Ontologies
Search-Optimized Quantization in Biomedical Ontology Alignment
Bouaggad, Oussama, Grabar, Natalia
In the fast-moving world of AI, as organizations and researchers develop more advanced models, they face challenges due to their sheer size and computational demands. Deploying such models on edge devices or in resource-constrained environments adds further challenges related to energy consumption, memory usage and latency. To address these challenges, emerging trends are shaping the future of efficient model optimization techniques. From this premise, by employing supervised state-of-the-art transformer-based models, this research introduces a systematic method for ontology alignment, grounded in cosine-based semantic similarity between a biomedical layman vocabulary and the Unified Medical Language System (UMLS) Metathesaurus. It leverages Microsoft Olive to search for target optimizations among different Execution Providers (EPs) using the ONNX Runtime backend, followed by an assembled process of dynamic quantization employing Intel Neural Compressor and IPEX (Intel Extension for PyTorch). Through our optimization process, we conduct extensive assessments on the two tasks from the DEFT 2020 Evaluation Campaign, achieving a new state-of-the-art in both. We retain performance metrics intact, while attaining an average inference speed-up of 20x and reducing memory usage by approximately 70%.
A Risk Ontology for Evaluating AI-Powered Psychotherapy Virtual Agents
Steenstra, Ian, Bickmore, Timothy W.
The proliferation of Large Language Models (LLMs) and Intelligent Virtual Agents acting as psychotherapists presents significant opportunities for expanding mental healthcare access. However, their deployment has also been linked to serious adverse outcomes, including user harm and suicide, facilitated by a lack of standardized evaluation methodologies capable of capturing the nuanced risks of therapeutic interaction. Current evaluation techniques lack the sensitivity to detect subtle changes in patient cognition and behavior during therapy sessions that may lead to subsequent decompensation. We introduce a novel risk ontology specifically designed for the systematic evaluation of conversational AI psychotherapists. Developed through an iterative process including review of the psychotherapy risk literature, qualitative interviews with clinical and legal experts, and alignment with established clinical criteria (e.g., DSM-5) and existing assessment tools (e.g., NEQ, UE-ATR), the ontology aims to provide a structured approach to identifying and assessing user/patient harms. We provide a high-level overview of this ontology, detailing its grounding, and discuss potential use cases. We discuss four use cases in detail: monitoring real user interactions, evaluation with simulated patients, benchmarking and comparative analysis, and identifying unexpected outcomes. The proposed ontology offers a foundational step towards establishing safer and more responsible innovation in the domain of AI-driven mental health support.
Ontology Creation and Management Tools: the Case of Anatomical Connectivity
Kokash, Natallia, de Bono, Bernard, Gillespie, Tom
Ontologies are essential for developing standardized vocabularies and defining relationships that help describe and interpret data from diverse sources. They are crucial for achieving semantic interoperability in many domains, allowing different systems to exchange data with a consistent and shared meaning. Ontologies are extensively used in biological and biomedical research Hoehndorf et al. (2015); Antezana et al. (2009), due to their ability to: provide standard identifiers for classes and relationships representing complex phenomena; include metadata to clarify the intended meaning of classes and relationships; include machine-readable definitions that allow computational access to class properties and relationships; standardize vocabulary across multiple data sources. Ontology-based data integration plays a vital role in neuroscience, where researchers synthesize knowledge across physiology, anatomy, molecular and developmental biology, cytology, and mathematical modeling to support accurate data representation, analysis, and simulation. A common challenge for many large neuroscience projects is the integration of data across a wide diversity of species, spatial resolutions, and temporal scales.
Integrating Activity Predictions in Knowledge Graphs
Hare, Forrest, Sculley, Alec, Stockton, Cameron
We argue that ontology - structured knowledge graphs can play a crucial role in generating predictions about future events. By leveraging the semantic framework provided by Basic Formal Ontology (BFO) and Common Core Ontologies (CCO), we demonstrate how data -- such as the movements of a fishing vessel -- can be organ ized in and retrieved from a knowledge graph. These query results are then used to create Markov chain models, allowing us to predict future states based on the vessel's history. To fully support this process, we introduce the term `spatiotemporal instant' to complete the necessary structural semantics. Additionally, we critique the prevailing ontological model of probability, according to which probabilities are about the future . We propose an alternative view, where at least some probabilities are treated as being about actual process profiles, which better captures the dynamics of real - world phenomena. Finally, we demonstrate how our Markov chain - based probability calculations can be seamlessly integrated back into the knowledge graph, enabling further an alysis and decision - making.
Automatic Mapping of AutomationML Files to Ontologies for Graph Queries and Validation
Westermann, Tom, Ramonat, Malte, Hujer, Johannes, Gehlhoff, Felix, Fay, Alexander
AutomationML has seen widespread adoption as an open data exchange format in the automation domain. It is an open and vendor neutral standard based on the extensible markup language XML. However, AutomationML extends XML with additional semantics that limit the applicability of common XML-tools for applications like querying or data validation. This article demonstrates how the transformation of AutomationML into OWL enables new use cases in querying with SPARQL and validation with SHACL. To support this, it provides practitioners with (1) an up-to-date ontology of the concepts defined in the AutomationML standard and (2) a declarative mapping to automatically transform any AutomationML model into RDF triples. A study on examples from the automation domain concludes that transforming AutomationML to OWL opens up new powerful ways for querying and validation that would have been impossible without this transformation.
