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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

A survey of Existing V&V, UQ and M&S Data and Knowledge Bases in Support of the Nuclear Energy - Knowledge base for Advanced Modeling and Simulation (NE-KAMS)

The Nuclear Energy - Knowledge base for Advanced Modeling and Simulation (NE-KAMS) is being developed at the Idaho National Laboratory in conjunction with Bettis Laboratory, Sandia National Laboratories, Argonne National Laboratory, Oak Ridge National Laboratory, Utah State University and others. The objective of this consortium is to establish a comprehensive knowledge base to provide Verification and Validation (V&V) and Uncertainty Quantification (UQ) and other resources for advanced modeling and simulation (M&S) in nuclear reactor design and analysis. NE-KAMS will become a valuable resource for the nuclear industry, the national laboratories, the U.S. NRC and the public to help ensure the safe operation of existing and future nuclear reactors. A survey and evaluation of the state-of-the-art of existing V&V and M&S databases, including the Department of Energy and commercial databases, has been performed to ensure that the NE-KAMS effort will not be duplicating existing resources and capabilities and to assess the scope of the effort required to develop and implement NE-KAMS. The survey and evaluation have indeed highlighted the unique set of value-added functionality and services that NE-KAMS will provide to its users. Additionally, the survey has helped develop a better understanding of the architecture and functionality of these data and knowledge bases that can be used to leverage the development of NE-KAMS.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Attention-based Aspect Reasoning for Knowledge Base Question Answering on Clinical Notes

Question Answering (QA) in clinical notes has gained a lot of attention in the past few years. Existing machine reading comprehension approaches in clinical domain can only handle questions about a single block of clinical texts and fail to retrieve information about different patients and clinical notes. To handle more complex questions, we aim at creating knowledge base from clinical notes to link different patients and clinical notes, and performing knowledge base question answering (KBQA). Based on the expert annotations in n2c2, we first created the ClinicalKBQA dataset that includes 8,952 QA pairs and covers questions about seven medical topics through 322 question templates. Then, we proposed an attention-based aspect reasoning (AAR) method for KBQA and investigated the impact of different aspects of answers (e.g., entity, type, path, and context) for prediction. The AAR method achieves better performance due to the well-designed encoder and attention mechanism. In the experiments, we find that both aspects, type and path, enable the model to identify answers satisfying the general conditions and produce lower precision and higher recall. On the other hand, the aspects, entity and context, limit the answers by node-specific information and lead to higher precision and lower recall.

Wang, Ping↗
DOE OSTI2014

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. Various computational models rely on random gene selection to infer such networks from microarray data. While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. The result is a directed and weighted network providing the individual contribution of each gene to its target. For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. Our model demonstrates significantly better fitness than the state-of-the-art model, which relies on an initial random selection of genes. Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. The p53 pathway results were manually validated in the literature. 60% of nonKEGG relationships were supported (74% for highly weighted interactions). The method was then applied to yeast data and our model again outperformed the comparison model. Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. This methodology can make a significant contribution to understanding the complex interactions involved in cellular behavior and molecular physiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

SU-E-J-71: Spatially Preserving Prior Knowledge-Based Treatment Planning

Purpose: Prior knowledge-based treatment planning is impeded by the use of a single dose volume histogram (DVH) curve. Critical spatial information is lost from collapsing the dose distribution into a histogram. Even similar patients possess geometric variations that becomes inaccessible in the form of a single DVH. We propose a simple prior knowledge-based planning scheme that extracts features from prior dose distribution while still preserving the spatial information. Methods: A prior patient plan is not used as a mere starting point for a new patient but rather stopping criteria are constructed. Each structure from the prior patient is partitioned into multiple shells. For instance, the PTV is partitioned into an inner, middle, and outer shell. Prior dose statistics are then extracted for each shell and translated into the appropriate Dmin and Dmax parameters for the new patient. Results: The partitioned dose information from a prior case has been applied onto 14 2-D prostate cases. Using prior case yielded final DVHs that was comparable to manual planning, even though the DVH for the prior case was different from the DVH for the 14 cases. Solely using a single DVH for the entire organ was also performed for comparison but showed a much poorer performance. Different ways of translating the prior dose statistics into parameters for the new patient was also tested. Conclusion: Prior knowledge-based treatment planning need to salvage the spatial information without transforming the patients on a voxel to voxel basis. An efficient balance between the anatomy and dose domain is gained through partitioning the organs into multiple shells. The use of prior knowledge not only serves as a starting point for a new case but the information extracted from the partitioned shells are also translated into stopping criteria for the optimization problem at hand.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods

