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DOE OSTI2023

FrESCO

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information and summary statistics about cancer prevalence to facilitate population level monitoring of cancer incidence. Extracting cancer phenotype from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating this information extraction process from cancer pathology reports has the potential to improve not only the quality of the data by extracting information in a consistent manner across registries, but to improve the quality of patient outcomes by reducing the time to assimilate new data and enabling time-sensitive applications such as precision medicine. Here we present FrESCO: Framework for Exploring Scalable Computational Oncology, a modular deep-learning natural language processing (NLP) library for extracting pathology information from clinical text documents.

Spannaus, Adam [Oak Ridge National Lab. (ORNL), Oa↗

DOE OSTI2024

Cosmology with persistent homology: a Fisher forecast

Abstract Persistent homology naturally addresses the multi-scale topological characteristics of the large-scale structure as a distribution of clusters, loops, and voids. We apply this tool to the dark matter halo catalogs from theQuijotesimulations, and build a summary statistic for comparison with the joint power spectrum and bispectrum statistic regarding their information content on cosmological parameters and primordial non-Gaussianity. Through a Fisher analysis, we find that constraints from persistent homology are tighter for 8 out of the 10 parameters by margins of 13–50%. The complementarity of the two statistics breaks parameter degeneracies, allowing for a further gain in constraining power when combined. We run a series of consistency checks to consolidate our results, and conclude that our findings motivate incorporating persistent homology into inference pipelines for cosmological survey data.

Astronomy & Astrophysics↗

DOE OSTI2026

Generative large language models for predictive maintenance planning

Maintenance planning and the generation of necessary components for tasks can prove time-consuming and complex. Automating the creation of recurring or similar tasks by leveraging previous planning packages and data, while uncovering insights to automate planning package generation, presents an opportunity to conserve valuable time and resources. This work aims to harness the textual and probabilistic capabilities of large language models (LLMs) to automate the generation of planning packages. Utilizing diverse data sources ranging from raw data to handwritten text, both singular and collaborative LLMs are trained and tested. Results demonstrate their capability to generate essential planning package components, effectively replicating the statistical patterns in the data. This demonstrates the use of these tools inside a digital asset for automated planning. This work outlines a methodology for constructing datasets, a training suite, and evaluation methods for LLM-based textual and conversational planning tools utilized in an asset digital twin. Results indicate that the fine-tuned models generate estimated planning information within the statistical ranges observed in real maintenance data. The models achieve high accuracy (>90%) in document question-answering and instruction generation tasks. Furthermore, the conversational retrieval-augmented generation (RAG) assistant system achieves 100% document retrieval accuracy, while conversational information capture exceeds 98% across the majority of work-package assistant modules.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Evidence of galaxy assembly bias in SDSS DR7 galaxy samples from count statistics

We present observational constraints on the galaxy–halo connection, focusing particularly on galaxy assembly bias from a novel combination of counts-in-cylinders statistics, P(N CIC ), with the standard measurements of the projected two-point correlation function w p (r p ), and number density n gal of galaxies. We measure n gal , w p (r p ), and P(N CIC ) for volume-limited, luminosity-threshold samples of galaxies selected from SDSS DR7, and use them to constrain halo occupation distribution (HOD) models, including a model in which galaxy occupation depends upon a secondary halo property, namely halo concentration. We detect significant positive central assembly bias for the M r < -20.0 and M r <-19.5 samples. Central galaxies preferentially reside within haloes of high concentration at fixed mass. Positive central assembly bias is also favoured in the M r < -20.5 and M r < -19.0 samples. We find no evidence of central assembly bias in the M r < -21.0 sample. We observe only a marginal preference for negative satellite assembly bias in the M r < -20.0 and M r < -19.0 samples, and non-zero satellite assembly bias is not indicated in other samples. Our findings underscore the necessity of accounting for galaxy assembly bias when interpreting galaxy survey data, and demonstrate the potential of count statistics in extracting information from the spatial distribution of galaxies, which could be applied to both galaxy–halo connection studies and cosmological analyses.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Prediction of the Al-rich part of the Al-Cu phase diagram using cluster expansion and statistical mechanics

