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At least 1,009 records · Page 56

Identifying Bayesian optimal experiments for uncertain biochemical pathway models

Abstract Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.

97 MATHEMATICS AND COMPUTING↗

The uncertainty in ozone calculations by a stratospheric photochemistry model

At present, there is an apparent conflict between one-dimensional stratospheric photochemistry models used in predicting ozone depletion and average data for stratospheric ozone. This conflict is in three particulars - column density of O3 and ozone density in the regions around 30 km and 50 km altitude. A study of the sensitivity of one such model to the values of reaction rates, boundary conditions, solar intensities, photolysis cross sections, and O(1D) yield parameters reveals that even at the 2-sigma uncertainty limit due to these input parameters, the model does not overlap the data for O3 density at 30 km and 50 km. The data is outside the 1-sigma model uncertainty limit for O3 column density. The study also shows the relative contribution of the various parameters studied to the imprecision in these model results.

Butler, D. M.↗

Parametrized uncertainties in the spectral function model of neutrino charged-current quasielastic interactions for oscillation analyses

A substantial fraction of systematic uncertainties in neutrino oscillation experiments stem from the lack of precision in modeling the nuclear target in neutrino-nucleus interactions. Whilst this has driven significant progress in the development of improved nuclear models for neutrino scattering, it is crucial that the models used in neutrino data analyses be accompanied by parameters and associated uncertainties that allow the coverage of plausible nuclear physics. Based on constraints from electron scattering data, we propose such a set of parameters, which can be applied to nuclear shell models, and test their application to the Benhar [] spectral function model. The parametrization is validated through a series of maximum likelihood fits to cross section measurements made by the T2K and MINERvA experiments, which also permit an exploration of the power of near-detector data to provide constraints on the parameters in neutrino oscillation analyses. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA Langley's Approach to the Sandia's Structural Dynamics Challenge Problem

The objective of this challenge is to develop a data-based probabilistic model of uncertainty to predict the behavior of subsystems (payloads) by themselves and while coupled to a primary (target) system. Although this type of analysis is routinely performed and representative of issues faced in real-world system design and integration, there are still several key technical challenges that must be addressed when analyzing uncertain interconnected systems. For example, one key technical challenge is related to the fact that there is limited data on target configurations. Moreover, it is typical to have multiple data sets from experiments conducted at the subsystem level, but often samples sizes are not sufficient to compute high confidence statistics. In this challenge problem additional constraints are placed as ground rules for the participants. One such rule is that mathematical models of the subsystem are limited to linear approximations of the nonlinear physics of the problem at hand. Also, participants are constrained to use these models and the multiple data sets to make predictions about the target system response under completely different input conditions. Our approach involved initially the screening of several different methods. Three of the ones considered are presented herein. The first one is based on the transformation of the modal data to an orthogonal space where the mean and covariance of the data are matched by the model. The other two approaches worked solutions in physical space where the uncertain parameter set is made of masses, stiffnesses and damping coefficients; one matches confidence intervals of low order moments of the statistics via optimization while the second one uses a Kernel density estimation approach. The paper will touch on all the approaches, lessons learned, validation 1 metrics and their comparison, data quantity restriction, and assumptions/limitations of each approach. Keywords: Probabilistic modeling, model validation, uncertainty quantification, kernel density

Horta, Lucas G.↗

End-Use Load Profiles for the U.S. Building Stock: Methodology and Results of Model Calibration, Validation, and Uncertainty Quantification

The United States is embarking on an ambitious transition to a 100% clean energy economy by 2050, which will require improving the flexibility of electric grids. One way to achieve grid flexibility is to shed or shift demand to align with changing grid needs. To facilitate this, it is critical to understand how and when energy is used. High- quality end-use load profiles (EULPs) provide this information, and can help cities, states, and utilities understand the time-sensitive value of energy efficiency, demand response, and distributed energy resources. Publicly available EULPs have traditionally had limited application because of age and incomplete geographic representation (Frick, Eckman, and Goldman 2017; Frick 2019). To help fill this gap, the U.S. Department of Energy (DOE) funded a three-year project - End-Use Load Profiles for the U.S. Building Stock - that culminated in the release of a publicly available dataset1 of simulated EULPs representing residential and commercial buildings across the contiguous United States. The motivation for this work is further detailed in a November 2019 report: Market Needs, Use Cases, and Data Gaps (Mims Frick et al. 2019). This Methodology and Results report provides detailed descriptions of how the dataset was developed, intended for an audience of dataset and model users interested in the technical details. These details include descriptions of all of the model improvements made for calibration and the final comparisons to empirical data sources. A companion report, End-Use Load Profiles for the U.S. Building Stock: Applications and Opportunities, will be published subsequently and will describe example applications and considerations for using the dataset, intended for an audience of general dataset users.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Sequential Design of Experiments for Pilot Testing of Novel Solvent System

