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DOE OSTI2021

Deep Bayesian local crystallography

Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Assessing the Reliability of Relevant Tweets and Validation Using Manual and Automatic Approaches for Flood Risk Communication

While Twitter has been touted as a preeminent source of up-to-date information on hazard events, the reliability of tweets is still a concern. Our previous publication extracted relevant tweets containing information about the 2013 Colorado flood event and its impacts. Using the relevant tweets, this research further examined the reliability (accuracy and trueness) of the tweets by examining the text and image content and comparing them to other publicly available data sources. Both manual identification of text information and automated (Google Cloud Vision, application programming interface (API)) extraction of images were implemented to balance accurate information verification and efficient processing time. The results showed that both the text and images contained useful information about damaged/flooded roads/streets. This information will help emergency response coordination efforts and informed allocation of resources when enough tweets contain geocoordinates or location/venue names. This research will identify reliable crowdsourced risk information to facilitate near real-time emergency response through better use of crowdsourced risk communication platforms.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Interferometric 4D-STEM for Lattice Distortion and Interlayer Spacing Measurements of Bilayer and Trilayer 2D Materials

Van der Waals materials composed of stacks of individual atomic layers have attracted considerable attention due to their exotic electronic properties that can be altered by, e.g., manipulating the twist angle of bilayer materials or the stacking sequence of trilayer materials. To fully understand and control the unique properties of these few-layer materials, a technique that can provide information about their local in-plane structural deformations, twist direction, and out-of-plane structure is needed. In principle, interference in overlap regions of Bragg disks originating from separate layers of a material encodes 3D information about the relative positions of atoms in the corresponding layers. Here, an interferometric 4D scanning transmission electron microscopy technique is described that utilizes this phenomenon to extract precise structural information from few-layer materials with nm-scale resolution. It is demonstrated how this technique enables measurement of local pm-scale in-plane lattice distortions as well as twist direction and average interlayer spacings in bilayer and trilayer graphene, and therefore provides a means to better understand the interplay between electronic properties and precise structural arrangements of few-layer 2D materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

A Quantum Leap for Dynamic Radiography

Dynamic radiography techniques have been instrumental in advancing the National Nuclear Security Administration's (NNSA) mission since WWII. This paper explores the transformative potential of quantum information science (QIS) to revolutionize dynamic radiography through enhanced image processing, tomographic reconstruction, statistics and uncertainty quantification (UQ), and artificial intelligence integration. By leveraging quantum algorithms to extract previously inaccessible information from existing datasets, this interdisciplinary approach promises unprecedented insights at the intersection of dynamic imaging, artificial intelligence, and quantum information technologies.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Leveraging Large Language Models for Real-World Data Evidence: A Framework for Automated Treatment Extraction and Data Harmonization

Background: The ability to comprehensively collect treatment information from cancer patient medical records would enable studies to evaluate real-world benefits and risks tied to specific treatments. Currently, it is difficult to system- atically collect high-quality treatment information because it is often stored in unstructured text. Manually extracting and standardizing drug and regimen data is time-intensive. Recent advances in large language models (LLMs) offer a potential solution for automated extraction of structured treatment information from clinical text. Objective: This study systematically evaluates the utility of four LLMs from the Llama family for automated extraction of oncology treatment information from clinical text. This information can guide researchers using cancer registry data to provide insights into cancer care and outcomes beyond clinical trials. Methods: Four instruction-tuned Llama models with varying parameter counts (1B, 3B, 8B, and 70B) were evaluated for their ability to extract treatment information from clinical documents. A unified oncology knowledge base integrating seven major public data sources was developed to standardize and normalize extracted entities—a critical step for harmonizing data from diverse sources. Extracted treatment data were compared against expert-annotated ground truth. Model performance was assessed using accuracy metrics (Precision, Recall, F1-Score) and opera- tional feasibility metrics, including processing speed and structural compliance of the output. Results: A strong positive correlation was observed between model size and extraction accuracy. F1-score improved from 0.609 for the 1B model to 0.710 (3B), 0.807 (8B), and 0.828 (70B). While larger models demonstrated superior accuracy and compliance, they incurred higher computational costs. The modest performance difference between 8B and 70B suggests diminishing returns with increasing model size. Conclusions: LLMs represent a viable technology for automating oncology treatment extraction. The 8B-parameter model emerged as a highly effective option, balancing high accuracy and computational efficiency. Selecting an appropriate LLM for deployment in cancer registries involves a trade-off between desired accuracy and available operational resources. Harmonizing extracted entities with the oncology knowledge base facilitates standardized integration into common data models, enhancing data quality for real-world evidence analyses.

