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At least 271 records · Page 15

Genesis Data Card Schema, Template and Supporting Tools

Genesis Data Cards provide a standardized template and schema for documenting scientific datasets in support of discovery, access, interoperability, reusability, governed use, and AI usability. This release of the Genesis Data Card repository includes a versioned Markdown template, a LinkML schema with generated Pydantic and JSON artifacts, schema documentation, and example completed data cards. Validation tooling is provided to ensure that completed data cards conform to the schema prior to submission. Accompanying documentation for the structured metadata is provided as a Field Reference Guide. The schema and accompanying template provided in this repository address the call for actionable context that enables humans and AI systems to find, access, interpret, cite, and reuse data, and, when appropriate, integrate it into AI and machine learning workflows. The data card is intended to serve as a common metadata artifact intended to support standardized, cross-program dataset documentation across Department of Energy (DOE)-aligned efforts, including but not limited to Genesis Mission-related implementations, the Office of Science, National Nuclear Security Administration (NNSA), and Advanced Simulation and Computing (ASC) data governance and stewardship initiatives.

data card↗

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

biocuration↗

Uncertainty guided online ensemble for non-stationary data streams in fusion science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior with distribution drifts, resulted by both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with such non-stationary data streams. Online learning techniques have been leveraged in other domains, however it has been largely unexplored for fusion applications. In this paper, we investigate online learning for continuous adaptation to drifting data streams in the prediction of Toroidal Field (TF) coils deflection at the DIII-D fusion facility. We further address the short-term performance degradation inherent to standard online learning, which arises because ground truth is unavailable at prediction time. To mitigate this issue, we propose an uncertainty-guided online ensemble framework. The method leverages the Deep Gaussian Process Approximation (DGPA) for calibrated uncertainty estimation and uses these uncertainty measures to guide a meta-algorithm that aggregates predictions from learners trained over different historical horizons. Our results show that online learning reduces prediction error by 80% compared to a static model. The online ensemble and the proposed uncertainty-guided ensemble further reduce error by approximately 6%, and 10% respectively, relative to standard single-model online learning, while also providing calibrated uncertainty estimates to support operational decision-making.

AI↗

Factorization Machine‐Based Active Learning for Functional Materials Design with Optimal Initial Data

The optimization of functional materials is important to enhance their properties, but their complex geometries pose great challenges to optimization. Data-driven algorithms efficiently navigate such complex design spaces by learning relationships between material structures and performance metrics to discover high-performance functional materials. Surrogate-based active learning, continually improving its surrogate model by iteratively including high-quality data points, has emerged as a cost-effective data-driven approach. Furthermore, it can be coupled with quantum computing to enhance optimization processes, especially when paired with a special form of surrogate model (i.e., quadratic unconstrained binary optimization), formulated by factorization machine (FM). However, current practices often overlook the variability in design space sizes when determining the initial data size for optimization. In this work, we investigate the optimal initial data sizes required for efficient convergence across various design space sizes. By employing averaged piecewise linear regression, we identify initiation points where convergence begins, highlighting the crucial role of employing adequate initial data in achieving efficient optimization. These results contribute to the efficient optimization of functional materials by ensuring faster convergence and reducing computational costs in FM-based active learning.

active learning↗

Accelerating kinetic plasma simulations with machine-learning-generated initial conditions

Computational models of plasma technologies often solve for the system operating conditions by time-stepping an initial value problem to a quasi-steady solution. However, the strongly nonlinear and multi-timescale nature of plasma dynamics often necessitate millions, or even hundreds of millions, of steps to reach convergence, reducing the effectiveness of these simulations for computer-aided engineering. We consider acceleration of kinetic plasma simulations via data-driven machine-learning-generated initial conditions, which initialize the simulations close to their final quasi-steady-state, thereby reducing the number of steps to reach convergence. Three machine-learning models are developed to predict the density and ion kinetic profiles of capacitively coupled plasma discharges relevant to the microelectronics industry. The models are trained on kinetic simulations over a range of device operating frequencies and pressures. Best performance was observed when simulations were initialized with ion kinetic profiles generated by a convolutional neural network, reducing the mean number of steps to reach convergence by 17.1× when compared to initialization with a zero-dimensional global model. We also outline a workflow for continuous data-driven model improvement and simulation speedup, with the aim of generating sufficient data for full device digital twins.