The CCSI2 program is supporting a six-month test campaign at the National Carbon Capture Center (NCCC) for evaluation of a novel water-lean solvent. This presentation describes CCSI2’s efforts in process modeling of the solvent system for both coal and natural gas-based flue gas sources and initial uncertainty quantification (UQ) work to estimate parametric uncertainty in key sub-models of interest (e.g., thermodynamics, mass transfer, reaction kinetics). Moreover, perspective is provided on how UQ and sequential design of experiments (SDoE) tools are used to assess the impact of model uncertainty on projected process performance, use this information to optimize data collection during the campaign, and refine process models through data collection. This framework is expected to reduce the overall model uncertainty, and thus risk associated with scale-up as the process moves towards commercialization.

Morgan, Joshua↗

Energy sector portfolio analysis with uncertainty

Governments are dealing with the challenge of how to efficiently invest in research and development portfolios related to energy technologies. Research and development investment decisions in the energy space are especially difficult due to numerous risks and uncertainties, and due to the complexity of energy's interactions with the broad economy. Historically, much of the U.S. Department of Energy's in-depth research and development analyses focused on assessing the impact of a research and development activity in isolation from other available opportunities and did not substantially consider risk and uncertainty. Endeavoring to combine integrated energy-economy modeling with uncertainty analysis and technology-specific research and development activities, the U.S. Department of Energy commissioned the development of the Stochastic Energy Deployment System to support and improve public energy research and development decision-making. The Stochastic Energy Deployment System draws from expert-elicited probability distributions for research and development-driven improvements in technology cost and performance, and it uses Monte Carlo simulations to evaluate the likelihood of outcomes within a system dynamics energy-economy model. The framework estimates the uncertain benefits and costs of various research and development portfolios and provides insight into the probability of meeting national technology goals, while accounting for interactions with the larger economy and for interactions among research and development investments spanning many energy sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Quantitative Feedback Theory (QFT) applied to the design of a rotorcraft flight control system

Quantitative Feedback Theory describes a frequency-domain technique for the design of multi-input, multi-output control systems which meet time or frequency domain performance criteria when specified uncertainty exists in the linear description of the vehicle dynamics. Quantitative Feedback Theory is applied to the design of the longitudinal flight control system for a linear uncertain model of the AH-64 rotorcraft. In this model, the uncertainty is assigned, and is assumed to be attributable to actual uncertainty in the dynamic model and to the changes in the vehicle aerodynamic characteristics which occur near hover. The model includes an approximation to the rotor and actuator dynamics. The design example indicates the manner in which handling qualities criteria may be incorporated into the design of realistic rotorcraft control systems in which significant uncertainty exists in the vehicle model.

Hess, R. A.↗

Sensitivity and uncertainty analysis of PWR spent fuel observables to operational and model parameters

Sensitivity and uncertainty analyses of spent nuclear fuel (SNF) observables - decay heat, neutron and γ-ray emission rate - to operational and model parameters have been performed. A 2D model representing a typical PWR 17x17 UO{sub 2} fuel assembly has been taken as reference. The Serpent code and ENDF/B-VII.1 evaluated nuclear data library have been used for the analyses. Relative uncertainty of decay heat, neutron and γ-ray emission rates due to Monte Carlo counting statistics, as well as the number of fuel pin radial regions required for an accurate characterization of SNF neutron emission, have been estimated. A parametric study has been carried out to investigate the impact of the homogenization to an average value of the fuel and moderator temperature, boron concentration power and burnup on the prediction of the selected observables. In addition, linear sensitivity coefficients have been calculated. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning

Tree training systems for temperate fruit have been developed throughout history by pomologists to improve light interception, fruit yield, and fruit quality. These training systems direct crown and branch growth to specific configurations. Quantifying crown architecture could aid the selection of trees that require less pruning or that naturally excel in specific growing/training system conditions. Regarding peaches [Prunus persica (L.) Batsch], access tools such as branching indices have been developed to characterize tree-crown architecture. However, the required branching data (BD) to develop these indices are difficult to collect. Traditionally, BD have been collected manually, but this process is tedious, time-consuming, and prone to human error. These barriers can be circumnavigated by utilizing terrestrial laser scanning (TLS) to obtain a digital twin of the real tree. TLS generates three-dimensional (3D) point clouds of the tree crown, wherein every point contains 3D coordinates (x, y, z). To facilitate the use of these tools for peach, we selected 16 young peach trees scanned in 2021 and 2022. These 16 trees were then modeled and quantified using the open-source software TreeQSM. As a result, “in silico” branching and biometric data for the young peach trees were calculated to demonstrate the capabilities of TLS phenotyping of peach tree-crown architecture. The comparison and analysis of field measurements (in situ) and in silico BD, biometric data, and quantitative structural model branch uncertainty data were utilized to determine the reconstructive model’s reliability as a source substitute for field measurements. Mean average deviation when comparing young tree (YT) height was approx. 5.93%, with crown volume was approx. 13.26% across both 2021 and 2022. All point clouds of the YTs in 2022 showed residuals lower than 12 mm to cylinders fitted to all branches, and mean surface coverage greater than 40% for both the trunk and primary branching orders.

