Results for “adaptive workflow” — Page 18

DOE OSTI2016

SU-F-J-194: Development of Dose-Based Image Guided Proton Therapy Workflow

Purpose: To implement image-guided proton therapy (IGPT) based on daily proton dose distribution. Methods: Unlike x-ray therapy, simple alignment based on anatomy cannot ensure proper dose coverage in proton therapy. Anatomy changes along the beam path may lead to underdosing the target, or overdosing the organ-at-risk (OAR). With an in-room mobile computed tomography (CT) system, we are developing a dose-based IGPT software tool that allows patient positioning and treatment adaption based on daily dose distributions. During an IGPT treatment, daily CT images are acquired in treatment position. After initial positioning based on rigid image registration, proton dose distribution is calculated on daily CT images. The target and OARs are automatically delineated via deformable image registration. Dose distributions are evaluated to decide if repositioning or plan adaptation is necessary in order to achieve proper coverage of the target and sparing of OARs. Besides online dose-based image guidance, the software tool can also map daily treatment doses to the treatment planning CT images for offline adaptive treatment. Results: An in-room helical CT system is commissioned for IGPT purposes. It produces accurate CT numbers that allow proton dose calculation. GPU-based deformable image registration algorithms are developed and evaluated for automatic ROI-delineation and dose mapping. The online and offline IGPT functionalities are evaluated with daily CT images of the proton patients. Conclusion: The online and offline IGPT software tool may improve the safety and quality of proton treatment by allowing dose-based IGPT and adaptive proton treatments. Research is partially supported by Mevion Medical Systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Technical Note: SCUDA: A software platform for cumulative dose assessment

Purpose: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (SCUDA) that can be seamlessly integrated into the clinical workflow. Methods: SCUDA consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our image PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. Results: The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. Conclusions: The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Leading magnetic fusion energy science into the big-and-fast data lane

To crack the code of unlimited clean energy from magnetic fusion, researchers collaborate among numerous facilities that are scattered around the globe. Probing hot fusion plasmas with sophisticated diagnostics, they routinely generate fast streams of high-dimensional time-series data. We present the adaptation of a production code-base for a plasma diagnostic to the big-and-fast data lane. The new code-base is used to stream measurements, made in Korea, into a Top-15 computing facility in the US for remote analysis. We discuss software and design choices made for this new HPC-enabled scientific workflow.

Kube, Ralph↗

NASA NTRS2014

Sentiment of Search: KM and IT for User Expectations

User perceived value is the number one indicator of a successful implementation of KM and IT collaborations. The system known as "Search" requires more strategy and workflow that a mere data dump or ungoverned infrastructure can provide. Monitoring of user sentiment can be a driver for providing objective measures of success and justifying changes to the user interface. The dynamic nature of information technology makes traditional usability metrics difficult to identify, yet easy to argue against. There is little disagreement, however, on the criticality of adapting to user needs and expectations. The Systems Usability Scale (SUS), developed by John Brook in 1986 has become an industry standard for usability engineering. The first phase of a modified SUS, polls the sentiment of representative users of the JSC Search system. This information can be used to correlate user determined value with types of information sought and how the system is (or is not) meeting expectations. Sentiment analysis by way of the SUS assists an organization in identification and prioritization of the KM and IT variables impacting user perceived value. A secondary, user group focused analysis is the topic of additional work that demonstrates the impact of specific changes dictated by user sentiment.

Berndt, Sarah Ann↗

NASA NTRSDate not supplied

Enhanced Simulation Techniques in Predicting Sonic Boom Loudness Using CFD

This paper outlines advancements in predicting sonic boom loudness within the Launch, Ascent, and Vehicle Aerodynamics (LAVA) computational framework. Traditionally, a two step process consisting of a steady state computational fluid dynamics problem for near-field analysis and a far-field propagation solver for calculation of loudness metrics has been used. Improvements to this process made in this work include utilizing a high-order space marching method for mid-field computations, developing a novel output-based mesh adaptation method targeting error in near-field pressure sig-natures, and developing a robust scripting system using curvilinear grids to increase robustness and simplify the process of running large databases of simulation cases. These advancements are detailed and applied to the simulation of the X-59, presenting comparative cost and timing analyses between the prior two step workflow and the current three step procedure. We achieve increased accuracy and robustness for loudness predictions with at least a50%computational cost reduction.