Artificial neural networks↗

Data Agnostic Feature-Target Analysis & Ranking Machine Learning Pipeline (DAFTAR-ML) v0.1.0

DAFTAR-ML is a specialized machine-learning pipeline that identifies relevant features based on their relationship to a target variable. Many ML pipelines focus solely on prediction, and feature ranking is often absent or lacks robust statistical methods. DAFTAR-ML performs its tasks with this outcome in mind. Model training is robust, using nested cross-validation and hyperparameter tuning. Instead of relying on native feature-importance scores, it employs SHAP (SHapley Additive exPlanations) to quantify feature importance. The pipeline also produces comprehensive results, including publication-quality visualizations.

Melie, Tina [Lawrence Berkeley National Laboratory↗

Machine learning for reactor power monitoring with limited labeled data

Real-time reactor power monitoring is critical for a variety of nuclear applications, spanning safety, security, operations, and maintenance. While machine learning methods have shown promise in monitoring reactor power levels, there is limited research on their efficacy in label-starved environments. The goal of this work is to assess the feasibility of classifying nuclear reactor power level using multisource data in scenarios with limited labels. Data were collected using low-resolution multisensors at four nuclear reactor facilities: two large research reactors and two TRIGA reactors. Within each pair, one reactor dataset served as the source and the other as the target in a transfer learning paradigm. Twenty-three supervised models were trained on labeled sequences of magnetic field and acceleration data from each of the target sites. Self-learning and transfer learning methods were applied to the top performing models to assess their classification performance with increasing amounts of labeled data. While reactor power level classification was achieved with a Matthews Correlation Coefficient of up to 0.739 ± 0.003 and 0.622 ± 0.009 with only 400 sequences per power state for the large research reactor and TRIGA target sites, respectively, self-learning and transfer learning leveraging source site data did not improve target classification performance. These findings suggest that alternative methods, such as higher sensitivity sensors, digital twins, or the use of physics-informed models, are required to enable high-performance classification in machine learning approaches to reactor monitoring with a dearth of target ground truth.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Resolving root causes of experiment discrepancies guided by machine learning

Abstract Scientists rely on accurate experimental data to explain nature and then harness this knowledge for applications addressing human needs. However, discrepancies between experiments of the same observable can impede scientific progress if one does not understand the underlying causes. Here, we developed a process that unravels data discrepancies by first using Bayesian machine learning to relate discrepancies to few of many, potentially biasing metadata features that encode experiment procedures. This machine learning output guides human experts to study discrepancy causes by simulating suspicious aspects of historical experiments or designing modern ones to address open questions. The study findings then lead to rejecting or correcting historical data on firm scientific bases. This process is demonstrated for the energy spectrum of neutrons emitted promptly (<1 ns) after fission of 252 Cf, a trusted nuclear physics Standard. It reduces the spread in experimental 252 Cf spectra by up to a factor of 6.

Neudecker, D. (ORCID:0000000339200627)↗

Estimating Fine-Resolution Shortwave Broadband Albedo of Croplands from Harmonized Landsat and Sentinel-2 Data

