite the higher computational cost, finetuned FMs demonstrate competitive performance compared to base models trained from scratch.

commercial buildings↗
DOE OSTI2022

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

Abstract. In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

ClimateNet: an expert-labeled open dataset and deep learning architecture for enabling high-precision analyses of extreme weather

Abstract. Identifying, detecting, and localizing extreme weather events is a crucial first step in understanding how they may vary under different climate change scenarios. Pattern recognition tasks such as classification, object detection, and segmentation (i.e., pixel-level classification) have remained challenging problems in the weather and climate sciences. While there exist many empirical heuristics for detecting extreme events, the disparities between the output of these different methods even for a single event are large and often difficult to reconcile. Given the success of deep learning (DL) in tackling similar problems in computer vision, we advocate a DL-based approach. DL, however, works best in the context of supervised learning – when labeled datasets are readily available. Reliable labeled training data for extreme weather and climate events is scarce. We create “ClimateNet” – an open, community-sourced human-expert-labeled curated dataset that captures tropical cyclones (TCs) and atmospheric rivers (ARs) in high-resolution climate model output from a simulation of a recent historical period. We use the curated ClimateNet dataset to train a state-of-the-art DL model for pixel-level identification – i.e., segmentation – of TCs and ARs. We then apply the trained DL model to historical and climate change scenarios simulated by the Community Atmospheric Model (CAM5.1) and show that the DL model accurately segments the data into TCs, ARs, or “the background” at a pixel level. Further, we show how the segmentation results can be used to conduct spatially and temporally precise analytics by quantifying distributions of extreme precipitation conditioned on event types (TC or AR) at regional scales. The key contribution of this work is that it paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data using a curated expert-labeled dataset – ClimateNet. ClimateNet and the DL-based segmentation method provide several unique capabilities: (i) they can be used to calculate a variety of TC and AR statistics at a fine-grained level; (ii) they can be applied to different climate scenarios and different datasets without tuning as they do not rely on threshold conditions; and (iii) the proposed DL method is suitable for rapidly analyzing large amounts of climate model output. While our study has been conducted for two important extreme weather patterns (TCs and ARs) in simulation datasets, we believe that this methodology can be applied to a much broader class of patterns and applied to observational and reanalysis data products via transfer learning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

An Open Combinatorial Diffraction Dataset Including Consensus Human and Machine Learning Labels with Quantified Uncertainty for Training New Machine Learning Models

Modern machine learning and autonomous experimentation schemes in materials science rely on accurate analysis of the data ingested by these models. Unfortunately, accurate analysis of the underlying data can be difficult, even for domain experts, complicating the training of the models intended to drive experiments. This is especially true when the goal is to identify the presence of weak signatures in diffraction or spectroscopic datasets. In this work, we examine a set of as-obtained diffraction data that track the phase transition from monoclinic to tetragonal in a Nb-doped VO2 film as a function of temperature and dopant concentration. We then task a set of domain experts and a set of machine learning experts with identifying which phase is present in each diffraction pattern manually and algorithmically, respectively; in both cases, the labels can vary dramatically, especially at the phase boundaries. We use the mode of the labels and the Shannon entropy as a method to capture, preserve and propagate consensus labels and their variance. Further we use the expert labels as a benchmark and demonstrate the use of Shannon entropy weighted scoring to test the performance of machine learning generated labels. Finally, we propose a material data challenge centered around generating improved labeling algorithms. This real-world dataset curated with expert labels can act as test bed for new algorithms. The raw data, annotations and code used in this study are all available online at data.gov and the interested reader is encouraged to replicate and improve the existing models

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Ontologizing health systems data at scale: making translational discovery a reality

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Identifying Genomic Islands with Deep Neural Networks

Background Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types. Results We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools. Conclusions We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.