CST↗

DOE OSTI2019

Software Defined Architectures for Data Analytics

Data analytics applications increasingly are complex workflows composed of phases with very different program behaviors (e.g., graph algorithms and machine learning, algorithms operating on sparse an dense data structures, etc). To reach the levels of efficiency required to process these workflows in real time, upcoming architectures will need to leverage even more workload specialization. If, at one end, we may find even more heterogenous processors composed by a myriad of specialized processing elements, at the other end we may see novel reconfigurable architectures, composed of sets of functional units and memories interconnected with (re)configurable on-chip networks, able to adapt dynamically to adapt the workload characteristics. Field Programmable Gate Arrays are more and more used for accelerating various workloads and, in particular, inferencing in machine learning, providing higher efficiency than other solutions. However, their fine grained nature still leads to issues for the design software and still makes dynamic reconfiguration impractical. Future, more coarse-grained architectures could offer the features to execute diverse workloads at high efficiency while providing better reconfiguration mechanisms for dynamic adaptability. Nevertheless, we argue that the challenges for reconfigurable computing remain in the software. In this position paper, we describe a possible toolchain for reconfigurable architectures targeted at data analytics.

FPGA, Dataflow, Reconfigurable Architectures, Soft↗

DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

DOE OSTI2015

Hybrid multiscale simulation of a mixing-controlled reaction

Not Available

Scheibe, Timothy D.↗

DOE OSTI2012

Towards a Global Monitoring System for CMS Computing Operations

The operation of the CMS computing system requires a complex monitoring system to cover all its aspects: central services, databases, the distributed computing infrastructure, production and analysis workflows, the global overview of the CMS computing activities and the related historical information. Several tools are available to provide this information, developed both inside and outside of the collaboration and often used in common with other experiments. Despite the fact that the current monitoring allowed CMS to successfully perform its computing operations, an evolution of the system is clearly required, to adapt to the recent changes in the data and workload management tools and models and to address some shortcomings that make its usage less than optimal. Therefore, a recent and ongoing coordinated effort was started in CMS, aiming at improving the entire monitoring system by identifying its weaknesses and the new requirements from the stakeholders, rationalise and streamline existing components and drive future software development. This contribution gives a complete overview of the CMS monitoring system and a description of all the recent activities that have been started with the goal of providing a more integrated, modern and functional global monitoring system for computing operations.

Bauerdick, L. A.T.↗

DOE OSTI2015

TU-E-BRB-00: Deformable Image Registration: Is It Right for Your Clinic

Deformable image registration (DIR) is developing rapidly and is poised to substantially improve dose fusion accuracy for adaptive and retreatment planning and motion management and PET fusion to enhance contour delineation for treatment planning. However, DIR dose warping accuracy is difficult to quantify, in general, and particularly difficult to do so on a patient-specific basis. As clinical DIR options become more widely available, there is an increased need to understand the implications of incorporating DIR into clinical workflow. Several groups have assessed DIR accuracy in clinically relevant scenarios, but no comprehensive review material is yet available. This session will also discuss aspects of the AAPM Task Group 132 on the Use of Image Registration and Data Fusion Algorithms and Techniques in Radiotherapy Treatment Planning official report, which provides recommendations for DIR clinical use. We will summarize and compare various commercial DIR software options, outline successful clinical techniques, show specific examples with discussion of appropriate and inappropriate applications of DIR, discuss the clinical implications of DIR, provide an overview of current DIR error analysis research, review QA options and research phantom development and present TG-132 recommendations. Learning Objectives: Compare/contrast commercial DIR software and QA options Overview clinical DIR workflow for retreatment To understand uncertainties introduced by DIR Review TG-132 proposed recommendations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