09 BIOMASS FUELS↗

Hyper Suprime-Cam Year 3 results: Cosmology from cosmic shear power spectra

Here, we measure weak lensing cosmic shear power spectra from the 3-year galaxy shear catalog of the Hyper Suprime-Cam (HSC) Subaru Strategic Program imaging survey. The shear catalog covers 416 deg 2 of the northern sky, with a mean i-band seeing of 0.59 arcsec and an effective galaxy number density of 15 arcmin —2 within our adopted redshift range. With an i-band magnitude limit of 24.5 mag, and four tomographic redshift bins spanning 0.3 ≤ z ph ≤ 1.5 based on photometric redshifts, we obtain a high-significance measurement of the cosmic shear power spectra, with a signal-to-noise ratio of approximately 26.4 in the multipole range 300 < ℓ < 1800. The accuracy of our power spectrum measurement is tested against realistic mock shear catalogs, and we use these catalogs to get a reliable measurement of the covariance of the power spectrum measurements. We use a robust blinding procedure to avoid confirmation bias, and model various uncertainties and sources of bias in our analysis, including point spread function systematics, redshift distribution uncertainties, the intrinsic alignment of galaxies and the modeling of the matter power spectrum. For a flat Λ CDM model, we find S 8 ≡ σ 8 (Ω m /0.3) 0.5 = ${0.776}_{—0.033}^{+0.032}$, which is in excellent agreement with the constraints from the other HSC Year 3 cosmology analyses, as well as those from a number of other cosmic shear experiments. This result implies a ~2σ-level tension with the Planck 2018 cosmology. We study the effect that various systematic errors and modeling choices could have on this value, and find that they can shift the best-fit value of S 8 by no more than ~ 0.5σ, indicating that our result is robust to such systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

Artificial intelligence models, photos, and data associated with the manuscript “Quantifying Streambed Grain Size, Uncertainty, and Hydrobiogeochemical Parameters Using Machine Learning Model YOLO” (v2)

This data package is associated with the manuscript “Quantifying Streambed Grain Size, Uncertainty, and Hydrobiogeochemical Parameters Using Machine Learning Model YOLO” published in Water Resources Research (Chen et al., 2024). This data package includes the training, validation, testing, and prediction data used by the artificial intelligence (AI) model for automated grain size and hydro-biogeochemistry quantification using streambed photos. The grain size data are extracted for each photo using You Look Only Once (YOLO), a pre-trained object detection model. This data package was originally published in October 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. Please see flmd.csv for a list of all files contained in this data package and descriptions for each. Please see dd.csv for a data dictionary that defines the column headers of .csv files in the data package. This dataset is comprised of one data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; and (4) six subfolders. Subfolders 1 to 4 include the training, validation, testing, and prediction data. Subfolder 5_Summary includes the summary results of different combinations of training, validation, testing, and prediction data. Subfolder 6_SupplementalData includes additional data downloaded from public sources (Kaufman et al., 2023a; Kaufman et al., 2023b; Garefalakis et al., 2023; Mair et al., 2024; https://github.com/river-corridors-sfa/Geospatial_variables). In total, the data package includes 110 folders and 44,283 files. These files include 9,047 .jpg photos, 1 .png photo, 3 .tif photos; 26,639 photo labels and individual grain sizes and probability from AI (.txt); 8,447 grain size distribution data (.dat); and 126 CSV files for results summary, and 14 required metadata files (.xlsx). The summary CSV files contain 68 columns and approximately 2,200 rows that represent photo names, site locations, recording time, GPS coordinates, grains sizes (D10, D50, D60, and D84), number of grains, and additional hydro-biogeochemical data such as water depth, flow velocity, Manning’s coefficient, friction factor, hydraulic conductivity, permeability, streambed interstitial velocity magnitude, mass transfer rate, and nitrate uptake velocity. The photos were obtained from 75 sites in the Yakima River Basin and the Columbia River shorelines, and other associated data from samples and sensors obtained when the photos were taken are publicly available (Fulton et al. 2022; Grieger et al. 2023). All files are .csv, .txt, .dat, .jpg, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