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DOE OSTI2018

Standard Lexicons, Coding Systems and Ontologies for Interoperability and Semantic Computation in Imaging

Standard clinical terms, codes, and ontologies promote clarity and interoperability. Within radiology, there is a variety of relevant content resources, tools and technologies. These provide the basis for fundamental imaging workflows such as reporting and billing, and also facilitate a range of applications in quality improvement and research. This article reviews the key characteristics of lexicons, coding systems, and ontologies. A number of standards are described, including International Classification of Diseases-10-Clinical Modification (ICD-10-CM), Current Procedural Terminology (CPT), Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), Logical Observation Identifiers Names and Codes (LOINC), and RadLex. Tools for accessing this material are reviewed, such as the National Center for Biomedical Ontology BioPortal system. Web services are discussed as a mechanism for semantic application development. Several example systems, workflows, and research applications using semantic technology are also surveyed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

A Hybrid Energy System Workflow for Energy Portfolio Optimization

This manuscript develops a workflow, driven by data analytics algorithms, to support the optimization of the economic performance of an Integrated Energy System. The goal is to determine the optimum mix of capacities from a set of different energy producers (e.g., nuclear, gas, wind and solar). A stochastic-based optimizer is employed, based on Gaussian Process Modeling, which requires numerous samples for its training. Each sample represents a time series describing the demand, load, or other operational and economic profiles for various types of energy producers. These samples are synthetically generated using a reduced order modeling algorithm that reads a limited set of historical data, such as demand and load data from past years. Numerous data analysis methods are employed to construct the reduced order models, including, for example, the Auto Regressive Moving Average, Fourier series decomposition, and the peak detection algorithm. All these algorithms are designed to detrend the data and extract features that can be employed to generate synthetic time histories that preserve the statistical properties of the original limited historical data. The optimization cost function is based on an economic model that assesses the effective cost of energy based on two figures of merit: the specific cash flow stream for each energy producer and the total Net Present Value. An initial guess for the optimal capacities is obtained using the screening curve method. The results of the Gaussian Process model-based optimization are assessed using an exhaustive Monte Carlo search, with the results indicating reasonable optimization results. The workflow has been implemented inside the Idaho National Laboratory’s Risk Analysis and Virtual Environment (RAVEN) framework. The main contribution of this study addresses several challenges in the current optimization methods of the energy portfolios in IES: First, the feasibility of generating the synthetic time series of the periodic peak data; Second, the computational burden of the conventional stochastic optimization of the energy portfolio, associated with the need for repeated executions of system models; Third, the inadequacies of previous studies in terms of the comparisons of the impact of the economic parameters. The proposed workflow can provide a scientifically defendable strategy to support decision-making in the electricity market and to help energy distributors develop a better understanding of the performance of integrated energy systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2014

An Integrated Development Environment for Adiabatic Quantum Programming

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware raises the question of how well quantum programs perform. Benchmarking behavior is challenging since the multiple steps to synthesize an adiabatic quantum program are highly tunable. We present an adiabatic quantum programming environment called JADE that provides control over all the steps taken during program development. JADE captures the workflow needed to rigorously benchmark performance while also allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation engine that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its use for benchmarking adiabatic quantum programs.

ISING MODEL↗
DOE OSTI2026

Implementing a unified solver for nonlinearly constrained optimization

SQP and interior-point methods (also referred to as Lagrange-Newton methods) typically share key algorithmic components, such as strategies for computing descent directions and mechanisms that promote global convergence. Building on this insight, we introduce a unifying framework with eight building blocks that abstracts the workflows of Lagrange-Newton methods. We then present Uno, a modular C++ solver that implements our unifying framework and allows the automatic combination of a wide range of strategies with no programming effort from the user. Uno is meant to (1) organize mathematical optimization strategies into a coherent hierarchy; (2) offer a wide range of efficient and robust methods that can be compared for a given instance; (3) enable researchers to experiment with novel optimization strategies; and (4) reduce the cost of development and maintenance of multiple optimization solvers. Uno’s software design allows user to compose new customized solvers for emerging optimization areas such as robust optimization or optimization problems with complementarity constraints, while building on reliable nonlinear optimization techniques. We demonstrate that Uno is highly competitive against state-of-the-art solvers filterSQP, IPOPT, SNOPT, MINOS, LANCELOT, LOQO, and CONOPT on a subset of 429 small problems from the CUTE collection. Uno is available as open-source software under the MIT license at https://github.com/cvanaret/Uno and via its C, Julia, Python, Fortran, and AMPL interfaces.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Strategies for connecting whole-building LCA to the low-carbon design process

