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DOE OSTI2025

ICAT: The Interactive Corpus Analysis Tool

The Interactive Corpus Analysis Tool (ICAT) is a Python library for creating dashboards to explore textual datasets and build simple binary classification models to help filter through them and focus on entries of interest. This tool uses a form of interactive machine learning (IML), a paradigm of “machine teaching” (Simard et al., 2017) that sits at the intersection of the fields of human computer interaction (HCI), visual analytics, and machine learning. The intent of ICAT is to allow subject matter experts (SME) with limited to no experience in machine learning to benefit from an iterative human-in-the-loop (HITL) approach to building their own model without needing to understand the details of the underlying algorithm. This interactivity is achieved by allowing the user to create features, label data points, and visually manipulate a representation of the features to manually cluster and investigate data, while a model is trained on the fly based on these actions. ICAT is built on top of the Panel (Holoviz, 2018) library, using a combination of Vega, a custom IPyWidget using D3, and ipyvuetify, and is intended to be used inside of a Jupyter environment.

Martindale, Nathan [Oak Ridge National Laboratory ↗

DOE OSTI2024

Dimensionally Aligned Signal Projection Algorithms Library

Dimensionally aligned signal projection (DASP) algorithms are used to analyze fast Fourier transforms (FFTs) and generate visualizations that help focus on the harmonics for specific signals. At a high level, these algorithms extract the FFT segments around each harmonic frequency center, and then align them in equally sized arrays ordered by increasing distance from the base frequency. This allows for a focused view of the harmonic frequencies, which, among other use cases, can enable machine learning algorithms to more easily identify salient patterns. This work seeks to provide an effective open-source implementation of the DASP algorithms proposed by Vann et al. (2018) as well as functionality to help explore and test how these algorithms work with an interactive dashboard and signal-generation tool. The DASP library is implemented in Python and contains four types of algorithms for implementing these feature engineering techniques: fixed harmonically aligned signal projection (HASP), decimating HASP, interpolating HASP, and frequency aligned signal projection (FASP). Each algorithm returns a numerical array, which can be visualized as an image. The HASP algorithms are variations of the algorithms originally presented by Vann et al. (2018). For consistency, FASP, which is the terminology used for the short-time Fourier transform (STFT), has been implemented as part of the library to provide a similar interface to the STFT of the raw signal. Additionally, the library contains an algorithm to generate artificial signals with basic customizations such as the base frequency, sample rate, duration, number of harmonics, noise, and number of signals. Finally, the library provides multiple interactive visualizations, each of which is implemented using IPyWidgets and works in a Jupyter environment. A dashboard-style visualization is provided, which contains some common signal-processing visual components (signal, FFT, spectogram) updating in unison with the HASP functions (see Figure 1 below). Separate from the dashboard, an independent visualization is provided for each of the DASP algorithms as well as for the artifical signal generator. These visualizations are included in the library to aid in developing an intuitive understanding how the algorithms are affected by different input signals and parameter selections.

harmonics↗

DOE OSTI2024

rox2vtk v0.1

For the development of magnets for particle accellerators, the tool ROXIE from CERN has become a de facto standard. This script interprets the output files of ROXIE and translates them into a VTK file that can be read in ParaView for visualization.

Messe, Christian↗

DOE OSTI2024

AEGIS (Air Emissions Grouped by Industrial Sectors) [SWR-24-49]

AEGIS is a robust framework designed to build and compile emissions inventories for various industrial sectors. It integrates multiple emissions databases provided by the USEPA – including GHGRP, NEI, and TRI – and leverages the STEWI and STEWICOMBO tools to retrieve, merge, and process data. The framework produces facility- and process-level inventories, identifies discrepancies (e.g., NAICS or FRS mismatches), and performs exploratory analysis including emission concentration calculations and visualization.

Atnoorkar, Swaroop↗

DOE OSTI2026

Data, model inputs, and analysis scripts associated with a manuscript on stream intermittency controls across spatial scales in Pacific Northwest watersheds