artificial intelligence↗

DOE OSTI2022

PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format

The layout of portable document format (PDF) files is constant to any screen, and the metadata therein are latent, compared to mark-up languages such as HTML and XML. No semantic tags are usually provided, and a PDF file is not designed to be edited or its data interpreted by software. However, data held in PDF files need to be extracted in order to comply with opensource data requirements that are now government-regulated. In the chemical domain, related chemical and property data also need to be found, and their correlations need to be exploited to enable data science in areas such as data-driven materials discovery. Such relationships may be realized using text-mining software such as the “chemistry-aware” natural-language-processing tool, ChemDataExtractor; however, this tool has limited data-extraction capabilities from PDF files. This study presents the PDFDataExtractor tool, which can act as a plug-in to ChemDataExtractor. It outperforms other PDF-extraction tools for the chemical literature by coupling its functionalities to the chemical-named entityrecognition capabilities of ChemDataExtractor. The intrinsic PDF-reading abilities of ChemDataExtractor are much improved. The system features a template-based architecture. This enables semantic information to be extracted from the PDF files of scientific articles in order to reconstruct the logical structure of articles. While other existing PDF-extracting tools focus on quantity mining, this template-based system is more focused on quality mining on different layouts. PDFDataExtractor outputs information in JSON and plain text, including the metadata of a PDF file, such as paper title, authors, affiliation, email, abstract, keywords, journal, year, document object identifier (DOI), reference, and issue number. With a self-created evaluation article set, PDFDataExtractor achieved promising precision for all key assessed metadata areas of the document text.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Exploring electron-beam induced modifications of materials with machine-learning assisted high temporal resolution electron microscopy

Directed atomic fabrication using an aberration-corrected scanning transmission electron microscope (STEM) opens new pathways for atomic engineering of functional materials. In this approach, the electron beam is used to actively alter the atomic structure through electron beam induced irradiation processes. One of the impediments that has limited widespread use thus far has been the ability to understand the fundamental mechanisms of atomic transformation pathways at high spatiotemporal resolution. Here, we develop a workflow for obtaining and analyzing high-speed spiral scan STEM data, up to 100 fps, to track the atomic fabrication process during nanopore milling in monolayer MoS 2 . An automated feedback-controlled electron beam positioning system combined with deep convolution neural network (DCNN) was used to decipher fast but low signal-to-noise datasets and classify time-resolved atom positions and nature of their evolving atomic defect configurations. Through this automated decoding, the initial atomic disordering and reordering processes leading to nanopore formation was able to be studied across various timescales. Using these experimental workflows a greater degree of speed and information can be extracted from small datasets without compromising spatial resolution. This approach can be adapted to other 2D materials systems to gain further insights into the defect formation necessary to inform future automated fabrication techniques utilizing the STEM electron beam.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Temporal Explosion Source Processes of Declared Nuclear Tests in the Democratic People’s Republic of Korea

In this work we highlight a preliminary temporal source analysis of the six declared Democratic People's Republic of Korea (DPRK) nuclear tests. We use regional seismic data to estimate relative source time functions (RSTFs) via iterative time-domain deconvolution (Ammon, 2006; Pippin, 2022) of vertical-component ground motions recorded within 2000 km of the source region. Since RSTFs are ideally independent of site and propagation effects, their amplitude spectrum is equivalent to the source spectral ratio, but they also retain phase information. We compare observed RSTFs (in the time and frequency domains) with synthetic RSTFs derived from the Mueller & Murphy (1971) explosion source model. The resolution of these time functions varies, however, we generally obtain high-quality results within the limitations of the recording broadband instrumentation. The results indicate that this method effectively preserves source time-history information that can be used for temporal analysis of remote nuclear explosions. This preliminary analysis is intended to assess the viability of using time-domain deconvolution methods for extracting temporal source information.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2021