In this work, the thermodynamic properties of α-Al and other phases (GP zones, θ'', θ' and θ) in the Al-rich part of the Al-Cu system have been obtained by means of the cluster expansion formalism in combination with statistical mechanics. This information was used to build the Al-rich part of the Al-Cu phase-diagram taking into account vibrational entropic contributions for θ', as those of the other phases were negligible. The simulation predictions of the phase boundaries between α-Al and either θ'', θ' or θ phases as a function of temperature are in good agreement with experimental data and extend the phase boundaries to a wider temperature range. The DFT calculations reveal the presence of a number of metastable Guinier-Preston-zone type configurations that may coexist with α-Al and θ'' at low temperatures. They also demonstrate that θ' is the stable phase below 550K but it is replaced by θ above this temperature due to the vibrational entropic contribution to the Gibbs energy of θ'. This work shows how the combination of cluster expansion and statistical mechanics can be used to expand our knowledge of the phase diagram of metallic alloys and to provide Gibbs free energies of different phases that can be used as input in mesoscale simulations of precipitation.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Dark Energy Survey Year 3 results: Cosmological constraints from galaxy clustering and galaxy-galaxy lensing using the MagLim lens sample

The cosmological information extracted from photometric surveys is most robust when multiple probes of the large scale structure of the Universe are used. Two of the most sensitive probes are the clustering of galaxies and the tangential shear of background galaxy shapes produced by those foreground galaxies, so-called galaxy-galaxy lensing. Combining the measurements of these two two-point functions leads to cosmological constraints that are independent of the way galaxies trace matter (the galaxy bias factor). The optimal choice of foreground, or lens, galaxies is governed by the joint, but conflicting requirements to obtain accurate redshift information and large statistics. We present cosmological results from the full 5000 deg 2 of the Dark Energy Survey’s first three years of observations (Y3) combining those two-point functions, using for the first time a magnitude-limited lens sample (MagLim) of 11 million galaxies, especially selected to optimize such combination, and 100 million background shapes. We consider two flat cosmological models, the Standard Model with dark energy and cold dark matter ( Λ CDM ) a variation with a free parameter for the dark energy equation of state ( w CDM ). Both models are marginalized over 25 astrophysical and systematic nuisance parameters. In Λ CDM we obtain for the matter density Ω m = 0.320 - 0.034 + 0.041 and for the clustering amplitude S 8 ≡ σ 8 ( Ω m / 0.3 ) 0.5 = 0.778 - 0.031 + 0.037 , at 68% C.L. The latter is only 1 σ smaller than the prediction in this model informed by measurements of the cosmic microwave background by the Planck satellite. In w CDM we find Ω m = 0.32 - 0.046 + 0.044 , S 8 = 0.777 - 0.051 + 0.049 and dark energy equation of state w = - 1.031 - 0.379 + 0.218 . We find that including smaller scales, while marginalizing over nonlinear galaxy bias, improves the constraining power in the Ω m - S 8 plane by 31% and in the Ω m - w plane by 41% while yielding consistent cosmological parameters from those in the linear bias case. These results are combined with those from cosmic shear in a companion paper to present full DES-Y3 constraints from the three two-point functions ( 3 × 2 pt ).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Accelerating high-strain continuum-scale brittle fracture simulations with machine learning

Failure in brittle materials under dynamic loading conditions is a result of the propagation and coalescence of microcracks. Simulating this discrete crack evolution at the continuum level is computationally expensive or, in some cases, intractable, resulting in the need to make broad assumptions or neglect key physics. In this work, we have developed an approach using machine learning that overcomes the current inability to represent meso-scale physics at the macro-scale. Our approach leverages damage and stress data from a computationally expensive high-fidelity model that explicitly resolves microcrack behavior to build an inexpensive machine learning emulator. Once trained, the machine learning emulator is used to predict the evolution of crack length statistics, which then informs a continuum-scale constitutive model. This results in a significant speed-up of the workflow by four orders of magnitude. Both the machine learning emulator and the continuum-scale model are validated against the high-fidelity model and experimental data, respectively, showing excellent agreement. There are two key findings. The first is that we can reduce the dimensionality of the problem, establishing that the machine learning emulator only needs the length of the longest crack and one of the maximum stress components to capture the necessary physics. Another compelling finding is that the emulator can be trained in one experimental setting and transferred successfully to predict behavior in a different setting.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Review of Onsite Temperature and Solar Forecasting Models to Enable Better Building Design and Operations

