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At least 487 records · Page 27

Materials Data Science Ontology(MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science

Ontologies have gained popularity in the scientific community as a way to standardize terminologies in organizations’ data. Although certain cohorts have created frameworks with rules and guidelines on creating ontologies, there exist significant variations in how Materials Science ontologies are currently developed. We seek to provide guidance in the form of a unified automated framework for developing interoperable and modular ontologies for Materials Data Science that simplifies the ontology terms matching by establishing a semantic bridge up to the Basic Formal Ontology(BFO). This framework provides key recommendations on how ontologies should be positioned within the semantic web, what knowledge representation language is recommended, and where ontologies should be published online to boost their findability and interoperability. Two fundamental components of the MDS-Onto framework are the bilingual package called FAIRmaterials for ontology creation and FAIRLinked, for FAIR data creation. To showcase the practical capabilities of FAIRmaterials, we present two exemplar domain ontologies of MDS-Onto: Synchrotron X-Ray Diffraction and Photovoltaics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

An in-depth field validation of “DUSST”: A novel low-maintenance soiling measurement device

This study presents indoor and field validation results for two versions of the “DUSST” optical soiling sensor, intended to be a low-cost and low-maintenance device for measuring photovoltaic soiling losses. Indoor testing covers irradiance calibration and temperature dependencies, which are necessary to achieve high accuracy, low uncertainty field measurements. Field testing includes an array of different environments including Saudi Arabia, California, Utah, and Colorado. DUSST versions include a configuration with a 530-nm light emitting diode (LED) (discussed in previous work) and a unit with seven white LEDs and a polycarbonate collimating optic. The new design increases light intensity fivefold and demonstrates a single linear calibration coefficient is effective to measure soiling losses as high as 75%. Field data from Utah and California demonstrate that daily soiling loss measurements and soiling rate calculations closely match both reference cell and full-size module measurements of soiling losses and soiling rates. Corrective methods employed on the Utah DUSST sensor suggest that it is possible to achieve measurement errors as low as ±0.1% at two standard deviations. Field data from both Colorado and Saudi Arabia demonstrate that LED lens soiling can occur and that further design optimizations are needed. The lesson learned from all the field deployment locations suggests directions for future design improvements.

14 SOLAR ENERGY↗

Filling data analysis gaps in time-resolved crystallography by machine learning

There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.

Trujillo, Justin (ORCID:0000000285505360)↗

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗

NWGraph: A Library of Generic Graph Algorithms and Data Structures in C++20

The C++ Standard Library is a valuable collection of generic algorithms and data structures that improves the usability and reliability of C++ software. Graph algorithms and data structures are notably absent from the standard library, and previous attempts to fill this gap have not gained widespread adoption. In this paper we show that the richness of graph algorithms and data structures can in fact be captured by straightforward composition of existing C++ mechanisms. Generic programming is algorithm-oriented. Accordingly, we apply a systematic approach to analyzing a broad set of graph algorithms, “lift” unnecessary constraints from them, and organize the resulting set of minimal common type requirements, i.e., concepts, for defining their interfaces. By using the newly available ranges and concepts in C++20, the type requirements for generic graph algorithms can be succinctly expressed. The generic algorithms and data structures resulting from our analysis are realized in NWGraph, in a modern, composable, and extensible C++ library.

graphs and networks, programming language, C++20↗

New U.S. Data Tools are Playing a Crucial Role in Decarbonizing Buildings at Speed, Scale, and Low Cost

Preparing buildings for retrofits traditionally requires expensive on-site audits or timeintensive simulation models. As a result, the majority of buildings fail to pursue cost-saving retrofits. To address these barriers, the U.S. Department of Energy (DOE) has introduced the Building Efficiency Targeting Tool for Energy Retrofits (BETTER)-a new, free, on-line tool that utilizes a data-driven analytical engine and user-friendly web interface to automatically analyze a building's monthly energy usage in response to weather conditions. The tool benchmarks a building's electric and fossil energy usage against peers; estimates energy, cost, and emissions reductions at the building and portfolio levels; recommends energy efficiency measures; and prioritizes buildings for net-zero energy retrofits. Thanks to interoperability with the DOE's Standard Energy Efficiency Data (SEED) platform, BETTER is supporting U.S. jurisdictions to prepare buildings for retrofit at speed, scale, and low cost to comply with energy policies. This paper discusses the use of BETTER and SEED by one of the branches of the California state government to streamline a retrofit program across 455 public non-residential buildings to align with state goals to reduce greenhouse gas emissions. It describes the organization's challenge to reduce energy consumption across a geographically diverse, aging portfolio; explores how BETTER and SEED improved workflow efficiency; presents preliminary results, including avoiding audit costs of $3.28 million and developing the groundwork for retrofit projects estimated to prevent emission of 2,271 t CO2e annually; and provides guidance for other jurisdictions seeking similar results.

