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DOE OSTI2025

Extremely Scalable Distributed Computation of Contour Trees via Pre-Simplification

Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains challenging due to scalability limitations. Recent developments in distributed hierarchical contour trees have addressed these challenges by enabling scalable computation across distributed systems. Building on these structures, advanced analytical tasks—such as volumetric branch decomposition and contour extraction—have been introduced to facilitate large-scale scientific analysis. Despite these advancements, such analytical tasks substantially increase memory usage, which hampers scalability. In this paper, we propose a pre-simplification strategy to significantly reduce the memory overhead associated with analytical tasks on distributed hierarchical contour trees. We demonstrate enhanced scalability through strong scaling experiments, constructing the largest known contour tree—comprising over half a trillion nodes with complex topology—in under 15 minutes on a dataset containing 550 billion elements.

Li, Mingzhe [University of Utah]↗

DOE OSTI2024

Learning epistatic polygenic phenotypes with Boolean interactions

Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1 , a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents

KBase has powerful tools for extracting microbial genomes from metagenomes and performing phylogenomic analysis and metabolic modeling. These tools can be used to predict key media ingredients for isolating uncultured members of microbiomes. Essential to this process are high-quality genomes extracted from metagenomic assemblies, and Kbase has a tool for assessing the quality of genomes too. Below we identify growth factors for a myxobacteria ("slime bacteria") yet to be isolated from the rhizosphere of Miscanthus xgiganteus (hybrid of "Silvergrass"), cultivated at the Kellogg Biological Station in Michigan. Data was transferred with Globus from JGI-IMG. This narrative and the "KBase Gold Case Study: Can you find Delftia?" make up the Silver and Gold Narrative Set for teaching metagenomics concepts to students in the BIT 477/577 course at North Carolina State University. This tutorial will guide the user through the process of extracting and annotating high-quality genomes from a metagenomic data, performing phylogenomic analysis, building a metabolic model, and using these to predict nutrient requirments for growth and isolation of corresponding microbes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2016

A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work will be needed to validate this approach in creating finite-element models.

gravitational physiology↗

DOE OSTI2026

OpenStudio®-MCP [SWR-26-035]

OpenStudio®-MCP is a Model Context Protocol (MCP) server that lets AI assistants perform building energy modeling through natural language. Rather than requiring users to learn the OpenStudio® SDK, EnergyPlus® scripting, or Ruby/Python automation, the server translates conversational requests into sequences of tool calls that create models, design HVAC systems, run simulations, and extract results — all within a single chat session. The server's 124 tools are organized into a skills architecture where each skill encapsulates a domain of building energy modeling (envelope, HVAC, loads, weather, simulation, results) behind typed, LLM-friendly interfaces. High-leverage operations like applying ASHRAE 90.1 baseline systems or generating standards-compliant typical buildings are exposed as single tool calls that internally wire dozens of OpenStudio® objects. Bundled measures from ComStock™ and Openstudio® -common-measures-gem are wrapped with dedicated tools and typed arguments rather than exposed through a generic measure interface, so AI models get consistent, error-resistant recipes without needing to discover measure arguments at runtime. A key design decision is structured results extraction: six SQL-based tools return surgical ~300–1,000 token responses (end-use breakdowns, envelope summaries, HVAC sizing, timeseries data) instead of requiring the AI to parse ~100K-token raw HTML reports, making iterative design exploration practical within context window limits. The codebase is designed as a reference implementation — explicit, well-commented, and modular — so that other simulation engines (EnergyPlus® standalone, TRNSYS, DOE-2) can use it as a template for building their own MCP servers.