Abstract Decarbonization is essential to meeting urgent climate goals. With the building sector in the United States accounting for 35% of total U.S. carbon emissions, reducing environmental impacts within the built environment is critical. Whole-building life cycle analysis (WBLCA) quantifies the impacts of a building throughout its life cycle. Despite being a powerful tool, WBLCA is not standard practice in the integrated design process. When WBLCA is used, it is typically either speculative and based on early design information or conducted only after design completion as an accounting measure, with virtually no opportunity to impact the actual design. This work proposes a workflow for fully incorporating WBLCA into the building design process in an iterative, recursive manner, where design decisions impact the WBLCA, which in turn informs future design decisions. We use the example of a negative-operational carbon modular building seeking negative upfront embodied carbon using bio-based materials for carbon sequestration as a case study for demonstrating the utility of the framework. Key contributions of this work include a framework of computational processes for conducting iterative WBLCA, using a combination of an existing building WBLCA tool (Tally) within the building information modeling superstructure (Revit) and a custom script (in R) for materials, life cycle stages, and workflows not available in the WBLCA tool. Additionally, we provide strategies for harmonizing the environmental impacts of novel materials or processes from various life cycle inventory sources with materials or processes in existing building WBLCA tool repositories. These strategies are useful for those involved in building design with an interest in reducing their environmental impact. For example, this framework would be useful for researchers who are conducting WBLCAs on projects that include new or unusual materials and for design teams who want to integrate WBLCA more fully into their design process in order to ensure the building materials are consciously chosen to advance climate goals, while still ensuring best performance by traditional measures.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

A machine-learning inverse model framework for rapid forecasting and history matching in unconventional reservoirs

Model-based optimization for real-time forecasting in unconventional reser-voirs requires novel methods and work?ows since the strategies and work?ows used in conventional reservoirs are either inapplicable, or prohibitively expen-sive and time-consuming. Insu?cient site data and computational expense of high-?delity simulations mean that work?ows with high-?delity simulations are not ideal for usage in comprehensive uncertainty quanti?cation stud-ies that require 1000s of forward model runs. We present an alternative, novel work?ow for unconventional reservoirs, based on the interplay between reduced-order models and machine-learning. Our physics-informed machine-learning (PIML) work?ow addresses the challenges to real-time reservoir management in uncoventionals, namely lack of data (the time-frame for which the wells have been producing), and computational expense of high-?delity modeling. We use the machine-learning paradigm of transfer-learning to bind together fast but less accurate reduced-order models with slow, but accurate high-?delity models and circumvent the di?culties inherent in the current state-of-the-art for unconventionals. Such a PIML work?ow, grounded in physics, is a viable candidate for real-time history matching and production forecasting in a fractured shale gas reservoir. The signi?cance of our approach is that while it is developed for a particu-lar well and site in the Marcelus Shale gas reservoir of the Appalachian basin (MSEEL), it is not wedded to it. We expect the same work?ow can be ap-plied to other shale formations (e.g., Woodford, Barnett, Utica, EagleFord) should site-data become available, using the same set of machine-learning techniques from transfer learning. Some ?ne-tuning (or minimal retraining of the neural networks) will be required to transfer knowledge across shale gas sites/formations but it is a clearly superior alternative to developing a new machine-learning model altogether when considering a di?erent site.