Computer Vision↗
DOE OSTI2020

Status Report on the Molten Salt Thermodynamic Database (MSTDB) Development (FY20)

The current status of the Molten Salt Thermodynamic Database (MSTDB) is reported. While a series of informational exchange meetings with Moten Salt Reactor (MSR) developers has given the NEAMS program insight into the systems of interest, the current effort is devoted to mining data already available in the literature for continued development of MSTDB. Many relevant systems have not been previously studied. Therefore, once the data from the literature is completely reviewed, curated, and used as inputs for MSTDB, new thermodynamic values will need to be generated using computational and experimental approaches.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2026

SimLBR: Learning to Detect Fake Images by Learning to Detect Real Images

The rapid advancement of generative models has made the detection of AI-generated images a critical challenge for both research and society. Recent works have shown that most state-of-the-art fake image detection methods overfit to their training data and catastrophically fail when evaluated on curated hard test sets with strong distribution shifts. In this work, we argue that it is more principled to learn a tight decision boundary around the real image distribution and treat the fake category as a sink class. To this end, we propose SimLBR, a simple and efficient framework for fake image detection with Latent Blending Regularization (LBR). Our method significantly improves cross-generator generalization, achieving up to +24.85% accuracy and +69.62% recall on the challenging Chameleon benchmark. SimLBR is also highly efficient, training orders of magnitude faster than existing approaches. Furthermore, we emphasize the need for reliability-oriented evaluation in fake image detection, introducing risk-adjusted metrics and worst-case estimates to better assess model robustness. All the code and models are availabe at: https://github.com/mvrl/SimLBR

Dhakal, Aayush [Washington University, St. Louis]↗
DOE OSTI2022

Hierarchical Conceptual Model Event and Activity Domains for Forecasting State-Sponsored Civil Nuclear Power Activities

In FY20, the Savannah River National Laboratory and the Sanghani Center for Artificial Intelligence and Data Analytics (Virginia Tech) entered a collaboration funded by the Department of Energy’s Office of Defense Nuclear Nonproliferation Research and Development to develop a machine learning based modeling pipeline to extract proliferation events of interest from open data sources. The prototype modeling pipeline that was developed relies on the use of time dependent word embedding models to identify contextual shifts in key words and phrases that act as indicators of events of interest. The FY20- 21 efforts were focused on a narrow topical domain of forecasting “fissile core fabrication” at the Savannah River Site prior to its official announcement in 2018. In FY22, the research team was funded to continue development of the modeling pipeline by applying it to the problem of forecasting new, and/or significant changes to existing, civil nuclear power reactors around the world. In this effort, the development will focus on proving applicability to a broader topical domain and in data environments that may contain more sparse information, relative to the United States. In this report, the worldwide landscape of civil nuclear reactors is outlined, the timeline of interest is defined, and a hierarchical conceptual model is established to identify the activity domains of interest and the event domains of interest. This preliminary effort will guide the curation of a glossary of key terms for data acquisition, as well as the downstream modeling efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗
DOE OSTI2026

Antarctic ice sheet model comparison with uncurated geological constraints shows that higher spatial resolution improves deglacial reconstructions

Accurately reconstructing past changes to the shape and volume of the Antarctic ice sheet relies on the use of physically based and thus internally consistent ice sheet modeling, benchmarked against spatially limited geologic data. The challenge in model benchmarking against geologic data is diagnosing whether model-data misfits are the result of an inadequate model, inherently noisy or biased geologic data, and/or incorrect association between modeled quantities and geologic observations. In this work we address this challenge by (i) the development and use of a new model-data evaluation framework applied to an uncurated data set of geologic constraints, and (ii) nested high-spatial-resolution modeling designed to test the hypothesis that model resolution is an important limitation in matching geologic data. While previous approaches to model benchmarking employed highly curated datasets, our approach applies an automated screening and quality control algorithm to an uncurated public dataset of geochronological observations (specifically, cosmogenic-nuclide exposure-age measurements from glacial deposits in ice-free areas). This optimizes data utilization by including more geological constraints, reduces potential interpretive bias, and allows unsupervised assimilation of new data as they are collected. We also incorporate a nested model framework in which high-resolution domains are downscaled from a continent-wide ice sheet model. We highlight the application of this framework by applying these methods to a small ensemble of deglacial ice-sheet model simulations, and demonstrate that the nested approach improves the ability of model simulations to match exposure age data collected from areas of complex topography and ice flow. We develop a range of diagnostic model-data comparison metrics to provide more insight into model performance than possible from a single-valued misfit statistic, showing that different metrics capture different aspects of ice sheet deflation.

Geosciences↗