BETTER↗

New U.S. Data Tools are Playing a Crucial Role in Decarbonizing Buildings at Speed, Scale, and Low Cost

Preparing buildings for retrofits traditionally requires expensive on-site audits or time- intensive simulation models. As a result, the majority of buildings fail to pursue cost-saving retrofits. To address these barriers, the U.S. Department of Energy (DOE) has introduced the Building Efficiency Targeting Tool for Energy Retrofits (BETTER)—a new, free, on-line tool that utilizes a data-driven analytical engine and user-friendly web interface to automatically analyze a building’s monthly energy usage in response to weather conditions. The tool benchmarks a building’s electric and fossil energy usage against peers; estimates energy, cost, and emissions reductions at the building and portfolio levels; recommends energy efficiency measures; and prioritizes buildings for net-zero energy retrofits. Thanks to interoperability with the DOE’s Standard Energy Efficiency Data (SEED) platform, BETTER is supporting U.S. jurisdictions to prepare buildings for retrofit at speed, scale, and low cost to comply with energy policies. This paper discusses the use of BETTER and SEED by one of the branches of the California state government to streamline a retrofit program across 455 public non-residential buildings to align with state goals to reduce greenhouse gas emissions. It describes the organization’s challenge to reduce energy consumption across a geographically diverse, aging portfolio; explores how BETTER and SEED improved workflow efficiency; presents preliminary results, including avoiding audit costs of $3.28 million and developing the groundwork for retrofit projects estimated to prevent emission of 2,271 t CO2e annually; and provides guidance for other jurisdictions seeking similar results.

Li, han↗

An Application for Validation of Power Distribution System Models in an ADMS Environment

An accurate model of a power distribution system is the foundation for model-based applications that ensure efficient and reliable grid operation in an advanced distribution management system (ADMS) environment. However, these models are error-prone and comprehensive model validation is challenging due to lack of standards-based systems, data originating from disparate databases and other sources, and the constantly evolving nature of modern power distribution systems. In this paper, a novel framework for comprehensive model validation is described. The proposed application, the Model Validator, ensures that a model is both consistent and feasible by validating the derivative static and operational network model. A modular architecture for the application has been implemented and integrated with an open-source standards-based platform for ADMS application development, GridAPPS-D, allowing new validation capability to be added with minimal time and effort. The Model Validator application is demonstrated on the IEEE 13-bus, 123-bus, and 8500-node test cases over three validation scenarios.

Poudel, Shiva↗

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES↗

Search for 𝐶⁢𝑃-Violating Neutrino Nonstandard Interactions with the NOvA Experiment

This Letter reports a search for charge-parity (𝐶⁢𝑃) symmetry violating nonstandard interactions (NSI) of neutrinos with matter using the NOvA Experiment, and examines their effects on the determination of the standard oscillation parameters. Data from 𝜈 𝜇 ⁡($\bar{𝜈}$ 𝜇 ) → 𝜈 𝜇 ⁡($\bar{𝜈}$ 𝜇 ) and 𝜈 𝜇 ⁡($\bar{𝜈}$ 𝜇 ) → 𝜈 𝑒 ⁡( $\bar{𝜈}$ 𝑒 ) oscillation channels are used to measure the effect of the NSI parameters 𝜖 𝑒⁢𝜇 and 𝜖 𝑒⁢𝜏 . With 90% CL the magnitudes of the NSI couplings are constrained to be |𝜖 𝑒⁢𝜇 | ≲0.3 and |𝜖 𝑒⁢𝜏 | ≲ 0.4. A degeneracy at |𝜖 𝑒⁢𝜏 | ≈ 1.8 is reported, and we observe that the presence of NSI limits sensitivity to the standard 𝐶⁢𝑃 phase 𝛿 𝐶⁢𝑃 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Search for top squarks in final states with many light-flavor jets and 0, 1, or 2 charged leptons in proton-proton collisions at $\sqrt{s}=13$ TeV