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript "Hydroclimatic Memory and Watershed Template Shape Stream Intermittency: Multi-scale Attribution Using Process-based Simulation and Explainable ML" by Niroula et al. (2026), submitted to Water Resources Research (WRR). The study investigates the dominant controls on stream intermittency across local, reach, and watershed scales using a coupled process-based simulation and explainable machine-learning framework. Long-term daily simulations from the Advanced Terrestrial Simulator (ATS) were used to generate wetness states and ponded-depth responses over river-corridor cells. These ATS outputs were then aggregated across scales and used to train XGBoost (eXtreme Gradient Boosting) models. SHAP (SHapley Additive exPlanations) was applied to quantify the relative importance of hydroclimatic forcings, watershed template attributes, and antecedent-memory effects in shaping intermittency behavior. The analysis is carried out for three contrasting Pacific Northwest watersheds: Oak Creek (OCW), American River Watershed (ARW), and H.J. Andrews (HJA). Across these testbeds, the package contains ATS-ready watershed inputs, ATS run configuration and selected output files, model-evaluation data products, intermittency-analysis datasets, machine-learning target-feature tables, SHAP outputs, and notebooks used to organize, analyze, and visualize results. At a high level, the package documents a workflow in which ATS provides the physically based simulation backbone and explainable machine learning is used as a post-processing attribution tool. The contents are intended to support interpretation of the manuscript figures and results, provide context for how intermittency metrics were generated at multiple scales, and preserve the key artifacts needed to understand and reuse the analysis workflow. The package contains a high-level directory summary file (`summary.txt`) and four main content folders (1) `evaluation_plots` contains evaluation figures and supporting evaluation datasets; (2) `intermittency_plots` contains intermittency-focused analysis notebook and prepared datasets; (3) `ml-training-and-shap_values_plots` contains ML training inputs, SHAP outputs, and figure-generation notebooks; and (4) `watershed_mesh_and_ats_input` contains ATS model setup materials, forcing inputs, geometry, and selected run files. More specifically, the `evaluation_plots` folder contains the notebook used for ATS evaluation plotting and site-specific evaluation datasets. These include evapotranspiration and water-balance products for three watersheds, as well as an Oak Creek field-measurement discharge file. The `intermittency_plots` folder contains the notebook used for intermittency analysis and the prepared datasets used to analyze intermittent and non-intermittent wetness behavior across the study watersheds. The `ml-training-and-shap_values_plots` folder contains notebooks and outputs for the machine-learning and explainability workflow. This includes the main XGBoost and SHAP notebook(s), a beeswarm plotting notebook, target-feature tables for machine-learning training, SHAP summary tables, and per-sample SHAP value archives. The `watershed_mesh_and_ats_input` folder contains ATS-related watershed inputs and supporting materials. This includes mesh and shape products, ATS-readable LAI and meteorological forcing inputs, selected ATS spinup and transient-run files, and a watershed workflow example notebook. Subdirectories are organized by watershed where applicable.All files are .cpg (codepage files), .csv (comma-separated values), .dbf (database files), .exo (Exodus mesh format), .h5 (HDF5 format), .ipynb (Jupyter notebooks), .pkl (Python pickle), .prj (projection files), .sh (shell scripts), .shp (shapefile geometry), .shx (shapefile index), .txt (text files), or .xml (markup data).

Advanced Terrestrial Simulator↗

DOE OSTI2024

TEAMER - Field Demonstration of MarineSitu’s Marine Energy Monitoring Tools - CRADA 664 (Abstract)

In order to effectively monitor for marine life around marine energy devices and thus minimize the risk of collision, multiple sensors working in coordination and augmented with around-the-clock automated monitoring algorithms need to be installed in challenging high-energy tidal and wave environments. Such systems are often too expensive for widespread adoption, or lack sufficient sensors or smarts to enable around-the-clock, real-time monitoring without human involvement. MarineSitu has been working to tackle this problem by developing a low-cost, combined sonar and stereo camera sensor array with connected real-time AI-based algorithms for automatically detecting marine life in these marine energy suitable environments. In this TEAMER project with Pacific Northwest National Lab (PNNL), MarineSitu will be testing this novel sensor system for the first time in the high-energy tidal channel environment at PNNL’s Marine and Coastal Research Lab. Throughout this deployment, MarineSitu will be monitoring their system and running analytics on the sensor’s data in real-time. Meanwhile, PNNL Data Scientists and Ocean Engineers, will be evaluating the system’s effectiveness and ease of use both as a tool for plug-and-play environmental monitoring and novel environmental monitoring research. In doing so, the team will improve MarineSitu’s system and software, produce insightful data products, and develop novel visualizations and AI algorithms for combining and analyzing the data produced by systems like MarineSitu’s.