Ball, Brian [National Laboratory of the Rockies (N↗

NASA NTRS2001

Extraction of Airport Features from High Resolution Satellite Imagery for Design and Risk Assessment

The LPA Group, consisting of 17 offices located throughout the eastern and central United States is an architectural, engineering and planning firm specializing in the development of Airports, Roads and Bridges. The primary focus of this ARC project is concerned with assisting their aviation specialists who work in the areas of Airport Planning, Airfield Design, Landside Design, Terminal Building Planning and design, and various other construction services. The LPA Group wanted to test the utility of high-resolution commercial satellite imagery for the purpose of extracting airport elevation features in the glide path areas surrounding the Columbia Metropolitan Airport. By incorporating remote sensing techniques into their airport planning process, LPA wanted to investigate whether or not it is possible to save time and money while achieving the equivalent accuracy as traditional planning methods. The Affiliate Research Center (ARC) at the University of South Carolina investigated the use of remotely sensed imagery for the extraction of feature elevations in the glide path zone. A stereo pair of IKONOS panchromatic satellite images, which has a spatial resolution of 1 x 1 m, was used to determine elevations of aviation obstructions such as buildings, trees, towers and fence-lines. A validation dataset was provided by the LPA Group to assess the accuracy of the measurements derived from the IKONOS imagery. The initial goal of this project was to test the utility of IKONOS imagery in feature extraction using ERDAS Stereo Analyst. This goal was never achieved due to problems with ERDAS software support of the IKONOS sensor model and the unavailability of imperative sensor model information from Space Imaging. The obstacles encountered in this project pertaining to ERDAS Stereo Analyst and IKONOS imagery will be reviewed in more detail later in this report. As a result of the technical difficulties with Stereo Analyst, ERDAS OrthoBASE was used to derive aviation obstruction measurements for this project. After collecting ancillary data such as GPS locations, South Carolina Geodetic Survey and Aero Dynamics ground survey points to set up the OrthoBASE Block File, measurements were taken of the various glide path obstructions and compared to the validation dataset. This process yielded the following conclusions: The IKONOS stereo model in conjunction with Imagine OrthoBASE can provide The LPA Group with a fast and cost efficient method for assessing aviation obstructions. Also, by creating our own stereo model we achieved any accuracy better currently available commercial products.

Robinson, Chris↗

DOE OSTI2020

High-Frequency, Multiclass Nonintrusive Load Monitoring for Grid-Interactive Residential Buildings

Smart buildings with net-load metering and control capabilities can provide valuable flexibility to grid operators. This article develops a novel approach for high-frequency, multiclass nonintrusive load monitoring (NILM) that enables effective net-load monitoring capabilities with minimal additional equipment and cost. Relative to existing NILM work, the proposed solution operates at a faster timescale, providing accurate multiclass state predictions for each 60-Hz ac cycle without relying on event-detection techniques. The approach is validated using a test bed with residential appliances and shown to have high accuracy, good generalization properties, and sufficient response time to support building grid-interactive control at fast timescales relevant to the provision of grid frequency support services.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Estimating ionization states and continuum lowering from ab initio path integral Monte Carlo simulations for warm dense hydrogen

Warm dense matter (WDM) is an active field of research, with applications ranging from astrophysics to inertial confinement fusion. Ionization degree and continuum lowering are important quantities to understand how materials behave under these conditions, but can be difficult to diagnose since experimental campaigns are limited and often require model-dependent analysis. This is especially true for hydrogen, which has a comparably low scattering cross section, making high-quality data particularly difficult to obtain. Consequently, building equation of state tables often relies on simulations in combination with untested approximations to extract properties from experiments. Here, we investigate an approach for extracting the ionization potential depression and ionization degree—quantities which are otherwise not directly accessible from the physical model—from first-principles path integral Monte Carlo (PIMC) simulations utilizing a chemical model. In contrast to experimental measurements, where noise and nonequilibrium effects add to the uncertainty of the inferred parameters, PIMC simulations provide a clean signal with well-defined thermodynamic conditions. Comparisons against commonly used models show a qualitative agreement, but we find deviations primarily for the high-density and high-temperature cases. We also demonstrate the decreasing sensitivity of the dynamic structure factor with respect to both ionization and continuum lowering for increasing scattering angles in x-ray Thomson scattering experiments. Our work has important implications for the design of future experiments, but also offers qualitative understanding of structure factors and the imaginary-time correlation function obtained from first-principles quantum Monte Carlo simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Digital holography for real-time non-invasive monitoring of larval fish at power plant intakes