Soybean (Glycine max) is a major source of vegetable oil and protein for both animal and human consumption. The completion of soybean genome sequence led to a number of transcriptomic studies (RNA-seq), which provide a resource for gene discovery and functional analysis. Several data-driven (e.g., based on gene expression data) and knowledge-based (e.g., predictions of molecular interactions) methods have been proposed and implemented. In order to better understand gene relationships and protein interactions, we applied probabilistic graphical methods, based on Bayesian network and knowledgebase constraints using gene expression data to reconstruct soybean metabolic pathways. The results show that this method can predict new relationships between genes, improving on traditional reference pathway maps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

SU-E-T-129: Are Knowledge-Based Planning Dose Estimates Valid for Distensible Organs?

Purpose: Knowledge-based planning programs have become available to assist treatment planning in radiation therapy. Such programs can be used to generate estimated DVHs and planning constraints for organs at risk (OARs), based upon a model generated from previous plans. These estimates are based upon the planning CT scan. However, for distensible OARs like the bladder and rectum, daily variations in volume may make the dose estimates invalid. The purpose of this study is to determine whether knowledge-based DVH dose estimates may be valid for distensible OARs. Methods: The Varian RapidPlan™ knowledge-based planning module was used to generate OAR dose estimates and planning objectives for 10 prostate cases previously planned with VMAT, and final plans were calculated for each. Five weekly setup CBCT scans of each patient were then downloaded and contoured (assuming no change in size and shape of the target volume), and rectum and bladder DVHs were recalculated for each scan. Dose volumes were then compared at 75, 60,and 40 Gy for the bladder and rectum between the planning scan and the CBCTs. Results: Plan doses and estimates matched well at all dose points., Volumes of the rectum and bladder varied widely between planning CT and the CBCTs, ranging from 0.46 to 2.42 for the bladder and 0.71 to 2.18 for the rectum, causing relative dose volumes to vary between planning CT and CBCT, but absolute dose volumes were more consistent. The overall ratio of CBCT/plan dose volumes was 1.02 ±0.27 for rectum and 0.98 ±0.20 for bladder in these patients. Conclusion: Knowledge-based planning dose volume estimates for distensible OARs are still valid, in absolute volume terms, between treatment planning scans and CBCT’s taken during daily treatment. Further analysis of the data is being undertaken to determine how differences depend upon rectum and bladder filling state. This work has been supported by Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

MO-D-BRC-00: In Memoriam of Jan Van De Geijn: Knowledge-Based Planning

Treatment planning is a central part of radiation therapy, including delineation in tumor volumes and critical organs, setting treatment goals of prescription doses to the tumor targets and tolerance doses to the critical organs, and finally generation of treatment plans to meet the treatment goals. National groups like RTOG have led the effort to standardize treatment goals of the prescription doses to the tumor targets and tolerance doses to the critical organs based on accumulated knowledge from decades of abundant clinical trial experience. The challenge for each clinical department is how to achieve or surpass these set goals within the time constraints of clinical practice. Using fifteen testing cases from different treatment sites such as head and neck, prostate with and without pelvic lymph nodes, SBRT spine, we will present clinically utility of advanced planning tools, including knowledge based, automatic based, and multiple criteria based tools that are clinically implemented. The objectives of this session are: Understand differences among these three advanced planning tools Provide clinical assessments on the utility of the advanced planning tools Discuss clinical challenges of treatment planning with large variations in tumor volumes and their relationships with adjacent critical organs. Ping Xia received research grant from Philips. Jackie Wu received research grant from Varian; P. Xia, Research support by Philips and Varian; Q. Wu, NIH, Varian Medical.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-D-BRC-03: Knowledge-Based Planning