Srinivasan, Shriram↗
DOE OSTI2015

Machine Learning and Understanding for Intelligent Extreme Scale Scientific Computing and Discovery. DOE Workshop Report, January 7–9, 2015, Rockville, MD

Large-scale parallel simulations and data analysis drive scientific discovery across many disciplines. To drive larger and more detailed simulations, and deal with larger data volumes, exascale machines capable of 1018 operations per second are expected within the next five to ten years. However, the complexity of developing and adapting modern simulation codes for these architectures is increasing rapidly. Workloads on exascale machines will be billion-way parallel. Exploiting the full capability of the machine will require carefully assigning application tasks to cores, accelerators, deep memories, and other heterogeneous compute resources, while simultaneously optimizing for time to solution, data movement, power, and resilience. Optimizations that improve performance on one machine may slow down another. Worse, applications themselves are dauntingly complex. Production simulations comprise millions of lines of code and use sophisticated, adaptive algorithms whose performance is input-dependent. Complex workflows can couple multi-physics simulation with data preprocessing and post-processing modules.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Co-design Framework for Online Data Analysis and Reduction

Science applications preparing for the exascale era are increasingly exploring in situ computations comprising of simulation-analysis-reduction pipelines coupled in-memory. Efficient composition and execution of such complex pipelines for a target platform is a codesign process that evaluates the impact and tradeoffs of various application- and system-specific parameters. In this article, we describe a toolset for automating performance studies of composed HPC applications that perform online data reduction and analysis. We describe Cheetah, a new framework for composing parametric studies on coupled applications, and Savanna, a runtime engine for orchestrating and executing campaigns of codesign experiments. Furthermore, this toolset facilitates understanding the impact of various factors such as process placement, synchronicity of algorithms, and storage versus compute requirements for online analysis of large data. Ultimately, we aim to create a catalog of performance results that can help scientists understand tradeoffs when designing next-generation simulations that make use of online processing techniques. We illustrate the design of Cheetah and Savanna, and present application examples that use this framework to conduct codesign studies on small clusters as well as leadership class supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Development Optimization and Uncertainty Analysis Methods for Oil and Gas Reservoirs

Uncertainty complicates the development optimization of oil and gas exploration and production projects, but methods have been devised to analyze uncertainty and its impact on optimal decision-making. This paper compares two methods for development optimization and uncertainty analysis: Monte Carlo (MC) simulation and stochastic programming. Two example problems for a gas field development and an oilfield development are solved and discussed to elaborate the advantages and disadvantages of each method. Development optimization involves decisions regarding the configuration of initial capital investment and subsequent operational decisions. Uncertainty analysis involves the quantification of the impact of uncertain parameters on the optimum design concept. The gas field development problem is designed to highlight the differences in the implementation of the two methods and to show that both methods yield the exact same optimum design. The results show that both MC optimization and stochastic programming provide unique benefits, and that the choice of method depends on the goal of the analysis. While the MC method generates more useful information, along with the optimum design configuration, the stochastic programming method is more computationally efficient in determining the optimal solution. Reservoirs comprise multiple compartments and layers with multiphase flow of oil, water, and gas. We present a workflow for development optimization under uncertainty for these reservoirs, and solve an example on the design optimization of a multicompartment, multilayer oilfield development.

02 PETROLEUM↗
DOE OSTI2024

Preliminary analysis of TREAT free-field experiments using openmc

This work analyses activation calculations for dosimetry materials during a steady-state irradiation in the Transient Reactor Test (TREAT) reactor core. Hence, we developed a workflow based on the Monte Carlo code OpenMC alongside a custom depletion solver. The irradiation-induced activity as a function of time is computed, and several sensitivity studies are performed to evaluate uncertainty. This study has shown activity computations are sensitive to flux amplitude, irradiation time, atoms quantity and microscopic cross sections. Stochastic uncertainties have been propagated to evaluate the activity uncertainty for each dosimetry material. Most uncertainties are below our target of 3%, which demonstrates OpenMC as a powerful predictive and analysis tool. The precise results obtained through this newly developed computation scheme will be used in future experiments to characterize quantities of interest when operating the TREAT reactor in new configurations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Overview of interpretive modelling of fusion performance in JET DTE2 discharges with TRANSP