Capturing the Physics of MaNGA Galaxies with Self-supervised Machine Learning

As available data sets grow in size and complexity, advanced visualization tools enabling their exploration and analysis become more important. In modern astronomy, integral field spectroscopic galaxy surveys are a clear example of increasing high dimensionality and complex data sets, which challenges the traditional methods used to extract the physical information they contain. Here, we present the use of a novel self-supervised machine-learning method to visualize the multidimensional information on stellar population and kinematics in the MaNGA survey in a 2D plane. Our framework is insensitive to nonphysical properties such as the size of the integral field unit and is therefore able to order galaxies according to their resolved physical properties. Using the extracted representations, we study how galaxies distribute based on their resolved and global physical properties. We show that even when exclusively using information about the internal structure, galaxies naturally cluster into two well-known categories, rotating main-sequence disks and massive slow rotators, from a purely data-driven perspective, hence confirming distinct assembly channels. Low-mass rotation-dominated quenched galaxies appear as a third cluster only if information about the integrated physical properties is preserved, suggesting a mixture of assembly processes for these galaxies without any particular signature in their internal kinematics that distinguishes them from the two main groups. The framework for data exploration is publicly released with this publication, ready to be used with the MaNGA or other integral field data sets.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Understanding Fission Gas Bubble Distribution and Zirconium Redistribution in Neutron-irradiated U-Zr Metallic Fuel Using Machine Learning

U-10wt.% Zr (U-10Zr) based metallic fuel is the leading candidate for next-generation sodium cooled fast reactor in United States. Currently, Idaho National Laboratory (INL) has been the leading national laboratory for research, development, and demonstration (RD&D) on metallic fuel. Advanced post-irradiation characterization will help to understand fuel microstructure and property change during irradiation, benefiting fuel qualification for commercial application. Characterization capabilities ranging from sub-nanometer to micrometer, such as scanning electron microscopy (SEM), focused ion beam (FIB) sampling, transmission electron microscopy (TEM) characterization, and local thermal conductivity microscopy (TCM), have been utilized recently on irradiated U-10Zr fuel samples to gain a better understanding of nuclear fuel microstructure and property evolution inside a reactor. The FIB/SEM coupled with energy dispersive X-ray spectroscopy (EDS) can capture the essential information to achieve better understanding of fuel behaviors. Inside a nuclear reactor, the phase and microstructure of U-10Zr is constantly changing under neutron bombardment. For example, the gaseous fission product atoms have a limited solubility inside fuel matrix and tend to precipitate out in bubble form, which not only contribute to fuel thermal conductivity degradation but also provide a shortcut for movement of fission products, i.e. lanthanides. The resultant deposition of lanthanides at the cladding inner surface will potentially trigger a chemical reaction/interaction between nuclear fuel and cladding at reactor operational conditions, threatening fuel integrity and safety. FIB/SEM coupled with EDS can provide the fission bubble information as well as probe into phase separation or Zr redistribution, which is fundamental to predict the fuel performance. With high velocity image data generating method, such as FIB/SEM, an automatic way to extract the microstructural information quantitively can better serve the needs from post irradiation characterization. A trained machine learning model, named Decision Tree, is employed to generate a bubble classifier and to categorize bubbles into three categories: isolated bubble, connected without lanthanides, and connected with lanthanides bubbles[3]. This work presents a showcase of this approach on six regions of a fuel cross-section along the radial temperature gradient. We obtained distributions of bubble categories and porosity rates along the six regions. Moreover, a secondary phase U-Zr2 was determined and found on regions 5 and 6. The secondary phase fraction was increasing from 15.61% in region 5 to 34.79% in region 6 based on this approach . This quantitative data offers insights into the lanthanide migration and potentially thermal conductivity degradation. This information from machine learning will be fed into fuel design code for better prediction of fuel performance.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Constraining Mornings and Evenings on Distant Worlds: A new Semianalytical Approach and Prospects with Transmission Spectroscopy

