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At least 397 records · Page 22

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

Measurement of the 28 Si ⁢(𝑛,𝑛′⁢𝛾) cross section with 𝑛, 𝛾, and correlated 𝑛−𝛾 angular distributions

Silicon has become an unavoidable element in the circuitry central to everyday life. In turn, the interactions of silicon isotopes with neutrons for nuclear physics applications, among other motivations, have become increasingly important to understand. The dominant isotope of silicon, 28 Si, is thus of primary interest for enhanced understanding for neutron transport calculations and related investigations. Unfortunately, the existing measurement database for neutron scattering reactions on 28 Si is minimal, and nuclear data evaluations on this topic have not been updated for decades. This article details new measurements of the 28 Si ⁢(𝑛,𝑛′⁢𝛾) reaction utilizing multiple analysis methods available within the correlated gamma neutron array for scattering (CoGNAC). Specifically, high-precision near-threshold results and high-incident-energy results were obtained using the 𝛾-only and correlated 𝑛−𝛾 techniques. First-ever measurements of the correlated 𝑛−𝛾 angular distribution for particles emitted following population of the first excited state in 28 Si were obtained as well, which provide unique insight into theoretical descriptions of the inelastic neutron scattering reaction mechanism itself and detailed guidance for nuclear reaction models. The results agree well with literature data where they exist, and substantially expand on the current database for neutron reactions on 28 Si .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

OmicsMLMentor: A Web Application for Guided Machine Learning Analysis of Omics Data

Expression-based omics technologies (e.g. proteomics, metabolomics, transcriptomics, etc.) increasingly rely on supervised and unsupervised machine learning (ML) models to find key biomolecules distinguishing conditions, identify natural groupings in biological data, or generate predictions for outcomes of interest. Fitting ML models to omics data presents several challenges, including handling missing data, selecting a normalization method, choosing a valid model, and optimizing hyperparameters, all requiring statistical programming skills to address these challenges. Thus, the open-source web application SLOPE was designed to lower the barrier to ML modeling for omics data. SLOPE supports the fitting of 15 ML models (10 supervised and 5 unsupervised) tailored to omics datasets, such as proteomics, metabolomics, lipidomics, and transcriptomics. SLOPE offers several omics-specific features, including methods for handling missingness (imputation, conversion, removal), normalization tests, ranking of models based on the structure of a user’s data and user input, and optimal hyperparameter selections using cross-validation splits. By streamlining ML workflows for omics analysis, SLOPE address critical gaps in existing online web tools, facilitating a broader adoption of these models for omics research. Here, SLOPE is applied to data from a lignin exposure study to highlight the workflow for fitting both supervised and unsupervised models to data.

lipidomics↗

PDV Methods and Analysis for Surveillance of Explosive Components

The Weapons Evaluation Test Laboratory (WETL) at Sandia is collaborating with Lawrence Livermore National Laboratory (LLNL) to enhance explosive surveillance testing by integrating Photon Doppler Velocimetry (PDV) data. This project has streamlined the testing environment, reducing hardware costs and training needs while improving data collection efficiency and usability for lab technicians.

Kress, Matthew Kip [Sandia National Laboratories (↗

Deep Learning-Based Dynamic Modeling of Three-Phase Voltage Source Inverters

Inverter-based resource (IBR) models are necessary to analyze modern power system stability and create effective control strategies. Modeling IBRs in converter-rich power systems is crucial, yet challenging due to the lack of commercial information on converter topologies and control parameters. This paper proposes novel convolutional neural network (CNN)–based data-driven techniques for modeling IBRs, addressing adaptability and proprietary concerns without requiring internal system physics knowledge. The proposed method is tested using real grid-tied commercial IBR transient data and demonstrates effectiveness and accuracy. Furthermore, the developed modeling approach is integrated and implemented in the open-source power distribution simulation and analysis tool, GridLAB-D, to illustrate the potentiality of dynamic analysis of large-scale power systems with high IBRs.

deep learning, artificial intelligence↗

A Unified Photometric Redshift Calibration for Weak Lensing Surveys Using the Dark Energy Spectroscopic Instrument

The effective redshift distribution n(z) of galaxies is a critical component in the study of weak gravitational lensing. Here, we introduce a new method for determining n(z) for weak lensing surveys based on high-quality redshifts and neural-network-based importance weights. Additionally, we present the first unified photometric redshift calibration of the three leading stage-III weak lensing surveys, the Dark Energy Survey (DES), the Hyper Suprime-Cam (HSC) survey, and the Kilo-Degree Survey (KiDS), with state-of-the-art spectroscopic data from the Dark Energy Spectroscopic Instrument (DESI). We verify our method using a new, data-driven approach and obtain n(z) constraints with statistical uncertainties of the order of $σ_z$ ~ 0.01 and smaller. Our analysis is largely independent of previous photometric redshift calibrations and, thus, provides an important cross-check in light of recent cosmological tensions. Overall, we find excellent agreement with previously published results on the DES Y3 and HSC Y1 data sets, while there are some differences on the mean redshift with respect to the previously published KiDS-1000 results. We attribute the latter to mismatches in photometric noise properties in the COSMOS field compared to the wider KiDS self-organizing map-gold catalog. At the same time, the new n(z) estimates for KiDS do not significantly change estimates of cosmic structure growth from cosmic shear. Finally, we discuss how our method can be applied to future weak lensing calibrations with DESI data.