Advanced building controls and energy optimization for new constructions and retrofits rely on accurate weather data. Traditionally, most studies utilize airport weather information as the decision inputs. However, most buildings are in environments that are quite different than those at the airport miles away. Tree cover, adjacent buildings, and micro-climate effects caused by the larger surrounding area can all yield deviations in air temperature, humidity, solar irradiance, and wind that are large enough to influence design and operation decisions. In order to overcome this challenge, there are many prior studies on developing weather forecasting algorithms from micro-to meso-scales. Additionally, this paper reviews and complies knowledge on common weather data resources, data processing methodologies and forecasting techniques of weather information. Commonly used statistical, machine learning and physical-based models are discussed and presented as two major categories: deterministic forecasting and probabilistic forecasting. Finally, evaluation metrics for forecasting errors are listed and discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Statistical 3D morphology characterization of vaterite microspheres produced by engineered Escherichia coli

Hollow vaterite microspheres are important materials for biomedical applications such as drug delivery and regenerative medicine owing to their biocompatibility, high specific surface area, and ability to encapsulate a large number of bioactive molecules and compounds. We demonstrated that hollow vaterite microspheres are produced by an Escherichia coli strain engineered with a urease gene cluster from the ureolytic bacteria Sporosarcina pasteurii in the presence of bovine serum albumin. We characterized the 3D nanoscale morphology of five biogenic hollow vaterite microspheres using 3D high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) tomography. Using automated high-throughput HAADF-STEM imaging across several sample tilt orientations, we show that the microspheres evolved from a smaller more ellipsoidal shape to a larger more spherical shape while the internal hollow core increased in size and remained relatively spherical, indicating that the microspheres produced by this engineered strain likely do not contain the bacteria. The statistical 3D morphology information demonstrates the potential for using biogenic calcium carbonate mineralization to produce hollow vaterite microspheres with controlled morphologies.

3D morphology↗

DOE OSTI2021

Reweighting the Sivers function with jet data from STAR

The reweighting procedure that using Bayesian statistics incorporates the information contained in a new data set, without the need of re-fitting, is applied to the quark Sivers function extracted from Semi-Inclusive Deep Inelastic Scattering (SIDIS) data. We exploit the recently published single spin asymmetry data for the inclusive jet production in polarized pp collisions from the STAR Collaboration at RHIC, which cover a much wider x region compared to SIDIS measurements. The reweighting method is extended to the case of asymmetric errors and the results show a remarkable improvement of the knowledge of the quark Sivers function.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Integration of ecosystem science into radioecology: A consensus perspective

In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This work is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A Machine Learning Assisted Development of a Model for the Populations of Convective and Stratiform Clouds

Abstract Traditional parameterizations of the interaction between convection and the environment have relied on an assumption that the slowly varying large‐scale environment is in statistical equilibrium with a large number of small and short‐lived convective clouds. They fail to capture nonequilibrium transitions such as the diurnal cycle and the formation of mesoscale convective systems as well as observed precipitation statistics and extremes. Informed by analysis of radar observations, cloud‐permitting model simulation, theory, and machine learning, this work presents a new stochastic cloud population dynamics model for characterizing the interactions between convective and stratiform clouds, with the goal of informing the representation of these interactions in global climate models. Fifteen wet seasons of precipitating cloud observations by a C‐band radar at Darwin, Australia are fed into a machine learning algorithm to obtain transition functions that close a set of coupled equations relating large‐scale forcing, mass flux, the convective cell size distribution, and the stratiform area. Under realistic large‐scale forcing, the derived transition functions show that, on the one hand, interactions with stratiform clouds act to dampen the variability in the size and number of convective cells and therefore in the convective mass flux. On the other, for a given convective area fraction, a larger number of smaller cells is more favorable for the growth of stratiform area than a smaller number of larger cells. The combination of these two factors gives rise to solutions with a few convective cells embedded in a large stratiform area, reminiscent of mesoscale convective systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Proton capture on 34 S in the astrophysical energy regime of O-Ne novae

Nuclear reaction sensitivity studies have shown that the final isotopic abundance of O-Ne nova nucleosynthesis is dependent on the 34 S(p,γ) 35 Cl reaction at astrophysical energies corresponding to peak nova burning temperatures of 0.1–0.4 GK. Isotopic ratios of the S, Cl, and Ar products are all used in various methods of cosmochemical analysis of presolar meteoritic grains. Due to the lack of direct experimental data, the 34 S+p reaction rate has been estimated using statistical modeling or information from indirect nucleon transfer experiments. In order to provide direct reaction information, here the resonance strengths of several low energy resonances, E c.m. = 272–495 keV, in the 34 S(p,γ) 35 Cl reaction were measured for the first time in inverse kinematics using the DRAGON recoil separator located at TRIUMF, Canada’s Particle Accelerator Centre in Vancouver.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Chiral edge state control of thermoelectric effects

