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At least 937 records · Page 52

GLEAM: Galaxy Line Emission & Absorption Modeling

We present Galaxy Line Emission & Absorption Modeling (gleam), a Python tool for fitting Gaussian models to emission and absorption lines in large samples of 1D extragalactic spectra. gleam is tailored to work well in batch mode without much human interaction. With gleam, users can uniformly process a variety of spectra, including galaxies and active galactic nuclei, in a wide range of instrument setups and signal-to-noise regimes. gleam also takes advantage of multiprocessing capabilities to process spectra in parallel. With the goal of enabling reproducible workflows for its users, gleam employs a small number of input files, including a central, user-friendly configuration in which fitting constraints can be defined for groups of spectra and overrides can be specified for edge cases. For each spectrum, gleam produces a table containing measurements and error bars for the detected spectral lines and continuum and upper limits for nondetections. For visual inspection and publishing, gleam can also produce plots of the data with fitted lines overlaid. In the present paper, we describe gleam’s main features, the necessary inputs, expected outputs, and some example applications, including thorough tests on a large sample of optical/infrared multi-object spectroscopic observations and integral field spectroscopic data. gleam is developed as an open-source project hosted at https://github.com/multiwavelength/gleam and welcomes community contributions.

79 ASTRONOMY AND ASTROPHYSICS↗

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

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

artificial intelligence↗

GPS-supported smartphone app-based integrated travel diary and time-use data collection: challenges and lessons learned

Travel behaviour and time-use data are two vital data sources for travel demand modelling. Travel behaviour is traditionally collected through household travel surveys, enhanced by using GPS-supported smartphone apps for passive location data collection. However, recruiting individuals willing to install these apps with sustained motivation to continue participation has been a critical challenge. This paper shares insights from a travel and time-use data collection procedure in Chicago and Sydney using the Fourstep app. Social media platforms were utilised as a solution to recruit participants in Chicago, where an international market research company failed to accomplish the task. This paper also discusses the challenges we faced and suggests ways to overcome them, offering valuable guidance to researchers in recruiting participants for smartphone application-based data collection. It also offers an analysis of travel, time-use, and travel-based multitasking behaviours based on the data collected from the Chicago and Sydney samples.

GPS-supported smartphone apps↗

How can a diverse set of integral and semi-integral measurements inform identification of discrepant nuclear data?

Nuclear data are used for a variety of applications, including criticality safety, reactor performance, and material safeguards. Despite the breadth of use-cases, the effective neutron multiplication factor, keff, of ICSBEP critical assemblies are primarily used for nuclear data validation; these are sensitive to specific energy regions and nuclides and are unable to uniquely constrain nuclear data. As a consequence, general-purpose nuclear data libraries, such as ENDF/B-VIII.0, may have deficiencies that, while not apparent in criticality applications, negatively impact other applications, such as non-destructive analysis of special nuclear material and neutron diagnosed subcritical experiments. Recent work by the Experiments Underpinned by Computational Learning for Improvements in Nuclear Data (EUCLID) project developed a machine learning tool, RAFIEKI, which uses random forests and the SHAP metric to determine which nuclear data contribute most to predicted bias between measured and simulated responses (e.g. keff). This paper contrasts RAFIEKI analysis applied to keff only against RAFIEKI analysis with keff paired with either LLNL pulsed sphere measurements or subcritical benchmarks. Two examples show that a) including pulsed sphere measurements substantially increases 9Be nuclear data importance to bias between 2 and 15 MeV, and b) including subcritical benchmarks has the potential for disentangling compensating errors between 240Pu (n,el) and (n,il) cross-sections between 0.1 and 10 MeV. These results show that RAFIEKI analysis applied to response sets that include, but go beyond, keff can aid nuclear data evaluators in identifying issues in nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Integrated package of electron cyclotron emission imaging data processing and forward modeling in OMFIT