Lange, J. U. [American Univ., Washington, DC (Unit↗

Monitoring the long-term performance of organic redox flow battery by a distribution of relaxation time analysis

Organic redox flow batteries hold great promise as an energy storage technology, but their intricate chemistry makes them vulnerable to various degradation mechanisms. Monitoring this degradation is essential for identifying the limiting processes within the cells. Electrochemical impedance spectroscopy (EIS) offers a straightforward, in-situ method for measuring the total resistance of an operating cell. However, to pinpoint the limiting processes during long-term cycling, EIS data must be complemented by other techniques. Distribution of relaxation time (DRT) analysis is particularly effective for differentiating resistance components. Here, in this study, we perform a comprehensive analysis of resistance evolution and the separation of anode and cathode contributions during long-term cycling of a full cell employing 7,8-dihydroxyphenazine-2-sulfonic acid (DHPS) as the anolyte. Separate analyses of the DHPS anolyte and ferri-/ferrocyanide catholyte were conducted using a symmetric cell setup. The relaxation times derived from symmetric cells facilitate the identification of peaks in the DRT profiles from the full cell. Importantly, the DRT profiles indicate a correlation between the evolution of charge transfer resistance and the chemical degradation of DHPS. The methodologies and results outlined in this study offer significant insights for developing diagnostic tools applicable to other types of redox flow batteries.

Distribution of relaxation time↗

An implementation of neural simulation-based inference for parameter estimation in ATLAS

Neural simulation-based inference (NSBI) is a powerful class of machine-learning-based methods for statistical inference that naturally handles high-dimensional parameter estimation without the need to bin data into low-dimensional summary histograms. Such methods are promising for a range of measurements, including at the Large Hadron Collider, where no single observable may be optimal to scan over the entire theoretical phase space under consideration, or where binning data into histograms could result in a loss of sensitivity. This work develops a NSBI framework for statistical inference, using neural networks to estimate probability density ratios, which enables the application to a full-scale analysis. It incorporates a large number of systematic uncertainties, quantifies the uncertainty due to the finite number of events in training samples, develops a method to construct confidence intervals, and demonstrates a series of intermediate diagnostic checks that can be performed to validate the robustness of the method. As an example, the power and feasibility of the method are assessed on simulated data for a simplified version of an off-shell Higgs boson couplings measurement in the four-lepton final states. This approach represents an extension to the standard statistical methodology used by the experiments at the Large Hadron Collider, and can benefit many physics analyses.

frequentist statistics↗

ASCR Workshop Position Paper: Challenges and Opportunities in High Energy Physics

High energy particle physics and cosmology concern themselves with estimating fundamental parameters of nature, such as the masses and interactions of fundamental particles like the Higgs boson and the rate of expansion of the universe. In doing so, they analyze exabyte-scale datasets, some of the largest in all of science, and face many challenges in subsequent data analysis. These challenges are shared between the two disciplines, but we focus on particle physics to highlight one specific domain. In particle physics, the standard method for estimating parameters involves performing Monte Carlo (MC) integration as a function of both parameters of interest and nuisance parameters using an expensive simulator, counting the number of observed collision events (i.i.d. samples) from an experiment in the corresponding integration domains, and forming a Poisson likelihood function. This likelihood function is then used in a Frequentist manner to construct a maximum likelihood point estimate (MLE) and confidence set for the parameters. To sufficiently populate the high-dimensional integration domains, simulators consume billions of CPU-hours annually and produce hundreds of petabytes of intermediate output data. Several techniques have been developed to: optimize definitions of the integration domains so as to be maximally sensitive to a particular subset of parameters, efficiently estimate the integrals, and build robust surrogate models by interpolating between integral evaluations at different parameter points. One can view this whole endeavor as classical Simulation-Based Inference (SBI).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data-driven model validation for neutrino-nucleus cross section measurements