Treatment planning is a central part of radiation therapy, including delineation in tumor volumes and critical organs, setting treatment goals of prescription doses to the tumor targets and tolerance doses to the critical organs, and finally generation of treatment plans to meet the treatment goals. National groups like RTOG have led the effort to standardize treatment goals of the prescription doses to the tumor targets and tolerance doses to the critical organs based on accumulated knowledge from decades of abundant clinical trial experience. The challenge for each clinical department is how to achieve or surpass these set goals within the time constraints of clinical practice. Using fifteen testing cases from different treatment sites such as head and neck, prostate with and without pelvic lymph nodes, SBRT spine, we will present clinically utility of advanced planning tools, including knowledge based, automatic based, and multiple criteria based tools that are clinically implemented. The objectives of this session are: Understand differences among these three advanced planning tools Provide clinical assessments on the utility of the advanced planning tools Discuss clinical challenges of treatment planning with large variations in tumor volumes and their relationships with adjacent critical organs. Ping Xia received research grant from Philips. Jackie Wu received research grant from Varian; P. Xia, Research support by Philips and Varian; Q. Wu, NIH, Varian Medical.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

A Knowledge-Based Approach to Improving and Homogenizing Intensity Modulated Radiation Therapy Planning Quality Among Treatment Centers: An Example Application to Prostate Cancer Planning

Purpose: Intensity modulated radiation therapy (IMRT) treatment planning can have wide variation among different treatment centers. We propose a system to leverage the IMRT planning experience of larger institutions to automatically create high-quality plans for outside clinics. We explore feasibility by generating plans for patient datasets from an outside institution by adapting plans from our institution. Methods and Materials: A knowledge database was created from 132 IMRT treatment plans for prostate cancer at our institution. The outside institution, a community hospital, provided the datasets for 55 prostate cancer cases, including their original treatment plans. For each “query” case from the outside institution, a similar “match” case was identified in the knowledge database, and the match case’s plan parameters were then adapted and optimized to the query case by use of a semiautomated approach that required no expert planning knowledge. The plans generated with this knowledge-based approach were compared with the original treatment plans at several dose cutpoints. Results: Compared with the original plan, the knowledge-based plan had a significantly more homogeneous dose to the planning target volume and a significantly lower maximum dose. The volumes of the rectum, bladder, and femoral heads above all cutpoints were nominally lower for the knowledge-based plan; the reductions were significantly lower for the rectum. In 40% of cases, the knowledge-based plan had overall superior (lower) dose–volume histograms for rectum and bladder; in 54% of cases, the comparison was equivocal; in 6% of cases, the knowledge-based plan was inferior for both bladder and rectum. Conclusions: Knowledge-based planning was superior or equivalent to the original plan in 95% of cases. The knowledge-based approach shows promise for homogenizing plan quality by transferring planning expertise from more experienced to less experienced institutions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

MO-G-304-01: FEATURED PRESENTATION: Expanding the Knowledge Base for Data-Driven Treatment Planning: Incorporating Patient Outcome Models

Purpose: To extend the capabilities of knowledge-based treatment planning beyond simple dose queries by incorporating validated patient outcome models. Methods: From an analytic, relational database of 684 head and neck cancer patients, 372 patients were identified having dose data for both left and right parotid glands as well as baseline and follow-up xerostomia assessments. For each existing patient, knowledge-based treatment planning was simulated for by querying the dose-volume histograms and geometric shape relationships (overlap volume histograms) for all other patients. Dose predictions were captured at normalized volume thresholds (NVT) of 0%, 10%, 20, 30%, 40%, 50%, and 85% and were compared with the actual achieved doses using the Wilcoxon signed-rank test. Next, a logistic regression model was used to predict the maximum severity of xerostomia up to three months following radiotherapy. Baseline xerostomia scores were subtracted from follow-up assessments and were also included in the model. The relative risks from predicted doses and actual doses were computed and compared. Results: The predicted doses for both parotid glands were significantly less than the achieved doses (p < 0.0001), with differences ranging from 830 cGy ± 1270 cGy (0% NVT) to 1673 cGy ± 1197 cGy (30% NVT). The modelled risk of xerostomia ranged from 54% to 64% for achieved doses and from 33% to 51% for the dose predictions. Relative risks varied from 1.24 to 1.87, with maximum relative risk occurring at 85% NVT. Conclusions: Data-driven generation of treatment planning objectives without consideration of the underlying normal tissue complication probability may Result in inferior plans, even if quality metrics indicate otherwise. Inclusion of complication models in knowledge-based treatment planning is necessary in order to close the feedback loop between radiotherapy treatments and patient outcomes. Future work includes advancing and validating complication models in the context of knowledge-based treatment planning. This work is supported by Philips Radiation Oncology Systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Evaluation of a Knowledge-Based Planning Solution for Head and Neck Cancer