Thermoelectric responses in two-dimensional electron gases subjected to magnetic fields have the potential to provide unique information about quasiparticle statistics. In this study, we show that chiral edge states play a key role in thermoelectric Hall bar measurements by completely controlling the direction of the internal thermal gradient. To this end, we perform measurements of the magnetothermoelectric responses of cadmium arsenide quantum wells. The magnetothermoelectric responses in the quantum Hall regime agree with theoretical predictions if one considers the role of chiral edge states, which flow in opposite directions on either side of the Hall bar and establish an internal temperature gradient that is perpendicular to the externally applied thermal gradient. We show that the results are self-consistent within this picture under different measurement conditions. We discuss potential applications of the findings, such as in nanoscale control of local temperature gradients and thermoelectric effects along with the characterization of other topological systems with chiral edges states.

Science & Technology - Other Topics↗

DOE OSTI2025

Hestia-SWIFL: hourly anthropogenic fossil fuel CO2 and heat on the 2km WRF grid, version 1.1

The Hestia-SWIFL version 1.1 anthropogenic heat (AH) and fossil fuel CO2 (FFCO2) emissions data product represent emissions due to the combustion of fossil fuel and cement production within the state of Arizona from 2019 to 2022. This product was developed as part of the Southwest Urban Corridor Integrated Field Laboratory (SW-IFL) project, which aims to provide new knowledge and tools that address extreme heat, air quality, climate change and related urban environmental issues by integrating high-resolution observations, modeling, and civic engagement. The emissions are generated using a bottom-up/engineering approach and are tied to results generated by the Vulcan Project version 4, an effort to quantify space/time-resolved FFCO2 & AH emissions for the entire United States landscape. A large number of data sources are combined to best estimate the emissions at fine scales such as air quality emissions data, traffic flow data, building information, sociodemographic information, and fuel statistics. The AH product provides emissions for two emissions sources (transportation and point source emissions) in units of Watts per hour per square meter (W/m2) per year (annual files) or per hour (hourly files). The FFCO2 product provides emissions from nine individual emission sectors as well as the total, and in units of tons of carbon (tC) per grid cell per year or per hour. The output made available here places the native spatial resolution of the Hestia FFCO2 & AH emissions data product (points, lines, and polygons) into a regularized 2km x 2km grid at hourly and annual temporal resolutions, and stored in netCDF files. The exact spatial extent is defined by the ASU Weather Research Forecast (WRF) simulation grid. All data are processed using R/Python pm high-performance computing system. 2-27-2026 updates: Bugs in airport hourly profile (both AH and FFCO2) and building spatial patterns (FFCO2 only) were fixed. Hourly emissions are reprocessed for all years to reflect those changes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

A Novel Standard Gibbs Energy of Formation Model for High-Enthalpy Water Systems

This work provides an advanced standard molar Gibbs energy of formation model, informed by molecular statistical thermodynamics (MST), and validated by mineral solubility and ion association reactions. This new model aligns with experimental data within uncertainties and highlights the role of specific MST interactions around the critical point. This work will provide a reliable tool for the optimization of industrial processes operating at the edges of the supercritical domain.

Hall, Derek↗

DOE OSTI2023

Earth mover’s distance as a measure of CP violation

We introduce a new unbinned two sample test statistic sensitive to CP violation utilizing the optimal transport plan associated with the Wasserstein (earth mover’s) distance. The efficacy of the test statistic is shown via two examples of CP asymmetric distributions with varying sample sizes: the Dalitz distributions of B 0 → K + π – π 0 and of D 0 → π + π – π 0 decays. The windowed version of the Wasserstein distance test statistic is shown to have comparable sensitivity to CP violation as the commonly used energy test statistic, but also retains information about the localized distributions of CP asymmetry over the Dalitz plot. For large statistic datasets we introduce two modified Wasserstein distance based test statistics — the binned and the sliced Wasserstein distance statistics, which show comparable sensitivity to CP violation, but improved computing time and memory scalings. Finally, general extensions and applications of the introduced statistics are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