Neutrino-nucleus cross section measurements are needed to improve interaction modeling to meet the precision needs of neutrino experiments in efforts to measure oscillation parameters and search for physics beyond the Standard Model. We review the difficulties associated with modeling neutrino-nucleus interactions that lead to a dependence on event generators in oscillation analyses and cross section measurements alike. We then describe data-driven model validation techniques intended to address this model dependence. The method relies on utilizing various goodness-of-fit tests and the correlations between different observables and channels to probe the model for defects in the phase space relevant for the desired analysis. These techniques shed light on relevant mismodeling, allowing it to be detected before it begins to bias the cross section results. We compare more commonly used model validation methods which directly validate the model against alternative ones to these data-driven techniques and show their efficacy with fake data studies. These studies demonstrate that employing data-driven model validation in cross section measurements represents a reliable strategy to produce robust results that will stimulate the desired improvements to interaction modeling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data-driven model validation for neutrino-nucleus cross section measurements

Neutrino-nucleus cross section measurements are needed to improve interaction modeling to meet the precision needs of neutrino experiments in efforts to measure oscillation parameters and search for physics beyond the Standard Model. We review the difficulties associated with modeling neutrino-nucleus interactions that lead to a dependence on event generators in oscillation analyses and cross section measurements alike. We then describe data-driven model validation techniques intended to address this model dependence. The method relies on utilizing various goodness-of-fit tests and the correlations between different observables and channels to probe the model for defects in the phase space relevant for the desired analysis. These techniques shed light on relevant mismodeling, allowing it to be detected before it begins to bias the cross section results. We compare more commonly used model validation methods which directly validate the model against alternative ones to these data-driven techniques and show their efficacy with fake data studies. These studies demonstrate that employing data-driven model validation in cross section measurements represents a reliable strategy to produce robust results that will stimulate the desired improvements to interaction modeling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Review of data-driven models for quantifying load shed by non-residential buildings in the United States

Shifting and shedding power demand in buildings can be cost-effective techniques for grids to function reliably and for end users to earn compensation. Grid operators reimburse customers in proportion to the quantity of load shed. Simple data-driven methods are used to quantify this shed, which is the difference between a measured load during the event and modeled "baseline" that would have occurred in absence of the event. These methods have evolved over the years and in many cases have been integrated with building physics, to make them a hybrid between physics based and empirical models. However, there is no comprehensive analysis that provides guidance to building operators, grid operators and researchers in selecting appropriate models based on their specific needs and available data. Here, this work aims to fill this gap by critically assessing the performance of baseline models put forward from the year 2000 through 2023. The literature reviewed includes reports generated by grid operators, reports from national laboratories and academic journal articles. The work outlines modeling features like the inputs, training period, estimation method, adjustments to fine tune the predictions and metrics to evaluate the performance. A comprehensive list of 50 models has been provided. For each model, the study explores the applicability of the model to weather sensitive buildings, variability in the building profile, timing of the event, and whether the building reduces energy consumption before an event. The work identifies the situations in which a particular model works and draws lessons based on evidence of performance. Finally, recommendations to aid in model selection are given.

97 MATHEMATICS AND COMPUTING↗

The DECADE cosmic shear project IV: cosmological constraints from 107 million galaxies across 5,400 deg$^2$ of the sky

We present cosmological constraints from the Dark Energy Camera All Data Everywhere (DECADE) cosmic shear analysis. This work uses shape measurements for 107 million galaxies measured through Dark Energy Camera (DECam) imaging of $5,\!412$ deg$^2$ of sky that is outside the Dark Energy Survey (DES) footprint. We derive constraints on the cosmological parameters $S_8 = 0.791^{+0.027}_{-0.032}$ and $Ω_{\rm m} =0.269^{+0.034}_{-0.050}$ for the $Λ$CDM model, which are consistent with those from other weak lensing surveys and from the cosmic microwave background. We combine our results with cosmic shear results from DES Y3 at the likelihood level, since the two datasets span independent areas on the sky. The combined measurements, which cover $\approx\! 10,\!000$ deg$^2$, prefer $S_8 = 0.791 \pm 0.023$ and $Ω_{\rm m} = 0.277^{+0.034}_{-0.046}$ under the $Λ$CDM model. These results are the culmination of a series of rigorous studies that characterize and validate the DECADE dataset and the associated analysis methodologies (Anbajagane et. al 2025a,b,c). Overall, the DECADE project demonstrates that the cosmic shear analysis methods employed in Stage-III weak lensing surveys can provide robust cosmological constraints for fairly inhomogeneous datasets. This opens the possibility of using data that have been previously categorized as ``unusable'' for cosmic shear analyses, thereby increasing the statistical power of upcoming weak lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Depletion Benchmark Analysis on a Lead Fast Reactor Using PyARC/OpenMC

PyARC is a user-friendly fast reactor analysis tool that automates multiphysics workflows using the “extended suite” of Argonne Reactor Computation (ARC) codes by providing a single common input for model definition, code execution, and output post-processing. A lead fast reactor (LFR) benchmark model is used to perform depletion calculations using the newly integrated OpenMC depletion capability in PyARC, building on previous analysis using the ARC codes through PyARC and Serpent. Results for core lifetime k-effective, shutdown decay heat, and end-of-life heavy-metal inventory are compared to verify the PyARC/OpenMC integration against the PyARC/ARC workflow and Serpent for depletion analysis of LFR designs. The results show satisfactory agreement among all three methods, with remaining discrepancies largely attributable to differences in nuclear data libraries and decay-chain modeling detail rather than to fundamental modeling limitations.