The technique of transmission spectroscopy—the variation of a planetary radius with wavelength due to opacity sources in the planet’s terminator region—has been one of the most successful in the characterization of exoplanet atmospheres to date, providing key insights into the composition and structure of these distant worlds. A common assumption made when using this technique, however, is that the variations are the same in the entire terminator region. In reality, the morning and evening terminators might have distinct temperature, pressure, and thus compositional profiles due to the inherent 3D nature of the planet, which would, in turn, give rise to different spectra on each side of it. Constraining those might be fundamental for our understanding of not only the weather patterns in these distant worlds but also the planetary formation signatures that might only be possible to extract once these features are well understood. Motivated by this physical picture, in this work, we perform a detailed study of the observational prospects of detecting this effect. We present an open-source semianalytical framework with which this information can be extracted directly from transit light curves and perform a detailed study of the prospects of detecting the effect with current missions, such as TESS, and upcoming ones, such as JWST. Our results show that these missions show great promise for the detection of this effect. Transmission spectroscopy studies with JWST, in particular, could provide spectra of each of the limbs, allowing us to convey 3D information previously accessible only via phase curves.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Efficient analysis of magnetic field line behavior in toroidal plasmas

The confinement of plasmas in tokamaks and stellarators depends on magnetic field lines lying in nested toroidal surfaces. The transition near the plasma edge away from the lines lying in magnetic surfaces defines properties of divertors. The transition in time defines properties of disruptions. Divertor design and disruption analyses require a detailed understanding of these transitions. The use of a Fourier transform coupled with a Gaussian window function allows far more information to be extracted about these transitions using far shorter field line integrations than can be obtained using traditional methods based on Poincaré plots. The physics of divertors and disruptions is reviewed to clarify why the type of information that can be gained from more efficient methods of analysis is of central importance to the fusion program based on magnetic confinement.

Boozer, Allen H. [Columbia Univ., New York, NY (Un↗

DOE OSTI2021

Quantum process tomography of a Mølmer-Sørensen gate via a global beam

Here, we present a framework for quantum process tomography of two-ion interactions that leverages modulations of the trapping potential and composite pulses from a global laser beam to achieve individual-ion addressing. Tomographic analysis of identity and delay processes reveals dominant error contributions from laser decoherence and slow qubit frequency drift during the tomography experiment. We use this framework on two co-trapped 40 Ca + ions to analyze both an optimized and an overpowered Mølmer–Sørensen gate and to compare the results of this analysis to a less informative Bell-state tomography measurement and to predictions based on a simplified noise model. These results show that the technique is effective for the characterization of two-ion quantum processes and for the extraction of meaningful information about the errors present in the system. The experimental convenience of this method will allow for more widespread use of process tomography for characterizing entangling gates in trapped-ion systems.

quantum computing↗

DOE OSTI2025

Deformable phrase level attention: A flexible approach for improving AI based medical coding

Objective: Improving the AI-driven automated medical encoding of clinical text plays a vital role in gathering information on the occurrence of diseases to improve population-level health. This work presents a novel attention mechanism designed to enhance text classification models and ensure appropriate classification of medical concepts in unstructured electronic health records. Materials and Methods: We developed a deformable, phrase-level attention mechanism to identify important lexical word-level and contextual phrase-level information from clinical text documents. We evaluated conventional and transformer-based deep learning models that we extended with our attention mechanism on the extraction of critical cancer information (e.g., site, subsite, laterality, histology, behavior) from 629,908 electronic pathology reports and on the automated medical encoding of 52,722 hospital discharge summaries. Results: Transformer-based models with the deformable, phrase-level attention mechanism achieved the best performance on the extraction of critical cancer information from pathology reports. Conventional- and transformer-based models show similar or better performance than their baseline counterparts on the automated medical encoding of clinical documents. Discussion: The addition of phrase-level information allowed models extended with our proposed method to outperform standard word-level attention. Our method showed favorable properties for the real-world application in terms of model robustness and phenotyping. These results indicate that our method is promising for automated data harmonization for common data models. Conclusion: This work proposes a novel deformable, phrase-level attention mechanism that enhances text classification models in the extraction of medical concepts from clinical text documents. We demonstrate strong performances on two clinical text datasets and showcase real-world deployability of our method.