An Electron Cyclotron Emission Imaging (ECEI) data analysis module has been developed for the OMFIT platform to accommodate the needs of users at the DIII-D tokamak for physics applications. The user can easily access the ECEI spatial observation windows in the plasma that are calculated based on the automatically retrieved hardware setup and available DIII-D equilibria, perform spectral analysis, and make 2D electron temperature fluctuation images. The module provides a powerful data post processing package for extracting important physics parameters from the 2D measurements, including the radial structure and poloidal mode number of Alfven Eigenmodes, as well as the frequency-vs-wavenumber dispersion relationship of broadband MHD. Lastly, the module propagates characterized synthetic fluctuations for the user, so one can perform forward modeling tasks with simple analytical fluctuations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Time and Frequency Analysis of Load Profile Data

Technology advancements and integration of modern advanced metering systems can monitor, forecast, inform, control, and operate the building's mechanical, electrical, and plumbing (MEP) systems. They offer a higher level of information, which can contribute to making smart buildings more energy efficient and to making them closer to becoming grid-interactive energy efficient buildings (GEB). This paper builds on the ongoing research on variability analysis of a case study building with a 1-minute load profile and examines the Discrete Wavelet Transform (DWT) process in the frequency domain to quantify the signal's energy in each bandwidth, with respect to each end-use category. Moreover, the amount of variability in the total variability is not similar among the end-use categories. This information is needed to understand the behavior of the variability in the frequency domain for future applications, such as generating synthetic load profiles with a similar frequency spectrum as the measured signal.

decomposition↗

How can a diverse set of integral and semi-integral measurements inform identification of discrepant nuclear data? [Slides]

Importance of nuclear data to bias changed significantly when including diverse measurement sets. LLNL pulsed sphere measurements provided information for 9 Be nuclear data above 2 MeV and subcritical benchmarks provided information for 240 Pu nuclear data between 100 keV and 10 MeV. Pulsed sphere leakage spectra and neutron noise observables are differently sensitive to nuclear data compared to critical benchmarks. Leakage spectra are sensitive to nuclear data above 5 MeV. Count rate and Feynman Y are more sensitive to nuclear data. A change in bias can help evaluators identify discrepant nuclear data. In the future, EUCLID plans to perform RAFIEKI analysis with additional benchmark and measurement sets.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Laue-DIALS: Open-source software for polychromatic x-ray diffraction data

Most x-ray sources are inherently polychromatic. Polychromatic (“pink”) x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure—ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

97 MATHEMATICS AND COMPUTING↗

Uncertainty Visualization Challenges in Decision Systems with Ensemble Data & Surrogate Models

Uncertainty visualization is a key component in translating important insights from ensemble simulation data into actionable decision-making by visually conveying various aspects of uncertainty within a system. With the recent advent of fast surrogate models trained on ensemble data, we can substitute computationally expensive simulations, which allows users to interact with more aspects of data spaces than ever before. However, the use of ensemble data with surrogate models in a decision-making tool brings up new challenges for uncertainty visualization, namely how to reconcile and communicate the new and different types of uncertainties brought in by surrogates and how to utilize these new data estimates in actionable ways. In this work, we examine these issues as they relate to high-dimensional data visualization, the integration of discrete datasets and the continuous representations of those datasets, and the unique difficulties associated with systems that allow users to iterate between input and output spaces. We assess the role of uncertainty visualization in facilitating intuitive and actionable interaction with ensemble data and surrogate models, and highlight key challenges in this new frontier of computational simulation.

ensemble data↗

Description of FY25 Theory and Simulation Performance Target: Development of an integrated modeling framework for fusion reactor design and assessment

