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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↗

NASA NTRS1984

Statistical analysis of Thematic Mapper Simulator data for the geobotanical discrimination of rock types in southwest Oregon

An evaluation of Thematic Mapper Simulator (TMS) data for the geobotanical discrimination of rock types based on vegetative cover characteristics is addressed in this research. A methodology for accomplishing this evaluation utilizing univariate and multivariate techniques is presented. TMS data acquired with a Daedalus DEI-1260 multispectral scanner were integrated with vegetation and geologic information for subsequent statistical analyses, which included a chi-square test, an analysis of variance, stepwise discriminant analysis, and Duncan's multiple range test. Results indicate that ultramafic rock types are spectrally separable from nonultramafics based on vegetative cover through the use of statistical analyses.

Morrissey, L. A.↗

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↗

NASA NTRS1984

Direct numerical simulation of curved turbulent channel flow

Low Reynolds number, mildly curved, turbulent channel flow has been simulated numerically without subgrid scale models. A new spectral numerical method developed for this problem was used, and the computations were performed with 2 million degrees of freedom. A variety of statistical and structural information has been extracted from the computed flow fields. These include mean velocity, turbulence stresses, velocity skewness, and flatness factors, space time correlations and spectra, all the terms in the Reynolds stress balance equations, and contour and vector plots of instantaneous velocity fields. The effects of curvature on this flow were determined by comparing the concave and convex sides of the channel. The observed effects are consistent with experimental observations for mild curvature. The most significant difference in the turbulence statistics between the concave and convex sides was in the Reynolds shear stress. This was accompanied by significant differences in the terms of the Reynolds shear stress balance equations. In addition, it was found that stationary Taylor-Gortler vortices were present and that they had a significant effect on the flow by contributing to the mean Reynolds shear stress, and by affecting the underlying turbulence.

Moser, R. D.↗

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↗

NASA NTRSDate not supplied

Natural Language Processing for Extracting Rich Disease Data Aligned To Satellite Meteorological Data

Global climate change is redefining our understanding of how diseases spread. In Sri Lanka, vector-borne diseases such as dengue fever, encephalitis, and leptospirosis historically surged during the monsoon seasons when temperatures were high enough for mosquito eggs to hatch. Unfortunately, due to rising temperatures and more erratic rainfall patterns, mosquito eggs can now hatch year-round and are increasingly unpredictable, leading to an alarmingly increasing number of hospitalizations and deaths. More data is needed to adapt our response to these diseases in an increasingly warmer world. In the contemporary landscape, a wealth of disease information is available, yet accessibility remains limited due to unstructured data formats such as PDFs. Therefore, converting unstructured disease reports into structured formats is necessary for effectively leveraging data. This paper introduces a comprehensive framework for collecting unstructured disease reports and transforming them into analyzable formats. By creating separate models tailored to each data format, we can ensure accuracy compared to general models. These straightforward models enhance accessibility and empower other researchers to use our tools. The returned structured data can then be harnessed for analysis, statistical purposes, and informing evidence-based public health interventions, thus facilitating more informed decision-making in healthcare. We deploy this framework to produce geospatial data for Sri Lanka and Brazil for many different conditions and align these data with satellite environmental data, providing for the first time a structured, aligned powerful dataset for disease modeling.

Open Source Open Science↗

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↗

NASA NTRSDate not supplied

Data Integrity Challenges in NASA Giovanni

The Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) is an online tool developed by the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), one of 12 NASA Science Mission Directorate Data Centers (DAACs) to analyze and visualize NASA remote sensing and model data without downloading data and software. As of this writing, over 2000 Earth satellite and model variables are available in Giovanni, including several well-known NASA satellite missions (e.g., TRMM, GPM) and projects (e.g., MERRA-2, GPCP). There are twenty-two plots provided by Giovanni that can be used to analyze, compare, and explore Earth data across disciplines. Results can be shared with colleagues and downloaded for further analysis. Giovanni has helped publish over 3000 referral papers over the years. As open science policies roll in, data integrity has become a major challenge for Giovanni and other tools. For integrity, both data and workflows must be transparent. FAIR-compliant data, including input, intermediate, and result products, as well as their associated statistics, metadata, and information, are needed. The NASA Data Product Development Guide for Data Producers provides a key resource on how to develop FAIR-compliant data products. Data quality information is also needed from data producers and analysis services like Giovanni. The workflow part is quite challenging and requires workflow management improvements, such as recording workflows and making them available to users. In this presentation, we will discuss the data integrity challenges in Giovanni.

data analysis, visualization↗

NASA NTRS1994

High-speed data search

The high-speed data search system developed for KSC incorporates existing and emerging information retrieval technology to help a user intelligently and rapidly locate information found in large textual databases. This technology includes: natural language input; statistical ranking of retrieved information; an artificial intelligence concept called semantics, where 'surface level' knowledge found in text is used to improve the ranking of retrieved information; and relevance feedback, where user judgements about viewed information are used to automatically modify the search for further information. Semantics and relevance feedback are features of the system which are not available commercially. The system further demonstrates focus on paragraphs of information to decide relevance; and it can be used (without modification) to intelligently search all kinds of document collections, such as collections of legal documents medical documents, news stories, patents, and so forth. The purpose of this paper is to demonstrate the usefulness of statistical ranking, our semantic improvement, and relevance feedback.

Driscoll, James N.↗

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↗