Effective evaluation of technological and operational approaches to reduce entrainment of marine organisms at cooling water intake structures (CWIS) requires accurate organism-sensing systems. Current detection methods lead to large temporal data gaps, require tedious manual analysis, and are fatal to organisms. In this report we describe integrating deep learning with a non-lethal, non-intrusive imaging method—digital holography—to rapidly detect fish larvae. Laboratory experiments demonstrated that the instrument could successfully image fish larvae at flow rates exceeding ranges seen in CWIS. Holograms of two fish larvae species, in the presence of bubbles and detritus, were collected to build a large database for training a lightweight convolutional neural network. The model achieves 97% extraction accuracy in quantifying larvae, and distinguishing them from other particles, including detritus and bubbles, when applied to a dataset of manually classified images, exceeding previous metrics for non-lethal, accurate, and real-time detection. These results demonstrate the potential of in situ holographic imaging for monitoring endangered larval fish species at power plant intake structures, and for high-fidelity, real-time applications in monitoring aquatic ichthyoplankton.

endangered species↗

DOE OSTI2022

Development and Demonstration of a Fuel-Efficient, Class 8 Tractor & Trailer Engine System (SuperTruck II)

Navistar presents the SuperTruck II (ST II) Final Report to the Unites States Department of Energy (US DOE), which covers the five Budget Periods (BPs) from 10-1-2016 through 6-30-2022. For ST II, Navistar built on the achievements of the SuperTruck I (ST I) Program as a catalyst to continue critical research, design and development, testing, and operations to reach the ambitious goals of the ST II project. This approach allowed Navistar to continue contributing to the essential needs of our nation for safe, efficient, and cost-effective delivery of goods and services, as we reduced negative environmental effects and improved operational productivity. This document contains information specified in DOE F 4600.2, Final Scientific/Technical Report DOE F 241.3, B. SCIENTIFIC/TECHNICAL REPORTS, explaining how we met and exceeded program requirements. Throughout this Final Report, Navistar extracted information from documents prepared during the project that represent our management, design and development, building, and testing efforts to meet and exceed SuperTruck II project goals. Navistar followed Plan requirements to achieve / exceed Project Objectives: a) >100% improvement in vehicle freight efficiency (FE) (on ton-MPG basis) relative to 2009 baseline with stretch goal of 140% improvement [actual: 170%); b) >55% engine brake thermal efficiency (BTE) demonstrated in operational engine at a 65-mph cruise point on a dynamometer – ≥31% increase from 2009 baseline [actual: 55.20% of combined BTE) ; and c) development and implementation of commercially cost effective technologies (in terms of a simple payback). Technology selection / development path focused on developing technologies applicable for production within 3-year approach, while ensuring technology readiness and cost of ownership for end users. The Program was organized into five budget periods: Requirements / Technology Assessment and Initial Hardware Testing; Technology Development and Concept Readiness Demonstration; Technology Finalization and Validation Tractor / Trailer Fabrication, Integration and Commissioning Demonstration; and Fuel Economy (FE) and Brake Thermal Efficiency (BTE) and Program Completion. Leadership was provided by DOE, with tasks performed by laboratories (Argonne National Laboratory, Lawrence Livermore National Laboratory); partners at Bosch, TPI, Dana, and J.B. Hunt; , and support from University of Michigan and Clemson University. Navistar lead this team with Principal Investigator / Contracting Officer; Project Manager (PM); Vehicle, Engine, and Aftertreatment Engineers; Finance Manager, Technical Program Leads, and Legal/IP; and other key personnel. Work also included personnel in risk management; funding / budget / finance. Work involved analysis, development, testing, and down selection of individual/system engine, aftertreatment, and vehicle technologies, with integration of selected technologies into a prototype vehicle for demonstration of fuel-efficiency gain. Work also included component/integrated system level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. As ST II progressed, Navistar performed computer-based modeling / simulations of technologies focused on the primary operational areas: Engine, Aftertreatment, and Vehicle. During the ST II Program, the COVID Virus outbreak unexpectedly challenged by the effects of, which affected staffing, scheduling, design, supplies, availability of materials, production procedures, and testing. The DOE responded by extending the program by three quarters to ensure that project tasks were completed for this vital project. Focus continued on analyzing, developing, testing, and down selecting individual-/system-level engine and vehicle technologies for integration of the final selected technologies into a prototype vehicle that would demonstrate fuel-efficiency gains made possible through these technologies. This included component/integrated system-level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, solar power, distributed and intelligent vehicle power, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. Throughout the program, function, reliability, and performance at all levels were ensured through testing. Proof of this approach was demonstrated in multiple, on-road demonstrations: Scenario A (Flatland) Fuel Economy, Scenario B (Hilly) Fuel Economy, and City Cycle Tests. Other benefits derived from ST II included new/improved products, publications, patents, and next-step capabilities related to electric/hydrogen vehicles and autonomous driving.