In the paper we present an overview of interpretive modelling of a database of JET-ILW 2021 D-T discharges using the TRANSP code. The main aim is to assess our capability of computationally reproducing the fusion performance of various D-T plasma scenarios using different external heating and D-T mixtures, and to understand the performance driving mechanisms. We find that interpretive simulations confirm a general power-law relationship between increasing external heating power and fusion output, which is supported by absolutely calibrated neutron yield measurements. A comparison of measured and computed D-T neutron rates shows that the calculations' discrepancy depends on the absolute neutron yield. The calculations are found to agree well with measurements for higher performing discharges with external heating power above ~20 MW, while low-neutron shots display an average discrepancy of around +40% compared to measured neutron yields. A similar trend is found for the ratio between thermal and beam-target fusion, where larger discrepancies are seen in shots with dominant beam-driven performance. We compare the observations to studies of JET-ILW D discharges, to find that on average the fusion performance is well modelled over a range of heating power, although an increased unsystematic deviation for lower-performing shots is observed. The ratio between thermal and beam-induced D-T fusion is found to be increasing weakly with growing external heating power, with a maximum value of ≳1 achieved in a baseline scenario experiment. An evaluation of the fusion power computational uncertainty shows a strong dependence on the plasma scenario type and fusion drive characteristics, varying between ±25% and 35%. D-T fusion alpha simulations show that the ratio between volume-integrated electron and ion heating from alphas is ≲10 for the majority of analysed discharges. Alphas are computed to contribute between ~15% and 40% to the total electron heating in the core of highest performing D-T discharges. An alternative workflow to TRANSP was employed to model JET D-T plasmas with the highest fusion yield and dominant non-thermal fusion component because of the use of fundamental radio-frequency heating of a large minority in the scenario, which is calculated to have provided ~10% to the total fusion power.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Data transfer for STAR grid jobs

The Solenoidal Tracker at RHIC (STAR) is a multipurpose experiment at the Relativistic Heavy Ion Collider (RHIC) with the primary goal to study the formation and properties of the quark-gluon plasma. STAR is an international collaboration of member institutions and laboratories from around the world. Yearly data-taking period produces PBytes of raw data collected by the experiment. STAR primarily uses its dedicated facility at BNL to process this data, but has routinely leveraged distributed systems, both high throughput (HTC) and high performance (HPC) computing clusters, to significantly augment the processing capacity available to the experiment. The ability to automate the efficient transfer of large data sets on reliable, scalable, and secure infrastructure is critical for any large-scale distributed processing campaign. For more than a decade, STAR computing has relied upon GridFTP with its x509-based authentication to build such data transfer systems and integrate them into its larger production workflow. The end of support by the community for both GridFTP and the x509 standard requires STAR to investigate other approaches to meet its distributed processing needs. In this study we investigate two multi-purpose data distribution systems, Globus.org and XRootD, as alternatives to GridFTP. We compare both their performance and the ease by which each service is integrated into the type of secure and automated data transfer systems STAR has previously built using GridFTP. The presented approach and study may be applicable to other distributed data processing use cases beyond STAR.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

CMed: Crowd Analytics for Medical Imaging Data

In this work, we present a visual analytics framework, CMed, for exploring medical image data annotations acquired from crowdsourcing. CMed can be used to visualize, classify, and filter crowdsourced clinical data based on a number of different metrics such as detection rate, logged events, and clustering of the annotations. CMed provides several interactive linked visualization components to analyze the crowd annotation results for a particular video and the associated workers. Additionally, all results of an individual worker can be inspected using multiple linked views in our CMed framework. We allow a crowdsourcing application analyst to observe patterns and gather insights into the crowdsourced medical data, helping him/her design future crowdsourcing applications for optimal output from the workers. We demonstrate the efficacy of our framework with two medical crowdsourcing studies: polyp detection in virtual colonoscopy videos and lung nodule detection in CT thin-slab maximum intensity projection videos. We also provide experts' feedback to show the effectiveness of our framework. Lastly, we share the lessons we learned from our framework with suggestions for integrating our framework into a clinical workflow.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