Purpose: Automated and knowledge-based planning techniques aim to reduce variations in plan quality. RapidPlan uses a library consisting of different patient plans to make a model that can predict achievable dose-volume histograms (DVHs) for new patients and uses those models for setting optimization objectives. We benchmarked RapidPlan versus clinical plans for 2 patient groups, using 3 different libraries. Methods and Materials: Volumetric modulated arc therapy plans of 60 recent head and neck cancer patients that included sparing of the salivary glands, swallowing muscles, and oral cavity were evenly divided between 2 models, Model{sub 30A} and Model{sub 30B}, and were combined in a third model, Model{sub 60}. Knowledge-based plans were created for 2 evaluation groups: evaluation group 1 (EG1), consisting of 15 recent patients, and evaluation group 2 (EG2), consisting of 15 older patients in whom only the salivary glands were spared. RapidPlan results were compared with clinical plans (CP) for boost and/or elective planning target volume homogeneity index, using HI{sub B}/HI{sub E} = 100 × (D2% − D98%)/D50%, and mean dose to composite salivary glands, swallowing muscles, and oral cavity (D{sub sal}, D{sub swal}, and D{sub oc}, respectively). Results: For EG1, RapidPlan improved HI{sub B} and HI{sub E} values compared with CP by 1.0% to 1.3% and 1.0% to 0.6%, respectively. Comparable D{sub sal} and D{sub swal} values were seen in Model{sub 30A}, Model{sub 30B}, and Model{sub 60}, decreasing by an average of 0.1, 1.0, and 0.8 Gy and 4.8, 3.7, and 4.4 Gy, respectively. However, differences were noted between individual organs at risk (OARs), with Model{sub 30B} increasing D{sub oc} by 0.1, 3.2, and 2.8 Gy compared with CP, Model{sub 30A}, and Model{sub 60}. Plan quality was less consistent when the patient was flagged as an outlier. For EG2, RapidPlan decreased D{sub sal} by 4.1 to 4.9 Gy on average, whereas HI{sub B} and HI{sub E} decreased by 1.1% to 1.5% and 2.3% to 1.9%, respectively. Conclusions: RapidPlan knowledge-based treatment plans were comparable to CP if the patient's OAR-planning target volume geometry was within the range of those included in the models. EG2 results showed that a model including swallowing-muscle and oral-cavity sparing can be applied to patients with only salivary gland sparing. This may allow model library sharing between institutes. Optimal detection of inadequate plans and population of model libraries requires further investigation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Knowledge-Based Hazardous Waste Determinations for Solar Photovoltaic (PV) Modules: A Foundational Study

