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As anyone even vaguely aware of current technology can tell you, machine learning (ML) and artificial intelligence (AI) have made exceptional breakthroughs in recent years. Generative artificial intelligence (GAI) emerged circa 2022 dominated by Large Language Models (LLMs) and generative tools for images emerged at about the same time.
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Validation and verification of engineering models is important to understand potential weaknesses and issues in the model. This is accomplished through the application of constraint logic to the model. These models and the constraints put upon them can be represented through a graph structure. Here we give a visualization system to aid users understanding, locating, and fixing constraint violations in their systems. We give users several ways to narrow down on the specific errors and parts of the graph they’re interested in. Users have the opportunity to choose the types of errors that will be shown in the graph. Clustering is applied to the graph to help users narrow down their searches. Several other graph interactions are given to support discovery of constraint violations.
While there are many tools for designing and modeling a single floating turbine, array level design and modeling has much more to consider. Designing floating wind arrays requires a coupled approach considering many variables, from bathymetry to installation and maintenance to failure and risk analysis. With all of these considerations, an array-level modeling tool is needed to quickly evaluate array designs. The Floating Array Model (FAModel) tool developed at the National Renewable Energy Laboratory was created to fill this gap in low-fidelity array modeling. FAModel is a python framework created to streamline holistic low-fidelity floating wind modeling for array-level analysis. FAModel integrates site data and models with a variety of open-source modeling tools developed by NREL, including FLORIS, RAFT, MoorPy, and anchor capacity models. The integration of these tools allows users to quickly and holistically design an array by considering forces, area analysis, visualization, annual energy production, failure modeling, and component costs.
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Digital engineering strategies typically assume that digital engineering models interoperate seamlessly across the multiple different engineering modeling software applications involved, such as model- based systems engineering (MBSE), mechanical computer-aided design (MCAD), electrical computer-aided design (ECAD), and other engineering modeling applications. The presumption is that the data schema in these modeling software applications are structured in the familiar flat- tabular schema like any other software application. Engineering domain-specific applications (e.g., systems, mechanical, electrical, simulation) are typically designed to solve domain-specific problems, necessarily excluding explicit representations of non-domain information to help the engineer focus on the domain problems (system definition, design, simulation). Such exclusions become problematic in inter-domain information exchange. The obvious assumptions of one domain might not be so obvious to experts in another domain. Ambiguity in domain-specific language can erode the ability to enable different domain modeling applications to interoperate, unless the underlying language is understood and used as the basis for translation from one application to another. The engineering modeling software application industry has struggled for decades to enable these applications to interoperate. Industry standards have been developed, but they have not unified the industry. Why is this? The authors assert that the industry has relied on traditional database integration methods. The basic issue prohibiting successful application integration then is that traditional database-driven integration does not consider the distinct languages of each domain. An engineering models meaning is expressed through the underlying language of that engineering domain. In essence, traditional integration methods do not retain the semantic context (meaning) of the model. The basis of this research stems from the widely held assumption that systems engineering models are (or can be) structured according to the underlying semantic ontology of the model. This assumption can be imagined from two thoughts. 1) Digital systems engineering models are often represented using graph theory (the graph of a complex systems model can contain millions of nodes and edges). When examining the nodes one at a time and following the outbound edges of each node one by one, one can end up with rudimentary statements about the model (i.e., node A relates to node B), as in a semantic graph. 2) Likewise, from the study of natural languages, a sentence can be structured into unambiguous triples of subject-predicate-object within formal and highly expressive semantic ontologies. The rudimentary statements about a systems model discerned with graph theory closely mimic the triples used in the ontologies that try to structure natural languages. In other words, a systems models semantic graph can be (or is) structured into an ontology. Additionally, it is well established in industry that through natural language processing (NLP), which provides the means to create language structures, that computers can interpret ontological graphs. Therefore, the authors hypothesized that if the integrity of the underlying semantic structure of a systems model is retained, the contextual meaning of the model is retained. By structuring system models into the triples of the underlying ontology during the transformation from one MBSE application to another, the authors have provided a proof of the concept that the meaning of a system model can be retained during transformation. The authors assert that this is the missing ingredient in effective systems model-to-model interoperability. ACKNOWLEDGEMENTS The authors would like to thank the FY19 Model Interoperability team members who provided a solid foundation for the FY20 team to leverage: John McCloud, for the work he did to guide us toward the right use of technology that will appropriately discover and manipulate ontologies. Carlos Tafoya, for the work he did to develop an application programming interface (API)/Adapter that would export ontology-based data from GENESYS. Peter Chandler, for the work he did to architect our overall integration solution, with an eye toward the future that would influence a large-scale federated production-level systems engineering digital model ecosystem.