16 TIDAL AND WAVE POWER↗

DOE OSTI2025

TEAMER – Field Demonstration of MarineSitu’s Marine Energy Monitoring (Abstract)

16 TIDAL AND WAVE POWER↗

DOE OSTI2026

Recent advances in plasma control and physics research in the Large Helical Device

The Large Helical Device (LHD), the largest superconducting helical system in the world, is equipped with advanced heating and diagnostic tools, facilitating plasma control and physics research. Data assimilation was employed for electron temperature control using a real-time Thomson scattering system and real time prediction code. A virtual LHD environment enabled visualization of escaping high-energy tritium ions and demonstrated that these ions impact the rear side of the divertor plate. Pioneering results crucial to plasma control have also been achieved. Real-time wall conditioning using Lithium granule dropping improved bulk ion energy and particle transport while simultaneously enhancing the heavy impurity transport. Progress has also been made in the investigation of turbulence-driven transport. At the confinement bifurcation, ion-scale turbulence decreased, while electron-scale turbulence increased. A change in the anisotropy of turbulent eddies was also observed at the confinement bifurcation. Coexistence of local and non-local turbulence was identified in electron-scale turbulence. Non-local turbulence exhibited the rapid spatial propagation of perturbations throughout the plasma, while local turbulence followed the temperature gradient. A transition between drift-wave turbulence and magnetohydrodynamics (MHD) turbulence was observed with the turbulence minimized at the transition condition. Machine learning analysis was employed to evaluate the temperate and density conditions of this turbulence transition. Then, real-time control of fueling and heating was applied to maintain the turbulence transition condition, improving the energy confinement enhancement factor by 20%. In addition, evidence was obtained for collisionless ion heating by energetic-ion-driven geodesic acoustic modes and MHD bursts. These achievements represent unique contributions to the development of fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Classification of Cloud Particle Imagery and Thermodynamics (COCPIT): A New Databasing Tool for the Characterization of Cloud Particle Images Captured During DOE Field Campaigns

The Department of Energy for decades has explored the earth system and atmosphere through research and deployment of in-situ and remote sensing platforms during field campaigns. Among these datasets exists a vast supply of cloud particle images that provide visual insight into the complex microphysics in the clouds that span our globe. The millions of images collected over decades of deployments provides a unique opportunity to further our understanding of our atmosphere down to the crystal size. This work over the past 5 years has sought to organize these images into digestible datasets that can then be used by scientists to further our understanding of microphysics. A machine learning model was developed that categorizes over 1.5 million images across 11 weather events with over 90% accuracy according to particle type. The database was then extended to include dimensional characteristics of the particle as well as co-location of environmental properties, such as temperature and water content. Then, to initialize the connection between these data and our understanding of how crystals form and grow, weather research and forecasting simulations were run to generate the growth histories of the classified crystals. This research culminates with 2 databases per event: (1) a database of all classified crystals and their dimensional and environmental properties and (2) simulated growth histories of each crystal. Finally, a user interface was created to allow researchers to explore data statistics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data

The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Visual Systems Mapping to Define and Compare Woody Biomass LCAs for Sustainable Systems

The challenge addressed in this research centres on the need to choose between several biomass sources and energy production processes, while supporting rural economies and resilience of forest systems. A key barrier to effective decision-making for strategies using biomass is the lack of standardized and transparent life cycle assessment (LCA) baselines. These baselines are critical for assessing the impacts of biomass strategies but often vary due to regional factors and chosen simplifying assumptions of the LCAs. However, omitting key variables can mean the LCA omits key feedback and balancing loops relevant to fully assessing impacts of the change or test scenario. To address these complexities, this project employs a systems engineering approach: visual systems mapping. This technique is used to define the boundaries and dynamic behaviours of LCA baselines, enhancing transparency. By examining five literature sources and their documented baseline scenarios, the systems mapping case-studies demonstrates an approach to documenting and archiving these baselines. Recommendations are that visual systems mapping should be used to document key assumptions, such as baselines, of LCAs. Further, where possible open data repositories should hold key information about LCA baselines and reproducible workflows (e.g., using open-source tools) should be used to improve transparency and comparability in LCAs. Given the consensus within the broader scientific community on the importance of replicable data practices, this research reinforces the need for standardized frameworks and systems engineering tools in LCAs. This research demonstrates a pathway to more transparent, standardized, and comparable LCAs, that may bolster decisions for biomass systems.

Davis, Maggie [ORNL] (ORCID:0000000181319328)↗

DOE OSTI2026

NREL OpenPATH: An Open-Source, Extensible Platform for Instrumenting Travel Behavior Data

NREL OpenPATH is an open-source, extensible platform that allows communities to instrument their own travel behavior data. The platform consists of a smartphone app, server and analysis pipeline, and enables collection of opt-in, multi-modal, end-to-end travel diaries. It makes the aggregate statistics available via a public dashboard, and allows deployers to download and visualize trip and trajectory data through the admin dashboard. It also allows for customization of the initial demographic survey and the trip-level qualitative information collected. Our goal is to provide an easy-to-use tool that can democratize travel behavior data collection by empower communities of all sizes to recruit participants and obtain a holistic picture of their travel patterns. The platform has been used by close to 40 partners, to collect data from thousands of participants. Upon signing a simple MOU, it is currently available for free to universities, non-profits and public agencies in the United States.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