This report explores using "generator knowledge" to determine whether a solar photovoltaic (PV) module must be managed as hazardous waste prior to recycling or landfilling. Generator knowledge is a legal term and existing regulatory pathway for making a hazardous waste determination that has been used by other industries but is a relatively unknown option to the PV industry. In the United States, a hazardous waste determination often acts as a pre-requisite to recycle or landfill a PV module. The results of the hazardous waste determination dictate whether the PV module must be managed as hazardous waste or nonhazardous solid waste. Managing a PV module as hazardous waste requires compliance with stringent U.S. federal and state hazardous waste law. In addition to increased management costs, which can be ten times higher, legal liability for PV modules regulated as hazardous waste is also heightened with both civil and criminal penalties for noncompliance which includes making an inaccurate or faulty hazardous waste determination. The most common reason a PV module would be regulated as hazardous is if it contains a regulated metal in an amount that equals or exceeds the toxicity characteristic limits. To determine whether a PV module exhibits a hazardous characteristic, the regulated person/entity must "apply knowledge...in light of the materials and processes used." In the absence of adequate knowledge to determine whether the PV module is hazardous, it must be tested using Test Method 1311 Toxicity Characteristic Leaching Procedure (TCLP) or an equivalent EPA-approved method. Although TCLP is the predominant method used to today to make a hazardous waste determination for PV modules, evidence from this study concludes it is not practical to TCLP test every PV module even in a single utility-scale installation, and a scalable solution is needed. This study finds that knowledge-based hazardous waste determinations may allow a regulated person/entity to make a hazardous waste determination for more than one PV module at one time - making this regulatory pathway a potential scalable solution. Through legal analysis and interviews with 44 experts, the authors explore what it means to make an accurate knowledge-based hazardous determination for PV modules considering sources and forms of information as well as potential limitations. The work aims to provide a foundation for building consensus on whether knowledge-based hazardous determinations are a viable, scalable industry approach for solar.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2015

SU-F-BRA-13: Knowledge-Based Treatment Planning for Prostate LDR Brachytherapy Based On Principle Component Analysis

Purpose: To create a knowledge-based algorithm for prostate LDR brachytherapy treatment planning that standardizes plan quality using seed arrangements tailored to individual physician preferences while being fast enough for real-time planning. Methods: A dataset of 130 prior cases was compiled for a physician with an active prostate seed implant practice. Ten cases were randomly selected to test the algorithm. Contours from the 120 library cases were registered to a common reference frame. Contour variations were characterized on a point by point basis using principle component analysis (PCA). A test case was converted to PCA vectors using the same process and then compared with each library case using a Mahalanobis distance to evaluate similarity. Rank order PCA scores were used to select the best-matched library case. The seed arrangement was extracted from the best-matched case and used as a starting point for planning the test case. Computational time was recorded. Any subsequent modifications were recorded that required input from a treatment planner to achieve an acceptable plan. Results: The computational time required to register contours from a test case and evaluate PCA similarity across the library was approximately 10s. Five of the ten test cases did not require any seed additions, deletions, or moves to obtain an acceptable plan. The remaining five test cases required on average 4.2 seed modifications. The time to complete manual plan modifications was less than 30s in all cases. Conclusion: A knowledge-based treatment planning algorithm was developed for prostate LDR brachytherapy based on principle component analysis. Initial results suggest that this approach can be used to quickly create treatment plans that require few if any modifications by the treatment planner. In general, test case plans have seed arrangements which are very similar to prior cases, and thus are inherently tailored to physician preferences.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

NRV web knowledge base on low-energy nuclear physics

Principles underlying the organization and operation of the NRV web knowledge base on low-energy nuclear physics (http://nrv.jinr.ru) are described. This base includes a vast body of digitized experimental data on the properties of nuclei and on cross sections for nuclear reactions that is combined with a wide set of interconnected computer programs for simulating complex nuclear dynamics, which work directly in the browser of a remote user. Also, the current situation in the realms of application of network information technologies in nuclear physics is surveyed. The potential of the NRV knowledge base is illustrated in detail by applying it to the example of an analysis of the fusion of nuclei that is followed by the decay of the excited compound nucleus formed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

The IAEA nuclear graphite knowledge base to support high temperature reactor deployment - 18643

Established in 1999, the International Atomic Energy Agency's (IAEA's) Nuclear Graphite Knowledge Base (NGKB) seeks to preserve and expand the scientific in-formation on the physical, chemical, mechanical, and other properties of graphite, which is relevant to nuclear power, nuclear safety, and other nuclear science and technology applications. The data archive NGKB contains has already proven itself invaluable to the nuclear graphite community. To date, NGKB data has supported a coordinated research project on irradiation creep in nuclear graphite and a number of individual member state research and reactor-life-extension activities. All NGKB records are stored on the Nucleus platform, which is based on the SharePoint environment. To add value to the user community, it is important to not only establish a comprehensive knowledge base but also develop a customized taxonomy that will facilitate advanced search functionalities and enhance the user experience, especially for non-expert members. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