The urgency to deliver fusion power is growing now more than ever, with increasing pressure for both public programs and private companies to meet milestones timelines and overcome significant remaining technical challenges to ensure growth of a nascent fusion industry in time to meet rapidly growing clean energy demands. With incredible advancements in computation and years of investment in fusion model development and validation, integrated modeling is poised to fill a key role in accelerating the timeline to a fusion pilot plant (FPP). Future fusion pilot plants will operate in regimes far beyond current experience, and device design will rely on physics-based prediction and extrapolation. Many concepts will also rely on simulation to assess safety (shielding, tritium management, materials activation and lifetimes), economics and scalability before the decision to build. Importantly, integrated simulation can be used to reveal and solve the complexities of system integration that may otherwise not be apparent in physical components or models developed in isolation. New experimental test facilities that produce relevant conditions to validate and resolve key technical challenges for various subsystems (materials, blankets, fuel cycle, etc.) have been repeatedly called for by the fusion community but are not yet realized. Integrated modeling has an important role in identifying realistic load conditions (thermal, electromagnetic, plasma, neutron and photon loads, etc.) and defining the components and experiments for these test facilities in order to ensure meaningful validation that sufficiently reduces modeling uncertainties and technical risk for the full integrated reactor. The Fusion REactor Design and Assessment (FREDA) SciDAC project is building a component-based integrated modeling framework & data structure to enable self-consistent, multi-fidelity, iterative optimization workflows for the fusion reactor design process. FREDA aims to shorten the time to viable designs by providing a set of flexible workflows to support the various stages of the design process using an integrated model hierarchy, ranging from the simple analytic descriptions to the highest fidelity, theory-based plasma and engineering modeling developed by the fusion and fission communities. These tools are expected to be needed for timely support of FPP design in the milestone program and in the FIRE collaboratives. The plasma simulation backbone of FREDA is IPS-FASTRAN with newly developed coupled Core-Edge Pedestal-SOL (CESOL) workflows, which is being extended to the far-SOL region up to the plasma facing components. FREDA incorporates the FERMI engineering modeling suite and will enable self-consistent evaluation of the thermal shields, limiters, blanket, magnets, and other surrounding structures with predictions of temperatures, erosion, dpa, activation, tritium generation and transport, creep, corrosion, material degradation, etc. Parametric generation of 3D CAD enables rapid iteration of component geometry in response to plasma and loading specifications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Leveraging 3D CAD and Virtual Reality in Design of the Calcine Disposition Project - 20512

Fluor Idaho's Calcine Disposition Project (CDP) is leveraging the power of three-dimensional (3D) visualization, light detection and ranging (Lidar), and virtual reality to improve designs and worker safety. With the use of computer-aided design (CAD) modeling software, the CDP has created 3D models of the facility and systems to aid in the design, development, and operation of its retrieval and transfer system. This by itself is nothing new and has been done in industry for years. The CDP project however is taking this a few steps farther with the use of Lidar and virtual reality software. The CRP is tasked with removing a radioactive granular material from stainless steel bins located in concrete vaults that were constructed in the late 1950's and early 1960's. While construction drawings are available, it is not certain that the drawings are as-built or how accurate they truly are. Part of the project requires precise placement of equipment on to bins around multiple pipe, electrical lines, and bin stiffeners. Relying solely on the existing drawings and models created from these drawings is highly risky and prone to failure. The first step to determine the precise location and orientation of all obstructions in the vault the project will use a Lidar system to scan the vault structure and precisely locate all vault and bin components. Once this information is obtained, the data will be integrated into the CAD model. The model will then be verified, and a true as-built model developed. Precise component location, size, and orientation will be used for final design and placement of retrieval components. The second step will be to take the verified 3D model and scan data and import it into virtual reality software creating a virtual world. While some work on the project requires all work to be completed remotely due to high radiation fields, some areas have low enough radiation levels that personnel can enter and perform work. With the use of a virtual reality headset, operators and technicians will be able to enter our virtual world and become familiar with the surroundings and perform work prior to ever entering the radiation environment. This training is expected to pay dividends by improving worker efficiency, reducing errors, and improving confidence that the work can be performed as expected. It will play a key aspect in as low as reasonably achievable (ALARA) principles. An additional aspect in using the Lidar scans and virtual environment, is that it will give engineers and managers an opportunity to revisit the facility, especially radiation areas, at any time to obtain design information and measurements that may be costly or impossible to obtain once the facility transitions into radiation operations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A library of AI-assisted FAIR water cycle and related disturbance datasets to enable model training, parameterization and validation