Automated medical encoding↗

DOE OSTI2023

Supplementary Material for ORNL_AISD-Ex

This dataset provides supplementary material for the previously published dataset ORNL_AISD-Ex (1), which is available at the following website: https://www.osti.gov/biblio/1907919 The dates comprises one compressed folder called ornl_aisd_ex.zip. The compressed folder ornl_aisd_ex.zip contains 1,000 CSV files, each of them titled ornl_aisd_ex_ID.csv, where ID is a number that ranges between 1 and 1,000. The information contained in ornl_aisd_ex_ID.csv corresponds to the information of the molecules compresses inside the ornl_aisd_ex_ID.tar.gz of the dataset ORNL_AISD-Ex. Each row in each .CSV file is associated with a molecule, and the columns contain the following information: 1) molecules ID 2) SMILES string representation 3) DFTB-PE (eV): formation energy 4) first 50 electronic excitation modes 5) oscillators strengths of the first 50 electronic excitation modes The compression of this information into CSV files will allow a more agile extraction and management of information to the users that do not have access to large scale HPC platforms. REFERENCES (1) Lupo Pasini, Massimiliano, Mehta, Kshitij, Yoo, Pilsun, and Irle, Stephan. ORNL_AISD-Ex: Quantum chemical prediction of UV/Vis absorption spectra for over 10 million organic molecules. United States: N. p., 2023. Web. doi:10.13139/OLCF/1907919.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Photo-zSNthesis: Converting Type Ia Supernova Lightcurves to Redshift Estimates via Deep Learning

Abstract Upcoming photometric surveys will discover tens of thousands of Type Ia supernovae (SNe Ia), vastly outpacing the capacity of our spectroscopic resources. In order to maximize the scientific return of these observations in the absence of spectroscopic information, we must accurately extract key parameters, such as SN redshifts, with photometric information alone. We present Photo- z SNthesis, a convolutional neural network-based method for predicting full redshift probability distributions from multi-band supernova lightcurves, tested on both simulated Sloan Digital Sky Survey (SDSS) and Vera C. Rubin Legacy Survey of Space and Time data as well as observed SDSS SNe. We show major improvements over predictions from existing methods on both simulations and real observations as well as minimal redshift-dependent bias, which is a challenge due to selection effects, e.g., Malmquist bias. Specifically, we show a 61× improvement in prediction bias 〈Δ z 〉 on PLAsTiCC simulations and 5× improvement on real SDSS data compared to results from a widely used photometric redshift estimator, LCFIT+Z. The PDFs produced by this method are well constrained and will maximize the cosmological constraining power of photometric SNe Ia samples.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Nucleon tomography and total angular momentum of valence quarks from synergy between lattice QCD and elastic scattering data

We present an exploratory work on integrating lattice-QCD results with experimental data for elastic scattering. Within the framework of generalized parton distributions, this approach allows for the extraction of detailed information about nucleon tomography and the total angular momentum carried by valence quarks. To accomplish this reliably, we introduce a new quantity, the “double ratio,” which significantly reduces the systematic uncertainties inherent in lattice QCD computations. Moreover, we introduce a “shadow” term in the extraction procedure, which is sensitive only to lattice-QCD results. This term allows us to investigate the model dependence of the extraction, providing a more flexible description of the nucleon that goes beyond the previously considered bell-shaped distribution.

Lattice QCD↗

DOE OSTI2022

1 H chemical shift anisotropy: a high sensitivity solid-state NMR dynamics probe for surface studies?

We report dynamics play significant roles in chemistry and biochemistry-molecular motions impact both large- and small-scale chemical reactions in addition to biochemical processes. In many systems, including heterogeneous catalysts, the characterization of dynamics remains a challenge. The most common approaches involve the solid-state NMR measurement of anisotropic interactions, in particular 2 H quadrupolar coupling and 1 H–X dipolar coupling, which generally require isotope enrichment. Due to the high sensitivity of 1 H NMR, 1 H chemical shift anisotropy (CSA) is a particularly enticing, and underexplored, dynamics probe. We carried out 1 H CSA and 1 H– 13 C dipolar coupling measurements in a series of model supported complexes to understand how 1 H CSA can be leveraged to gain dynamic information for heterogeneous catalysts. Mathematical descriptions are given for the dynamic averaging of the CSA tensor, and its dependence on orientation and asymmetry. The variability of the orientation of the tensor in the molecular frame, in addition to its magnitude and asymmetry, negatively impacts attempts to extract quantitative dynamic information. Nevertheless, 1 H CSA measurements can reveal useful qualitative insights into the motions of a particularly dilute site, such as from a surface species.

1H chemical shift anisotropy↗