TU-E-BRB-02: DIR QA Options and Research Development

Deformable image registration (DIR) is developing rapidly and is poised to substantially improve dose fusion accuracy for adaptive and retreatment planning and motion management and PET fusion to enhance contour delineation for treatment planning. However, DIR dose warping accuracy is difficult to quantify, in general, and particularly difficult to do so on a patient-specific basis. As clinical DIR options become more widely available, there is an increased need to understand the implications of incorporating DIR into clinical workflow. Several groups have assessed DIR accuracy in clinically relevant scenarios, but no comprehensive review material is yet available. This session will also discuss aspects of the AAPM Task Group 132 on the Use of Image Registration and Data Fusion Algorithms and Techniques in Radiotherapy Treatment Planning official report, which provides recommendations for DIR clinical use. We will summarize and compare various commercial DIR software options, outline successful clinical techniques, show specific examples with discussion of appropriate and inappropriate applications of DIR, discuss the clinical implications of DIR, provide an overview of current DIR error analysis research, review QA options and research phantom development and present TG-132 recommendations. Learning Objectives: Compare/contrast commercial DIR software and QA options Overview clinical DIR workflow for retreatment To understand uncertainties introduced by DIR Review TG-132 proposed recommendations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

TU-E-BRB-03: Overview of Proposed TG-132 Recommendations

Deformable image registration (DIR) is developing rapidly and is poised to substantially improve dose fusion accuracy for adaptive and retreatment planning and motion management and PET fusion to enhance contour delineation for treatment planning. However, DIR dose warping accuracy is difficult to quantify, in general, and particularly difficult to do so on a patient-specific basis. As clinical DIR options become more widely available, there is an increased need to understand the implications of incorporating DIR into clinical workflow. Several groups have assessed DIR accuracy in clinically relevant scenarios, but no comprehensive review material is yet available. This session will also discuss aspects of the AAPM Task Group 132 on the Use of Image Registration and Data Fusion Algorithms and Techniques in Radiotherapy Treatment Planning official report, which provides recommendations for DIR clinical use. We will summarize and compare various commercial DIR software options, outline successful clinical techniques, show specific examples with discussion of appropriate and inappropriate applications of DIR, discuss the clinical implications of DIR, provide an overview of current DIR error analysis research, review QA options and research phantom development and present TG-132 recommendations. Learning Objectives: Compare/contrast commercial DIR software and QA options Overview clinical DIR workflow for retreatment To understand uncertainties introduced by DIR Review TG-132 proposed recommendations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

Certification Considerations for Adaptive Stress Testing of Airborne Software

eduAdaptive Stress Testing (AST) has shown promise in identifying errant corner cases in complex software used in aerospace applications including Flight Management Systems (FMS). The strength of AST is performing test-based verification of complex aerospace software intensive systems at scale in simulated operational environments.Simulating and capturing the realistic operational complexities in integrated verification environments may exposeflaws in the softwareprior to field deployment, whereas the software may perform just fine to traditional requirements-basedunit and component level testing.AST can be used to test the whole system.Individual components may behave safely, but together can result in complex interactions and emergent failures, so it is important to test at the integrated system level.Motivated by the observed benefitsat the prototype proof of concept scale, this paper considers how AST may be integrated into a production workflow and used to generate objective evidence in a processthat delivers certified aerospace software.The research includes evaluation of alignment with both DO-178C and Overarching Properties(OP). The paper addresses questions such as “where should AST fit in the Plan for Software Aspects of Certification (PSAC) and Software Verification Plan (SVP), what aspects of AST do not fit, and what objectives does it satisfy?” The paper concludes that AST is in fact useful at locating errors in complex airborne application software and in doing so provides benefits to suppliers and end users. Furthermore, AST appears appropriate to add value in both DO-178Cbased and Overarching Properties based certification approaches.

certification↗

DOE OSTI2025

VISION: a modular AI assistant for natural human-instrument interaction at scientific user facilities

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an x-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instruments and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex—a synthetic extension to the cognition of scientists—may radically transform scientific practice and discovery.