Altered surface albedo due to land-cover conversions and management is a significant driver of global climate change. Albedo can be directly measured at ground stations, and remote sensing data can be used to scale-up albedo values to regional and global levels. Some previous studies have retrieved fine-resolution (10–30 m) instantaneous albedo and coarse-resolution (500–1000 m) daily mean albedo from remote sensing data, but they all required the input of Moderate Resolution Imaging Spectroradiometer (MODIS) albedo information at 500-m resolution, and none have assembled both instantaneous and daily albedo based exclusively on fine-resolution satellite data. Here, to address this issue, we compiled 387 instantaneous and 346 daily albedo records using field net radiometer measurements from the bioenergy croplands at the W. K. Kellogg Biological Station in southwest Michigan. We then connected these albedo records with a suite of variables derived from harmonized Landsat and Sentinel-2 data through two machine learning algorithms (random forest regression and extreme gradient boosting) to retrieve clear-sky instantaneous and daily shortwave broadband albedo. The performance statistics indicate reasonable accuracy of model results [root-mean-square error (RMSE)] around or below 0.03 except for snow-covered surfaces), suggesting that the retrieval of both instantaneous and daily albedo based exclusively on fine-resolution satellite data is promising. To facilitate the use of fine-resolution albedo products at the global level, future efforts need to include more albedo records of diverse surface cover types, as well as to accurately model daily albedo for cloudy days to address the “clear-sky bias.”

Harmonized Landsat and Sentinel-2↗

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗

Machine Learning-Enhanced Multiphase CFD for Carbon Capture Modeling Run Data

Repository for the data generated as part of the 2023-2024 ALCC project "Machine Learning-Enhanced Multiphase CFD for Carbon Capture Modeling." The data was generated with MFIX-Exa's CFD-DEM model. The problem of interest is gravity driven, particle-laden, gas-solid flow in a triply-periodic domain of length 2048 particle diameters with an aspect ratio of 4. The mean particle concentration ranges from 1% to 40% and the Archimedes number ranges from 18 to 90. The particle-to-fluid density ratio, particle-particle restitution and friction coefficients and domain aspect ratio are held constant at values of 1000, 0.9, 0.25 and 4, respectively. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 using NERSC award ALCC-ERCAP0025948.

AMReX↗

Using supervised machine-learning approaches to understand abiotic stress tolerance and design resilient crops

Abiotic stresses such as drought, heat, cold, salinity and flooding significantly impact plant growth, development and productivity. As the planet has warmed, these abiotic stresses have increased in frequency and intensity, affecting the global food supply and making it imperative to develop stress-resilient crops. In the past 20 years, the development of omics technologies has contributed to the growth of datasets for plants grown under a wide range of abiotic environments. Integration of these rapidly growing data using machine-learning (ML) approaches can complement existing breeding efforts by providing insights into the mechanisms underlying plant responses to stressful conditions, which can be used to guide the design of resilient crops. In this review, we introduce ML approaches and provide examples of how researchers use these approaches to predict molecular activities, gene functions and genotype responses under stressful conditions. Finally, we consider the potential and challenges of using such approaches to enable the design of crops that are better suited to a changing environment. This article is part of the theme issue ‘Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the ‘Resilience Revolution’?’.

abiotic stress↗

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

Out-of-Distribution Detection and Radiological Data Monitoring Using Statistical Process Control

Abstract Machine learning (ML) models often fail with data that deviates from their training distribution. This is a significant concern for ML-enabled devices as data drift may lead to unexpected performance. This work introduces a new framework for out of distribution (OOD) detection and data drift monitoring that combines ML and geometric methods with statistical process control (SPC). We investigated different design choices, including methods for extracting feature representations and drift quantification for OOD detection in individual images and as an approach for input data monitoring. We evaluated the framework for both identifying OOD images and demonstrating the ability to detect shifts in data streams over time. We demonstrated a proof-of-concept via the following tasks: 1) differentiating axial vs. non-axial CT images, 2) differentiating CXR vs. other radiographic imaging modalities, and 3) differentiating adult CXR vs. pediatric CXR. For the identification of individual OOD images, our framework achieved high sensitivity in detecting OOD inputs: 0.980 in CT, 0.984 in CXR, and 0.854 in pediatric CXR. Our framework is also adept at monitoring data streams and identifying the time a drift occurred. In our simulations tracking drift over time, it effectively detected a shift from CXR to non-CXR instantly, a transition from axial to non-axial CT within few days, and a drift from adult to pediatric CXRs within a day—all while maintaining a low false positive rate. Through additional experiments, we demonstrate the framework is modality-agnostic and independent from the underlying model structure, making it highly customizable for specific applications and broadly applicable across different imaging modalities and deployed ML models.

Zamzmi, Ghada↗