Shapes of Cognition for Computational Cognitive Modeling
McShane, Marjorie, Nirenburg, Sergei, Oruganti, Sanjay, English, Jesse
Shapes of cognition is a new conceptual paradigm for the computational cognitive modeling of Language - Endowed Intelligent Agents (LEIAs) . S hapes are remembered constellations of sensory, linguistic, conceptual, episodic, and procedural knowledge that allow agents to cut through the complexity of real life the same way as people do: by expecting things to be typical, recognizing patterns, acting by habit, reasoning by analogy, satisficing, and generally minimizing cognitive load to the degree situations permit . Atypical outcomes are treated using shapes - based recovery method s, such as learning on the fly, asking a human partner for help, or seeking an actionable, even if imperfect, situational understanding . Although shapes is an umbrella term, it is not vague: shapes - based modeling involves particular objectives, hypotheses, modeling strategies, knowledge bases, and actual models of wide - ranging phenomena, all implemented within a particular cognitive architecture . Such s pecificity is needed both to vet the our hypotheses and to achieve our practical aims of building useful agent systems that are explainable, extensible, and worthy of our trust, even in critical domains . However, a lthough the LEIA example of shapes - based modeling is specific, the principles can be applied more broadly, giving new life to knowledge - based and hybrid AI .
Executable Ontologies: Synthesizing Event Semantics with Dataflow Architecture
This paper presents boldsea, Boldachev's semantic-event approach -- an architecture for modeling complex dynamic systems using executable ontologies -- semantic models that act as dynamic structures, directly controlling process execution. We demonstrate that integrating event semantics with a dataflow architecture addresses the limitations of traditional Business Process Management (BPM) systems and object-oriented semantic technologies. The paper presents the formal BSL (boldsea Semantic Language), including its BNF grammar, and outlines the boldsea-engine's architecture, which directly interprets semantic models as executable algorithms without compilation. It enables the modification of event models at runtime, ensures temporal transparency, and seamlessly merges data and business logic within a unified semantic framework.
Measuring Visual Understanding in Telecom domain: Performance Metrics for Image-to-UML conversion using VLMs
Ranjani, HG, Prabhudesai, Rutuja
Telecom domain 3GPP documents are replete with images containing sequence diagrams. Advances in Vision-Language Large Models (VLMs) have eased conversion of such images to machine-readable PlantUML (puml) formats. However, there is a gap in evaluation of such conversions - existing works do not compare puml scripts for various components. In this work, we propose performance metrics to measure the effectiveness of such conversions. A dataset of sequence diagrams from 3GPP documents is chosen to be representative of domain-specific actual scenarios. We compare puml outputs from two VLMs - Claude Sonnet and GPT-4V - against manually created ground truth representations. We use version control tools to capture differences and introduce standard performance metrics to measure accuracies along various components: participant identification, message flow accuracy, sequence ordering, and grouping construct preservation. We demonstrate effectiveness of proposed metrics in quantifying conversion errors across various components of puml scripts. The results show that nodes, edges and messages are accurately captured. However, we observe that VLMs do not necessarily perform well on complex structures such as notes, box, groups. Our experiments and performance metrics indicates a need for better representation of these components in training data for fine-tuned VLMs.
Aligning ESG Controversy Data with International Guidelines through Semi-Automatic Ontology Construction
Iwata, Tsuyoshi, Comte, Guillaume, Flores, Melissa, Kondo, Ryoma, Hisano, Ryohei
The growing importance of environmental, social, and governance data in regulatory and investment contexts has increased the need for accurate, interpretable, and internationally aligned representations of non-financial risks, particularly those reported in unstructured news sources. However, aligning such controversy-related data with principle-based normative frameworks, such as the United Nations Global Compact or Sustainable Development Goals, presents significant challenges. These frameworks are typically expressed in abstract language, lack standardized taxonomies, and differ from the proprietary classification systems used by commercial data providers. In this paper, we present a semi-automatic method for constructing structured knowledge representations of environmental, social, and governance events reported in the news. Our approach uses lightweight ontology design, formal pattern modeling, and large language models to convert normative principles into reusable templates expressed in the Resource Description Framework. These templates are used to extract relevant information from news content and populate a structured knowledge graph that links reported incidents to specific framework principles. The result is a scalable and transparent framework for identifying and interpreting non-compliance with international sustainability guidelines.
Investigating Language Model Capabilities to Represent and Process Formal Knowledge: A Preliminary Study to Assist Ontology Engineering
Recent advances in Language Models (LMs) have failed to mask their shortcomings particularly in the domain of reasoning. This limitation impacts several tasks, most notably those involving ontology engineering. As part of a PhD research, we investigate the consequences of incorporating formal methods on the performance of Small Language Models (SLMs) on reasoning tasks. Specifically, we aim to orient our work toward using SLMs to bootstrap ontology construction and set up a series of preliminary experiments to determine the impact of expressing logical problems with different grammars on the performance of SLMs on a predefined reasoning task. Our findings show that it is possible to substitute Natural Language (NL) with a more compact logical language while maintaining a strong performance on reasoning tasks and hope to use these results to further refine the role of SLMs in ontology engineering.