36 MATERIALS SCIENCE↗

DOE OSTI2014

PLAStiCC: Predictive Look-Ahead Scheduling for Continuous dataflows on Clouds

Scalable stream processing and continuous dataflow systems are gaining traction with the rise of big data due to the need for processing high velocity data in near real time. Unlike batch processing systems such as MapReduce and workflows, static scheduling strategies fall short for continuous dataflows due to the variations in the input data rates and the need for sustained throughput. The elastic resource provisioning of cloud infrastructure is valuable to meet the changing resource needs of such continuous applications. However, multi-tenant cloud resources introduce yet another dimension of performance variability that impacts the application’s throughput. In this paper we propose PLAStiCC, an adaptive scheduling algorithm that balances resource cost and application throughput using a prediction-based look-ahead approach. It not only addresses variations in the input data rates but also the underlying cloud infrastructure. In addition, we also propose several simpler static scheduling heuristics that operate in the absence of accurate performance prediction model. These static and adaptive heuristics are evaluated through extensive simulations using performance traces obtained from public and private IaaS clouds. Our results show an improvement of up to 20% in the overall profit as compared to the reactive adaptation algorithm.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A Geo-Data Science Method for Assessing Unconventional Rare-Earth Element Resources in Sedimentary Systems

Abstract Rare-earth elements (REEs) supply raw materials that constitute many of our modern critical infrastructure, defense, technology, and electrification needs. Despite REE accumulations occurring in conventional bedrock and ion-adsorption deposits sourced from weathering of igneous rocks, unconventional host materials such as coal and related sedimentary strata have been identified as promising sources of REEs to meet growing demand. To maximize the potential of unconventional resources such as REE-coal systems, new approaches are needed overcome challenges from mineral systems with no known deposits and areas with sparse geochemical data. This article presents a systematic knowledge-data resource assessment method for predicting and identifying REE resource potential and occurrence in these unconventional systems. The method utilizes a geologic and geospatial knowledge-data approach informed and guided by REE accumulation mechanisms to systematically assess and identify areas of higher enrichment. An assessment of the Powder River Basin is presented as a test case to demonstrate the method workflow and results. The key output is a potential enrichment score map reported with varying confidence levels based on the amount of supporting evidence. Results from the test case indicate several locations with promising potential for different types of coal-REE deposits, demonstrating the viability of the method for exploration and assessment of unconventional REE resources. The method is flexible by design and, with sufficient applicable knowledge and data, can be adapted for assessing critical mineral systems in other sedimentary systems as well.

58 GEOSCIENCES↗

DOE OSTI2019

The Data Quality Monitoring Software for the CMS experiment at the LHC: past, present and future

The Data Quality Monitoring software is a central tool in the CMS experiment. It is used in the following key environments: (i) Online, for real-time detector monitoring; (ii) Offline, for the prompt-offline-feedback and final fine-grained data quality analysis and certification; (iii) Validation of all the reconstruction software production releases; (iv) Validation in Monte Carlo productions. Though the basic structure of the Run1 DQM system remains the same for Run2, between the Run1 and Run2 periods, the DQM system underwent substantial upgrades in many areas, not only to adapt to the surrounding infrastructure changes, but also to provide improvements to meet the growing needs of the collaboration with an emphasis on more sophisticated methods for evaluating data quality. We need to cope with the higher-energy and -luminosity proton-proton collision data, as well as the data from various special runs, such as Heavy Ion runs. In this contribution, we will describe the current DQM software, structure and workflow in the different environments. We then discuss the performance and our experiences with the DQM system in Run2. The main technical challenges which we have encountered and the solutions adopted during Run2 will also be discussed, including efficient use of memory in multithreading environments. Finally, we present the prospect of a future DQM upgrade with emphasis on functionality and long-term robustness for LHC Run3.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