The purpose of this research is to develop a first-of-a-kind framework for integrating Big Data capability into the daily activities of our current fleet of nuclear power plants. Big Data is traditionally defined as data sets with high volume, velocity, and heterogeneity, and the existing Big Data analytics capabilities are now widely popular in fields such as finance, weather, e-commerce, healthcare and sports. In the nuclear industry, while the volume and velocity of data may present computational challenges for existing analytics capabilities, data heterogeneity are seen to present the major challenge. This research project mainly focuses on incorporating the wide range of data heterogeneities in nuclear power plants into an integrated Big Data Analytics capability. The primary end-product of this project is a Big Data framework that is capable of dealing with the large volume and heterogeneity of the data found in nuclear power plants to extract timely and valuable information on equipment performance. The framework can generate system insights that are actionable relations between measurable impacts and the corresponding maintenance action plans and enable optimization of plant operation and maintenance based on the extracted information. The developed framework is capable of handling heterogeneous data including both image data and time-series sensor data. Specifically, this developed framework includes the following components. The first component is an overarching maintenance ontology which includes system insights required by maintenance optimization. The maintenance ontology interacts with other components in the developed framework. The second component handles Piping & Instrumentation Diagram (P&ID) data. It can be used to extract system components and their relations automatically from the P&IDs. This extracted information is stored in the first component, i.e., maintenance ontology, and is also used as input to the third component, i.e., a tool for generating the fault tree for the corresponding system. The generated fault tree in turn is stored in the ontology for assessing risk that is used as a criterion in maintenance policy optimization. The fourth component is a tool for inferring the parameters in the Markov degradation model for a nuclear system. It uses basic information from the ontology. The fifth component is a tool for assessing the degradation level using sensor measurement data, for example, pressure, flowrate. This tool can be used for determining corrective maintenance actions. The results obtained from components four and five are returned to the ontology. The sixth component of the framework is a tool for optimizing the maintenance policy for a nuclear system of interest. It takes certain basic information from the ontology, e.g., costs of maintenance actions and system failures, as input, and returns the optimal maintenance policy to the ontology. This tool can be used for determining predictive maintenance actions. A set of experiments have also been conducted to verify the algorithms developed in this project for nuclear system degradation monitoring. The experiments are based on four solenoid valves, similar to the ones used in nuclear power plants. The analyses based on the experimental data using two algorithms, i.e., the Randomized Window Decomposition (RWD) algorithm and the particle filtering algorithm, and the results are introduced in the report. The Big Data framework developed in this project can be used as a support tool in daily activities of plant operation and maintenance and will reduce current costs while maintaining or improving safety levels. Overall, the project will not only benefit existing reactors, however it will open new frontiers to realize the long overdue value of Big Data Analytics in the nuclear sphere.
Research in occupant behaviour is now using a more elaborate framework of building occupant interaction. Researchers often face challenges in collecting data, particularly for the data to meet the minimum number of required data points and the data interoperability requirements. Researchers address the first issue with the synthetic population and the latter with data ontologies. While synthetic population is commonly used to address the first issue, data ontology development is used to address the latter. The two solutions are complementary to each other. One of the known ontologies in building occupant behaviour research is the Drivers-Needs-Actions-Systems (DNAS) ontology, which has been used by building modelers to describe energy-related occupant behaviour. This paper describes the ontology-based synthetic population generation that can be used in the agent-based modeling (ABM) applications. This paper considers multiple data sources, including ASHRAE Thermal Comfort DB II and IEA Annex 66 data sets. A case study of an office building is used to present the workflow of DNAS framework expansion, synthetic population generation, and agent-based modeling.
Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.
Background Large language models (LLMs) are increasingly used medicine for diverse applications including differential diagnostic support. The training data used to create LLMs such as the Generative Pretrained Transformer (GPT) predominantly consist of English-language texts, but LLMs could be used across the globe to support diagnostics if language barriers could be overcome. Initial pilot studies on the utility of LLMs for differential diagnosis in languages other than English have shown promise, but a large-scale assessment on the relative performance of these models in a variety of European and non-European languages on a comprehensive corpus of challenging rare-disease cases is lacking. Methods We created 4917 clinical vignettes using structured data captured with Human Phenotype Ontology (HPO) terms with the Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema. These clinical vignettes span a total of 360 distinct genetic diseases with 2525 associated phenotypic features. We used translations of the Human Phenotype Ontology together with language-specific templates to generate prompts in English, Chinese, Czech, Dutch, French, German, Italian, Japanese, Spanish, and Turkish. We applied GPT-4o, version gpt-4o-2024-08-06, and the medically fine-tuned Meditron3-70B to the task of delivering a ranked differential diagnosis using a zero-shot prompt. An ontology-based approach with the Mondo disease ontology was used to map synonyms and to map disease subtypes to clinical diagnoses in order to automate evaluation of LLM responses. Findings For English, GPT-4o placed the correct diagnosis at the first rank 19.9% and within the top-3 ranks 27.0% of the time. In comparison, for the nine non-English languages tested here the correct diagnosis was placed at rank 1 between 16.9% and 20.6%, within top-3 between 25.4% and 28.6% of cases. The Meditron3 model placed the correct diagnosis within the first 3 ranks for 20.9% of cases in English and between 19.9% and 24.0% for the other nine languages. Interpretation The differential diagnostic performance of LLMs across a comprehensive corpus of rare-disease cases was largely consistent across the ten languages tested. This suggests that the utility of LLMs in clinical settings may extend to non-English clinical settings.
General Entity Model (GEM) is an extensible, upper-level ontology. An ontology is simply a collection of concepts and their relationships and properties and can be used as a schema or data model to describe some domain. As an upper-level ontology, GEM is intended to be used as a foundation for building domain-specific ontologies (such as energy, manufacturing, etc).
CEMENTO is a component python package of the larger SDLE FAIR application suite of tools for creating scientific ontologies more efficiently. This package provides functional interfaces for converting draw.io diagrams of ontologies into RDF triple file formats and vice versa. This package is able to provide term matching between reference ontology files and terms used in draw.io diagrams allowing for faster ontology deployment while maintaining robust cross-references.
Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.
Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.
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.