Zukouski, Russ↗

NASA NTRS1997

Efficient algorithms for robust feature matching

One of the basic building blocks in any point-based registration scheme involves matching feature points that are extracted from the sensed image to their counterparts in the reference image. This leads to the fundamental problem of point matching: given two sets of points, find the affine transformation that transforms one point set so that its distance from the other point set is minimized. Because of measurement errors and the presence of outlying data points, it is important that the distance measure between two point sets be robust to these effects. We measure distances using the generalized Hausdorff distance. Point matching can be a computationally intensive task, and there have been a number of algorithms and approaches proposed for solving this problem both theoretical and applied. We present two approaches to the point matching problem, in an attempt to reduce the computational complexity of the problem, while still providing guarantees on the quality of the final match. Our first method is an approximation algorithm, which is loosely based on a branch-and-bound approach due to Huttenlocher and Rucklidge. We show that by varying the approximation error bounds, it is possible to achieve a tradeoff between the quality of the match and the running time of the algorithm. Our second method involves a Monte Carlo method for accelerating the search process used in the first algorithm. With high probability this method succeeds in finding an approximately optimal match. We establish the efficiency of our approaches empirically.

Mount, David M.↗

NASA NTRS1994

Automated Scalability Analysis Tools for Message Passing Parallel Programs

In order to develop scalable parallel applications, a number of programming decisions have to be made during the development of the program. Performance tools that help in making these decisions are few, if existent. Traditionally, performance tools have focused on exposing performance bottlenecks of small-scale executions of the program. However, it is common knowledge that programs that perform exceptionally well on small processor configurations, more often than not, perform poorly when executed on larger processor configurations. Hence, new tools that predict the execution characteristics of scaled-up programs are an essential part of an application developers toolkit. In this paper we discuss important issues that need to be considered in order to build useful scalability analysis tools for parallel programs. We introduce a simple tool that automatically extracts scalability characteristics of a class of deterministic parallel programs. We show with the help of a number of results on the Intel iPSC/860, that predictions are within reasonable bounds.

Sarukkai, Sekhar R.↗

NASA NTRS1997

Wavelet Methods Developed to Detect and Control Compressor Stall

A "wavelet" is, by definition, an amplitude-varying, short waveform with a finite bandwidth (e.g., that shown in the first two graphs). Naturally, wavelets are more effective than the sinusoids of Fourier analysis for matching and reconstructing signal features. In wavelet transformation and inversion, all transient or periodic data features (as in compressor-inlet pressures) can be detected and reconstructed by stretching or contracting a single wavelet to generate the matching building blocks. Consequently, wavelet analysis provides many flexible and effective ways to reduce noise and extract signals which surpass classical techniques - making it very attractive for data analysis, modeling, and active control of stall and surge in high-speed turbojet compressors. Therefore, fast and practical wavelet methods are being developed in-house at the NASA Lewis Research Center to assist in these tasks. This includes establishing user-friendly links between some fundamental wavelet analysis ideas and the classical theories (or practices) of system identification, data analysis, and processing.

Le, Dzu K.↗

DOE OSTI2021

Identifying build orientation of 3D-printed materials using convolutional neural networks

The advent of additive manufacturing (AM) processes brought with it intense research into various materials and manufacturing processes. At the same time, the need for validation of material properties, as well as study and forecasting of aging, has arisen. Modern imaging techniques, like X-ray computed tomography (XCT), are a convenient vehicle for such studies; however, the large datasets they produce require novel analysis techniques to efficiently extract critical information. Here, we present our work on developing a 3D extension of the ResNet architecture to distinguish between two build orientations of tensile bars produced by AM. Using only information from XCT, our method achieves a 99.3% correct classification at a misidentification of 1%.

