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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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All sourcesNASA NTRSDOE OSTI
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 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 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 OSTI2023

Improving Knowledge Base with Network Architecture Diagrams

In order to ensure Cyber Security Team (CST) has access to updated and in-depth information regarding Fermilab systems, capabilities, procedures, tools, and training, the CST created the Knowledge Base. This consists of a wealth of information for current and future CST employees to improve knowledge retention and transfer. The Knowledge Base, however, uses outdated network diagrams that lack many of the previous and upcoming changes to the architecture. For this reason, updated diagrams have been created to reflect the current position of the CST capabilities. By employing the knowledge learned at Fermi National Accelerator Laboratory, three diagrams have been created to highlight the current state of the CST’s operations and capabilities.

Blum, Ethan↗
DOE OSTI2022

An adaptive knowledge-based data-driven approach for turbulence modeling using ensemble learning technique under complex flow configuration: 3D PWR sub-channel with DNS data

This work describes a new approach to increase the accuracy of Reynolds-averaged Navier–Stokes (RANS) in modeling turbulence flow leveraging the machine learning technique. Traditionally, different turbulence models for Reynolds stress are developed for different flow patterns based on human knowledge. Each turbulence model has a certain application domain and prediction uncertainty. In recent years, with the rapid improvements of machine learning techniques, researchers start to develop an approach to compensate for the prediction discrepancy of traditional turbulence models with statistical models and data. However, the approach has deficiencies in several aspects. For example, the amount of human knowledge introduced to the statistical model couldn’t be controlled, which makes the statistical model learn from a very naïve stage and limits its application. In this work, a new approach is developed to address those deficiencies. Here, the new approach uses the “ensemble learning” technique to control the amount of human knowledge introduced into the statistical model. Therefore, the new approach could be adaptive to the multiple application domains. In conclusion, according to the results of case study, the new approach shows higher accuracy than both traditional turbulence models and the previous machine learning approach.

42 ENGINEERING↗
DOE OSTI2025

Enhancing EV Motor Design Through Knowledge-Based AI and Hierarchical Fuzzy Logic Model

This work presents a novel approach to optimizing electric vehicle motor design through the integration of Knowledge-Based Artificial Intelligence (KB-AI) and Hierarchical Fuzzy Logic. Traditional motor design processes are time-intensive, relying heavily on iterative simulations and domain-specific expertise. These processes are further complicated by the nonlinear relationships between key design parameters. The proposed framework addresses these challenges by systematically encoding expert knowledge from scientific literature into a fuzzy logic system, allowing for the efficient handling of complex design variables. The hierarchical fuzzy logic model reduces computational complexity by decomposing the nonlinear relationships into manageable rule sets while maintaining design accuracy. The proposed methodology was applied to the design of a 100 kW motor, yielding optimal values for key parameters. This resulted in a compact motor design with a volume of 2.2 liters, showcasing the framework’s ability to deliver high-performance, application-specific motor configurations.

Kumar, Praveen [ORNL] (ORCID:0000000291877857)↗
DOE OSTI2021

Wide-Scale Clinical Implementation of Knowledge-Based Planning: An Investigation of Workforce Efficiency, Need for Post-automation Refinement, and Data-Driven Model Maintenance

Our purpose was to investigate the effect of automated knowledge-based planning (KBP) on real-world clinical workflow efficiency, assess whether manual refinement of KBP plans improves plan quality across multiple disease sites, and develop a data-driven method to periodically improve KBP automated planning routines.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)

Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Biochemistry & Molecular Biology↗
DOE OSTI2022

A Knowledge-based Framework for Building Energy Model Performance Verification

Building energy modeling (BEM) has been widely used by researchers, regulators, and engineers to quantify building energy performance. Quality assurance (QA) and quality control (QC) of the model's performance are essential parts of such analysis. Currently, QA/QC is done in a manual and ad-hoc manner, which is tedious, error-prone, and time-consuming when QA/QC a large number of models. To solve these challenges, we propose a a dAta-driveN buIlding perforMance verificATion framEwork (ANIMATE), which conducts automated output-based verification of building operations requirements (especially for time-series output-based verification of control requirements). While this framework was developed for verifying energy model performance, it can be extended for other applications such as BEM software testing and performance verification of real buildings in the field.

Chen, Yan↗
DOE OSTI2022

Knowledge-matching based computational framework for genome-scale metabolic model refinement

Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Identification and Evaluation of Thermal Transport Components for Integrated Energy Systems

A proper evaluation and selection of component technologies is a critical aspect in the development of Integrated Energy System (IES). This study aims to investigate the key components and associated technologies required to build high-temperature heat transport systems for IES. Of particular interest is the component technologies needed to design and construct IES that combines advanced nuclear reactors with high-temperature industrial processes. This study particularly delved into knowledge base, evaluation metrics, and state-of-the-art commercial technologies, aiming to facilitate the evaluation and selection process of various thermal transport components. In addition, an evaluation process was proposed in order to assist in the optimal selection of the thermal transport components based on the knowledge base and evaluation metrics investigated through this study.

42 ENGINEERING↗