Several new physics models including versions of supersymmetry (SUSY) characterized by R-parity violation (RPV) or with additional hidden sectors predict the production of events with top quarks, low missing transverse momentum, and many additional quarks or gluons. The results of a search for top squarks decaying to two top quarks and six additional light-flavor quarks or gluons are reported. The search employs a novel machine learning method for background estimation from control samples in data using decorrelated discriminators. The search is performed using events with 0, 1, or 2 electrons or muons in conjunction with at least six jets. No requirement is placed on the magnitude of the missing transverse momentum. The result is based on a sample of proton-proton collisions at $\sqrt{s}=13$ TeV corresponding to 138 fb −1 of integrated luminosity collected with the CMS detector at the LHC in 2016–2018. With no statistically significant excess of events observed beyond the expected contributions from the standard model, the data are used to determine upper limits on the top squark pair production cross section in the frameworks of RPV and stealth SUSY. Models with top squark masses less than 700 (930) GeV are excluded at 95% confidence level for RPV (stealth) SUSY scenarios.

Hadron-Hadron Scattering↗

Thresholding Analysis and Feature Extraction from 3D Ground Penetrating Radar Data for Noninvasive Assessment of Peanut Yield

This study explores the efficacy of utilizing a novel ground penetrating radar (GPR) acquisition platform and data analysis methods to quantify peanut yield for breeding selection, agronomic research, and producer management and harvest applications. Sixty plots comprising different peanut market types were scanned with a multichannel, air-launched GPR antenna. Image thresholding analysis was performed on 3D GPR data from four of the channels to extract features that were correlated to peanut yield with the objective of developing a noninvasive high-throughput peanut phenotyping and yield-monitoring methodology. Plot-level GPR data were summarized using mean, standard deviation, sum, and the number of nonzero values (counts) below or above different percentile threshold values. Best results were obtained for data below the percentile threshold for mean, standard deviation and sum. Data both below and above the percentile threshold generated good correlations for count. Correlating individual GPR features to yield generated correlations of up to 39% explained variability, while combining GPR features in multiple linear regression models generated up to 51% explained variability. The correlations increased when regression models were developed separately for each peanut type. This research demonstrates that a systematic search of thresholding range, analysis window size, and data summary statistics is necessary for successful application of this type of analysis. The results also establish that thresholding analysis of GPR data is an appropriate methodology for noninvasive assessment of peanut yield, which could be further developed for high-throughput phenotyping and yield-monitoring, adding a new sensor and new capabilities to the growing set of digital agriculture technologies.

54 ENVIRONMENTAL SCIENCES↗

Benchmark calculations of pure neutron matter with realistic nucleon-nucleon interactions

Here, we report benchmark calculations of the energy per particle of pure neutron matter as a function of the baryon density using three independent many-body methods: Brueckner–Bethe–Goldstone, Fermi hypernetted chain/single-operator chain, and auxiliary-field diffusion Monte Carlo. Significant technical improvements are implemented in the latter two methods. The calculations are made for two distinct families of realistic coordinate-space nucleon-nucleon potentials fit to scattering data, including the standard Argonne v 18 interaction and two of its simplified versions, and four of the new Norfolk Δ -full chiral effective field theory potentials. Primarily because of the advancements in the auxiliary-field diffusion Monte Carlo, we observe good agreement among the three many-body techniques up to nuclear saturation density—the maximum difference in the energy per particle is within 1.5 MeV for all the potentials we consider. At higher densities, the divergences become more important, and are mainly driven by the Fermi hypernetted chain/single-operator calculations. We also study the connection between nucleon-nucleon scattering data and the energy per particle of pure neutron matter. Our results suggest that fitting to higher-energy nucleon-nucleon scattering helps reduce the spread of energies among the models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Extracting Resilience Metrics From Distribution Utility Data Using Outage and Restore Process Statistics

Resilience curves track the accumulation and restoration of outages during an event on an electric distribution grid. We show that a resilience curve generated from utility data can always be decomposed into an outage process and a restore process and that these processes generally overlap in time. We use many events in real utility data to characterize the statistics of these processes, and derive formulas based on these statistics for resilience metrics such as restore duration, customer hours not served, and outage and restore rates. The formulas express the mean value of these metrics as a function of the number of outages in the event. We also give a formula for the variability of restore duration, which allows us to predict a maximum restore duration with 95% confidence. Overall, we give a simple and general way to decompose resilience curves into outage and restore processes and then show how to use these processes to extract resilience metrics from standard distribution system data.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Enabling probabilistic learning on manifolds through double diffusion maps