Kiesling, Kalin R.↗

Elastic Changepoint Detection for Globally-indexed Functional Time Series Data with Climate Applications

Changepoint detection is a vital tool in the application of climate data analysis. Numerous types of climate observation data are most properly represented by functional time series, implying a need for accurate changepoint detection methods applicable to functional time series data. Such data taken at a global scale often contain both spatial heterogeneity and dependence as well as phase (time) misalignment. In this report, we present methods which can detect spatially-dependent changepoints while allowing different estimates of change time and change strength depending on location. Additionally, we provide extensions to this spatially-predicted model which controls for phase variability among observations. Our methods provide the ability to detect a single change, or control for epidemic changes (where a “return-to-normal” change is more likely to be detected than the initial change). We showcase results analyzing the June 1991 eruption of Mt. Pinatubo, where our methods demonstrate the ability to accurately detect both single and epidemic changepoints even in the presence of strong seasonal variability. We find that our spatially-predicted model improves the detection of relevant changepoints versus methods which do not take spatial information into account, and we find that controlling for phase variability helps to control the false discovery rate during the detection process.

54 ENVIRONMENTAL SCIENCES↗

Exploring the Energy Frontier through Precision Tests and Fast Tracking with the CMS Detector (Final Technical Report)

This Early Career Award supported a research program using the CMS experiment at the CERN LHC to probe physics beyond the Standard Model in the top quark and Higgs boson sectors, alongside detector and trigger developments for the High-Luminosity LHC (HL-LHC) upgrade. The program (i) searched for charged lepton flavor violation (LFV) in the top quark sector with the full CMS Run-2 data set, placing the world’s strongest limits to date on the $t → eµq\ (q = u/c)$ branching fraction; (ii) developed preliminary analysis methods toward a boosted $t\bar{t}H(b\bar{b})$ measurement of the top quark Yukawa coupling and its CP properties; (iii) made leading contributions to the hardware-based Level-1 (L1) track finding system for the upgraded CMS detector for HL-LHC; and (iv) developed novel L1 trigger algorithms, notably a displaced vertex trigger enabling new searches for exotic long-lived particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Model Based Approach to Extract Health Information from Textual Data

In current nuclear power plants (NPPs) a large amount of condition-based data is being generated and stored to assess and monitor component health and performance. The format of this data can be either numeric (e.g., pump vibration data) or textual (e.g., condition report which assess component health). While assessing component health from numeric data can be performed with a large variety of methods, the extraction of information from textual data still remains a challenge. Natural language processing (NLP) methods are starting to be deployed in current NPPs mainly to filter out incident reports (IRs) that are not safety related by employing supervised machine learning methods. However, these methods do not really provide the quantitative information that might be contained in IRs. This paper presents an approach to extract information from textual data (e.g., from IRs, maintenance reports) that is based on NLP data analytics methods coupled with model-based system engineer (MBSE) models. NLP methods are employed to perform syntactic and semantic analyses. Syntactic analysis analyzes the grammatical structure of a sentence; such analysis includes: part of speech (POS) tagging (i.e., identification of grammatic elements of each string - e.g., nouns, verbs), named entity recognition (i.e., identification of text entities - e.g., names, dates, events), and relation extraction (e.g., coreference resolution). On the other hand, semantic analysis is designed to analyze the logic structure of a sentence. Through a specific set of rules, our methods can identify whether a sentence contains health information of a component (e.g., degraded performance, anomaly behavior) or the causal relationship between two events (i.e., a cause-effect pair). An innovative element of our approach is that semantic analysis relies on MBSE models to identify links between textual elements. MBSE are diagrams designed to represent system and component dependencies (from both a form and functional point of view). In our approach, MBSE models emulate system engineer knowledge about component/system architecture. This paper presents in detail how the integration of NLP methods and MBSE models is performed. Few analysis examples focusing on centrifugal pumps are presented.

97 - MATHEMATICS AND COMPUTING↗

Use of AI for Interpreting Technical Specifications for Power Uprates in Nuclear Power Plants

Powerpoint presentation. Background information provided on power plant uprates. Discussion of the current and proposed approaches to power plant uprates. Explanation of what data is used to draft a LAR. Methods such as retrieval augmented generation (RAG) and fine-tuning are discussed. Use case analysis is performed. Different failure types are examined. Conclusions are drawn from the analysis. Future work is proposed.

97 - MATHEMATICS AND COMPUTING↗