DancePartner: Python Package to Mine Multiomics Relationship Networks from Literature and Databases

A goal of multi-omics experiments is to understand how mechanistic molecular biology is altered between conditions, typically a control group and experimental groups. Oftentimes this involves studying changes in biomolecule relationships (e.g. interactions, metabolic relationships) of several types of biomolecules (e.g. proteins, lipids, metabolites). Though several databases contain relationships between biomolecules, understudied species may have little to no relationship information in databases and thus must be mined from literature. There are several challenges to literature mining, including automated full-text extraction, duplicate biomolecule term collapsing, and implementing complex machine learning tools. To make relationship extraction more accessible to the community, a python package called DancePartner was developed to allow for the extraction of relationships from literature and databases, with functions to map biomolecule synonyms to standardized identifiers and visualize and characterize the resulting multi-omics network. Here, in this study, an example dataset involving Caenorhabditis elegans is presented, where relationships are mined from 1443 publications using DancePartner. These relationships are combined with relationships from KEGG, WikiPathways, UniProt, and LipidMaps, and visualized.

BERT↗

DOE OSTI2025

Breaking the barrier of human-annotated training data for machine learning-aided plant research using aerial imagery

Machine learning (ML) can accelerate biological research. However, the adoption of such tools to facilitate phenotyping based on sensor data has been limited by (i) the need for a large amount of human-annotated training data for each context in which the tool is used and (ii) phenotypes varying across contexts defined in terms of genetics and environment. This is a major bottleneck because acquiring training data is generally costly and time-consuming. This study demonstrates how a ML approach can address these challenges by minimizing the amount of human supervision needed for tool building. A case study was performed to compare ML approaches that examine images collected by an uncrewed aerial vehicle to determine the presence/absence of panicles (i.e. “heading”) across thousands of field plots containing genetically diverse breeding populations of 2 Miscanthus species. Automated analysis of aerial imagery enabled the identification of heading approximately 9 times faster than in-field visual inspection by humans. Leveraging an Efficiently Supervised Generative Adversarial Network (ESGAN) learning strategy reduced the requirement for human-annotated data by 1 to 2 orders of magnitude compared to traditional, fully supervised learning approaches. The ESGAN model learned the salient features of the data set by using thousands of unlabeled images to inform the discriminative ability of a classifier so that it required minimal human-labeled training data. This method can accelerate the phenotyping of heading date as a measure of flowering time in Miscanthus across diverse contexts (e.g. in multistate trials) and opens avenues to promote the broad adoption of ML tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

pixelvar79/ESGAN-Flowering-Detection-paper

Varela, Sebastian↗

DOE OSTI2024

SMART – A Comprehensive Research and Development Program to Demonstrate Application of Machine Learning for Supporting CCS Deployment

Presentation material for a paper presented at the GHGT-17 conference, Calgary, Canada, October 20-24, 2024. The objective of the US Department of Energy’s SMART Initiative, i.e., Science-informed Machine Learning (ML) for Accelerating Real-Time Decisions in Subsurface Applications, is to showcase how the utilization of ML can significantly improve efficiency and effectiveness of field-scale commercial carbon storage operations. This paper will present the results from the current phase of SMART (field deployment) for demonstrating the applicability of ML-based tools and workflows for: (a) virtual learning during the pre-injection permitting phase, (b) advanced storage reservoir imaging to better characterize fractures and faults, and (c) dynamic storage reservoir modelling and optimization to inform operational decision making and visualization of system evolution.

CO2 geologic storage↗

DOE OSTI2024

SMART – A Comprehensive Research and Development Program to Demonstrate Application of Machine Learning for Supporting CCS Deployment

The objective of the US Department of Energy’s SMART Initiative, i.e., Science-informed Machine Learning (ML) for Accelerating Real-Time Decisions in Subsurface Applications, is to showcase how the utilization of ML can significantly improve efficiency and effectiveness of field-scale commercial carbon storage operations. This paper will present the results from the current phase of SMART (field deployment) for demonstrating the applicability of ML-based tools and workflows for: (a) virtual learning during the pre-injection permitting phase, (b) advanced storage reservoir imaging to better characterize fractures and faults, and (c) dynamic storage reservoir modelling and optimization to inform operational decision making and visualization of system evolution.

Siriwardane, Hema↗

DOE OSTI2025

Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation

The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.

15 GEOTHERMAL ENERGY↗