This whitepaper is responsive to focal area Data acquisition and assimilation enabled by machine learning, AI, and advanced methods. Here we describe how FAIR (Findable, Accessible, Reusable, Interoperable) datasets related to water cycle extremes are essential for successful implementation of ML in Earth System and other models. We also describe how AI can be used to acquire and integrate water cycle data related to extreme events to create a library of FAIR datasets for training and evaluating algorithms.

58 GEOSCIENCES↗

Equation-based and data-driven modeling: Open-source software current state and future directions

Here, a review of current trends in scientific computing reveals a broad shift to open-source and higher-level programming languages such as Python and growing career opportunities over the next decade. Open-source modeling tools accelerate innovation in equation-based and data-driven applications. Significant resources have been deployed to develop data-driven tools (PyTorch, TensorFlow, Scikit-learn) from tech companies that rely on machine learning services to meet business needs while keeping the foundational tools open. Open-source equation-based tools such as Pyomo, CasADi, Gekko, and JuMP are also gaining momentum according to user community and development pace metrics. Integration of data-driven and principles-based tools is emerging. New compute hardware, productivity software, and training resources have the potential to radically accelerate progress. However, long-term support mechanisms are still necessary to sustain the momentum and maintenance of critical foundational packages.

97 MATHEMATICS AND COMPUTING↗

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

ABSTRACT The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a ‘big data’ resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

60 APPLIED LIFE SCIENCES↗

Evaluation and Suitability of Using SERI QC Software for Estimating Measurement Uncertainty

SERI QC is a robust solar data quality assessment software tool that has been in continuous use for more than three decades. This report (the first of six in the Data Quality and Uncertainty Integration project) reviews and evaluates the software to determine its suitability for determining the estimated expanded measurement uncertainty of solar measurement data by including operational factors. Using redundancy incorporated in three-component (global, direct, diffuse) solar measurements, SERI QC can quantify the standard uncertainty estimates for estimating uncertainty. With minor modifications, SERI QC will provide an operational uncertainty to be used in conjunction with the National Renewable Energy Laboratory method for instrument uncertainty to provide an integrated estimate of solar measurement data sets. These modifications will capitalize on SERI QC's evaluation of data quality, including data input validation and a variety of built-in solar routines, and will further develop the utility of the software.

14 SOLAR ENERGY↗

Measurement of quark- and gluon-like jet fractions using jet charge in PbPb and pp collisions at 5.02 TeV

The momentum-weighted sum of the electric charges of particles inside a jet, known as jet charge, is sensitive to the electric charge of the particle initiating the parton shower. This paper presents jet charge distributions in $ \sqrt{s_{\mathrm{NN}}} $ = 5.02 TeV lead-lead (PbPb) and proton-proton (pp) collisions recorded with the CMS detector at the LHC. These data correspond to integrated luminosities of 404 μb$^{−1}$ and 27.4 pb$^{−1}$ for PbPb and pp collisions, respectively. Leveraging the sensitivity of the jet charge to fundamental differences in the electric charges of quarks and gluons, the jet charge distributions from simulated events are used as templates to extract the quark- and gluon-like jet fractions from data. The modification of these jet fractions is examined by comparing pp and PbPb data as a function of the overlap of the colliding Pb nuclei (centrality). This measurement tests the color charge dependence of jet energy loss due to interactions with the quark-gluon plasma. No significant modification between different centrality classes and with respect to pp results is observed in the extracted quark- and gluon-like jet fractions.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