36 MATERIALS SCIENCE↗

DOE OSTI2020

High-Frequency, Multiclass Nonintrusive Load Monitoring for Grid-Interactive Residential Buildings

27 ARPA - Advanced Research Projects Agency-Energy↗

DOE OSTI2020

A methodology for generating reduced-order models for large-scale buildings using the Krylov subspace method

Developing a computationally efficient but accurate building energy simulation (BES) model is important for many purposes. Model order reduction (MOR) methods are attractive and much more reliable than identification approaches, since it directly extract a lower-dimensional model from a detailed physics-based model without any pre-simulations. However, because of computational and data storage requirements, there are challenges of applying these methods to a large-scale building. To overcome the problem, this work introduces the Krylov subspace method to the building science field. Technical issues of applying the method to building applications are addressed and a suitable algorithm that overcomes those challenges is presented. Furthermore, to demonstrate the reliability of the algorithm, comparisons between the resulted reduced-order model (ROM) and a high-fidelity model from a commercial BES software for a 60-zone case study building are provided. The ROM was a factor of 100 faster than the high fidelity model but with high accuracy.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Different CT slice thickness and contrast‐enhancement phase in radiomics models on the differential performance of lung adenocarcinoma

Abstract Background To investigate the effects of computed tomography (CT) reconstruction slice thickness and contrast‐enhancement phase on the differential diagnosis performance of radiomic signature in lung adenocarcinoma. Methods A total of 187 patients who had been pathologically confirmed with lung adenocarcinoma and nonadenocarcinoma were divided into a training cohort ( n = 149) and validation cohort ( n = 38). All the patients underwent contrast‐enhanced CT and the images were reconstructed with different slice thickness. The radiomic features were extracted from different slice thickness and scan phase. The logistic regression (LR) algorithm was used to build a machine learning model for each group. The area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve and DeLong test was used to evaluate its discriminating performance. Results Finally, 34 image features and five semantic features were selected to establish a radiomics model. Based on the three contrast‐enhanced CT phases and four reconstruction slice thickness, 12 groups of radiomics models showed good discrimination ability with the AUCs range from 0.9287 to 0.9631, sensitivity range from 0.8349 to 0.9083, specificity range from 0.825 to 0.925 in the training group. Similar results were observed in the validation group. However, there was no statistical significance between the different CT scan phase groups and different slice thickness ( p > 0.05). Conclusions The radiomic analysis of contrast‐enhanced CT can be used for the differential diagnosis of lung adenocarcinoma. Moreover, different slice thickness and contrast‐enhanced scan phase did not affect the discriminating ability in the radiomics models.

Wang, Yang↗

NASA NTRS2000

Tidal Energy Dissipation from Topex/Poseidon

In a recent paper ({\it Nature, 405,} 775, 2000) we concluded that 25 to 30\% of the ocean's tidal energy dissipation, or about 1 terawatt, occurs in the deep ocean, with the remaining 2.6 TW in shallow seas. The physical mechanism for deep-ocean dissipation is apparently scattering of the surface tide into internal modes; Munk and Wunsch have suggested that this mechanism may provide half the power needed for mixing the deep-ocean. This paper builds further evidence for $1\pm 0.2$ TW of deep-ocean dissipation. The evidence is extracted from tidal elevations deduced from seven years of Topex/Poseidon satellite altimeter data. The dissipation rate Is formed as a balance between the rate of working by tidal forces and the energy flux divergence. While dynamical assumptions are required to compute fluxes, area integrals of the energy balance are, owing to the tight satellite constraints, remarkably insensitive to these assumptions. A large suite of tidal solutions based on a wide range of dynamical assumptions, on perturbations to bathymetric models, and on simulated elevation data are used to assess this sensitivity. These and Monte Carlo error fields from a generalized inverse model are used to establish error uncertainties.

Ray, Richard D.↗