MO-G-BRE-09: Validating FMEA Against Incident Learning Data: A Study in Stereotactic Body Radiation Therapy

Purpose: Though FMEA (Failure Mode and Effects Analysis) is becoming more widely adopted for risk assessment in radiation therapy, to our knowledge it has never been validated against actual incident learning data. The objective of this study was to perform an FMEA analysis of an SBRT (Stereotactic Body Radiation Therapy) treatment planning process and validate this against data recorded within an incident learning system. Methods: FMEA on the SBRT treatment planning process was carried out by a multidisciplinary group including radiation oncologists, medical physicists, and dosimetrists. Potential failure modes were identified through a systematic review of the workflow process. Failure modes were rated for severity, occurrence, and detectability on a scale of 1 to 10 and RPN (Risk Priority Number) was computed. Failure modes were then compared with historical reports identified as relevant to SBRT planning within a departmental incident learning system that had been active for two years. Differences were identified. Results: FMEA identified 63 failure modes. RPN values for the top 25% of failure modes ranged from 60 to 336. Analysis of the incident learning database identified 33 reported near-miss events related to SBRT planning. FMEA failed to anticipate 13 of these events, among which 3 were registered with severity ratings of severe or critical in the incident learning system. Combining both methods yielded a total of 76 failure modes, and when scored for RPN the 13 events missed by FMEA ranked within the middle half of all failure modes. Conclusion: FMEA, though valuable, is subject to certain limitations, among them the limited ability to anticipate all potential errors for a given process. This FMEA exercise failed to identify a significant number of possible errors (17%). Integration of FMEA with retrospective incident data may be able to render an improved overview of risks within a process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Baycal

Bayesian Model Calibration (BayCal) toolkit is a software plugin for Risk Analysis Virtual Environment (RAVEN) framework, arming at inversely quantifying the uncertainties associated with simulation model parameters based on available experiment data. BayCal seeks statistical inference of the uncertain input parameters that are consistent with the available measurement data or observed data. The unique feature of BayCal is the capability to be linked with RAVEN to build corresponding calibration workflows for complex multi-physics simulations. In addition to be able to use the machine learning capability of RAVEN to significantly reduce the computational cost of expensive simulation models, another distinctive feature of BayCal is the capability to deal with high-dimensional correlated model outputs, such as time series observations at multiple locations, via principal component analysis (PCA) technique.

Wang, Congjian↗
DOE OSTI2024

Bottom-up design of actinide materials from molecular clusters: Demonstration of a general-purpose simulation capability leveraging machine-learned atomic potentials

Actinide thin-film coatings such as uranium dioxide (UO 2 ) play an important role in nuclear reactors and other mission-relevant applications, but realization of their potential requires a deep fundamental understanding of the chemical vapor deposition (CVD) processes used for their growth. The slow experimental progress can be attributed, in part, to the standard safety guidelines associated with handling uranium byproducts, which are often corrosive, toxic, and radioactive. Accurate simulation techniques, when used in concert with experiment, can improve laboratory safety, material durability, and deliverable timeframes. However, state-of-the-art computational methods are either insufficiently accurate or intractably expensive. To remedy this situation, in this project we suggested a machine-learning (ML) accelerated workflow for simulating molecular clustering toward deposition. As a benchmark test case, we considered molecular clustering in steam and assessed independent components of our workflow by comparing with measured thermodynamic properties of water. After analyzing each component individually and finding no fundamental barrier to realization of the workflow, we attempted to integrate the ML component, a Sandia-developed tool called FitSNAP. As this was the first application of FitSNAP to atoms and molecules in the gas phase at Sandia, the method required more fitting data than was originally anticipated. Systematic improvements were made by including in the fit data diatomic potentials, molecular single-bond-breaking curves, and symmetry-constrained intermolecular potentials. We concluded that our strategy provides a feasible pathway toward modeling CVD and related processes, but that extensive training data must be generated before it can be of practical use.

36 MATERIALS SCIENCE↗