Here, we present a generative learning framework for probabilistic sampling that extends Probabilistic Learning on Manifolds (PLoM), which is designed to generate statistically consistent realizations of a random vector in a finite-dimensional Euclidean space, informed by a (representative) set of observations. In its original form, PLoM constructs a reduced-order probabilistic model by combining three main components: (a) kernel density estimation to approximate the underlying probability measure, (b) Diffusion Maps to characterize the manifold of the data, and (c) a reduced-order Itô Stochastic Differential Equation (ISDE) to sample from the learned distribution. However, its sampling dynamics are posed in the ambient space and the retained number of reduced coordinates is chosen by projection-reconstruction error. In practice, this often (i) requires more coordinates than the data’s intrinsic dimension to achieve stable sampling and (ii) lacks a smooth, basis-independent lifting back to the data domain; moreover, standard Diffusion Maps emphasize harmonic eigenfunctions and can miss non-harmonic latent structure. We address these limitations by decoupling geometry learning from sampling: a first Diffusion Maps pass identifies non-harmonic coordinates on which we formulate a full-order ISDE directly in the latent space, while Double Diffusion Maps captures multiscale geometric features and Geometric Harmonics (GH) learns a smooth lifting map to the ambient variables that is independent of the particular diffusion basis. This hybrid design preserves the system’s dynamical richness with a compact geometric representation and enables principled out-of-sample inference. The effectiveness and robustness of the proposed method are illustrated through two numerical studies: one based on data generated from two-dimensional Hermite polynomial functions and another based on high-fidelity simulations of a detonation wave in a reactive flow.

Double diffusion maps↗

Tidal Energy Resource Characterization, Bottom Lander Measurements, Cook Inlet, AK, 2021

These datasets are from tidal resource characterization measurements collected on the Terrasond High Energy Oceanographic Mooring (THEOM) from 1 July 2021 to 30 August 2021 (60 days) in Cook Inlet, Alaska. The lander was deployed at 60.7207031 N, 151.4294998 W in ~50 m of water. The dataset contains raw and processed data from the following two instruments: 1. A Nortek Signature 500 kHz acoustic Doppler current profiler (ADCP). Data were recorded in 4 Hz in the beam coordinate system from all 5 beams. Processed data has been averaged into 5 minutes bins and converted to the East-North-Up (ENU) coordinate system. 2. A Nortek Vector acoustic Doppler velocimeter (ADV). Data were recorded at 8 Hz in the beam coordinate system. Processed data has been averaged into 5 minutes bins and converted to the Streamwise - Cross-stream - Vertical (Principal) coordinate system. Turbulence statistics were calculated from 5-minute bins, with an FFT length equal to the bin length, and saved in the processed dataset. Data was read and analyzed using the DOLfYN (version 1.0.2) python package and saved in MATLAB (.mat) and netCDF (.nc) file formats. Files containing analyzed data (".b1") were standardized using the TSDAT (version 0.4.2) python package. NetCDF files can be opened using DOLfYN (e.g., `dat = dolfyn.load(''*.nc")`) or the xarray python package (e.g. `dat = xarray.open_dataset("*.nc"). All distances are in meters (e.g., depth, range, etc), and all velocities in m/s. See the DOLfYN documentation linked in the submission, and/or the Nortek documentation for additional details.

16 TIDAL AND WAVE POWER↗

GSplit: Scaling Graph Neural Network Training on Large Graphs via Split-Parallelism

Graph neural networks (GNNs), an emerging class of machine learning models for graphs, have gained popularity for their superior performance in various graph analytical tasks. Mini-batch training is commonly used to train GNNs on large graphs, and data parallelism is the standard approach to scale mini-batch training across multiple GPUs. Data parallel approaches contain redundant work as subgraphs sampled by different GPUs contain significant overlap. To address this issue, we introduce a hybrid parallel mini-batch training paradigm called Split parallelism. Split parallelism avoids redundant work by splitting the sampling, loading, and training of each mini-batch across multiple GPUs. Split parallelism, however, introduces communication overheads that can be more than the savings from removing redundant work. We further present a lightweight partitioning algorithm that probabilistically minimizes these overheads. We implement spllit parllelism in GSplit and show that it outperforms state-of-the-art mini-batch training systems like DGL, Quiver, and P3.

Lim, Seung-Hwan [ORNL] (ORCID:0000000194616866)↗