Large Language Models (LLMs) possess intricate internal representations of the world, yet these latent structures are notoriously difficult to interpret or repurpose beyond the original prediction task. Building on our earlier work (Rothenfusser, 2025), which introduced the concept of vector ontologies as a framework for translating high-dimensional neural representations into interpretable geometric structures, this paper provides the first empirical validation of that approach. A vector ontology defines a domain-specific vector space spanned by ontologically meaningful dimensions, allowing geometric analysis of concepts and relationships within a domain. We construct an 8-dimensional vector ontology of musical genres based on Spotify audio features and test whether an LLM's internal world model of music can be consistently and accurately projected into this space. Using GPT-4o-mini, we extract genre representations through multiple natural language prompts and analyze the consistency of these projections across linguistic variations and their alignment with ground-truth data. Our results show (1) high spatial consistency of genre projections across 47 query formulations, (2) strong alignment between LLM-inferred genre locations and real-world audio feature distributions, and (3) evidence of a direct relationship between prompt phrasing and spatial shifts in the LLM's inferred vector ontology. These findings demonstrate that LLMs internalize structured, repurposable knowledge and that vector ontologies offer a promising method for extracting and analyzing this knowledge in a transparent and verifiable way.

This paper presents SEGO (Semantic Graph Ontology), a cognitive mapping architecture designed to integrate geometric perception, semantic reasoning, and explanation generation into a unified framework for human-centric collaborative robotics. SEGO constructs dynamic cognitive scene graphs that represent not only the spatial configuration of the environment but also the semantic relations and ontological consistency among detected objects. The architecture seamlessly combines SLAM-based localization, deep-learning-based object detection and tracking, and ontology-driven reasoning to enable real-time, semantically coherent mapping.

We explore the role of ontologies in enhancing hybrid modeling and simulation through improved semantic rigor, model reusability, and interoperability across systems, disciplines, and tools. By distinguishing between methodological and referential ontologies, we demonstrate how these complementary approaches address interoperability challenges along three axes: Human-Human, Human-Machine, and Machine-Machine. Techniques such as competency questions, ontology design patterns, and layered strategies are highlighted for promoting shared understanding and formal precision. Integrating ontologies with Semantic Web Technologies, we showcase their dual role as descriptive domain representations and prescriptive guides for simulation construction. Four application cases - sea-level rise analysis, Industry 4.0 modeling, artificial societies for policy support, and cyber threat evaluation - illustrate the practical benefits of ontology-driven hybrid simulation workflows. We conclude by discussing challenges and opportunities in ontology-based hybrid M&S, including tool integration, semantic alignment, and support for explainable AI.

The implementation of transformational pedagogy in secondary education classrooms requires a broad multiliteracy approach. Due to limited planning time and resources, high school English Literature teachers often struggle to curate diverse, thematically aligned literature text sets. This study addresses the critical need for a tool that provides scaffolds for novice educators in selecting literature texts that are diverse -- in terms of genre, theme, subtheme, and author -- yet similar in context and pedagogical merits. We have developed a recommendation system, Teaching Text Expansion for Teacher Scaffolding (T-TExTS), that suggests high school English Literature books based on pedagogical merits, genre, and thematic relevance using a knowledge graph. We constructed a domain-specific ontology using the KNowledge Acquisition and Representation Methodology (KNARM), transformed into a knowledge graph, which was then embedded using DeepWalk, biased random walk, and a hybrid of both approaches. The system was evaluated using link prediction and recommendation performance metrics, including Area Under the Curve (AUC), Mean Reciprocal Rank (MRR), Hits@K, and normalized Discounted Cumulative Gain (nDCG). DeepWalk outperformed in most ranking metrics, with the highest AUC (0.9431), whereas the hybrid model offered balanced performance. These findings demonstrate the importance of semantic, ontology-driven approaches in recommendation systems and suggest that T-TExTS can significantly ease the burden of English Literature text selection for high school educators, promoting more informed and inclusive curricular decisions. The source code for T-TExTS is available at: https://github.com/koncordantlab/TTExTS

The growing volume of omics and clinical data generated for neurodegenerative diseases (NDs) requires new approaches for their curation so they can be ready-to-use in bioinformatics. NeuroEmbed is an approach for the engineering of semantically accurate embedding spaces to represent cohorts and samples. The NeuroEmbed method comprises four stages: (1) extraction of ND cohorts from public repositories; (2) semi-automated normalization and augmentation of metadata of cohorts and samples using biomedical ontologies and clustering on the embedding space; (3) automated generation of a natural language question-answering (QA) dataset for cohorts and samples based on randomized combinations of standardized metadata dimensions and (4) fine-tuning of a domain-specific embedder to optimize queries. We illustrate the approach using the GEO repository and the PubMedBERT pretrained embedder. Applying NeuroEmbed, we semantically indexed 2,801 repositories and 150,924 samples. Amongst many biology-relevant categories, we normalized more than 1,700 heterogeneous tissue labels from GEO into 326 unique ontology-aligned concepts and enriched annotations with new ontology-aligned terms, leading to a fold increase in size for the metadata terms between 2.7 and 20 fold. After fine-tuning PubMedBERT with the QA training data augmented with the enlarged metadata, the model increased its mean Retrieval Precision from 0.277 to 0.866 and its mean Percentile Rank from 0.355 to 0.896. The NeuroEmbed methodology for the creation of electronic catalogues of omics cohorts and samples will foster automated bioinformatic pipelines construction.

Semantic Spacetime (SST) is a discrete, graph theoretic'agent' representation of configurations and process phenomena, used for modelling scenarios that include knowledge representations, in the form of labelled directed graphs [1-4]. It enables both qualitative and quantitative interpretations of processes by combining physical and virtual concepts (from physics and information science) into a Promise Theoretic agent model [5]. Promise Theory principles emphasize the autonomy or locality of causal behaviour, so there are clear motivations for modelling phenomena in this way. As a graph theoretical structure, a Semantic Spacetime is a collection of nodes (agents) joined by links (channels for process information), both of which may have annotations and numerical values associated with them. A key application for Semantic Spacetime in artificial systems is to represent'knowledge' (in its simplified sense) and process structures, such as those normally associated with indexing methods or Semantic Webs, like the triple store approaches of the Resource Description Framework (RDF) [6].

Recent advances in Large Language Models have demonstrated their capabilities across a variety of tasks. However, automatically extracting implicit knowledge from natural language remains a significant challenge, as machines lack active experience with the physical world. Given this scenario, semantic knowledge graphs can serve as conceptual spaces that guide the automated text generation reasoning process to achieve more efficient and explainable results. In this paper, we apply a logic-augmented generation (LAG) framework that leverages the explicit representation of a text through a semantic knowledge graph and applies it in combination with prompt heuristics to elicit implicit analogical connections. This method generates extended knowledge graph triples representing implicit meaning, enabling systems to reason on unlabeled multimodal data regardless of the domain. We validate our work through three metaphor detection and understanding tasks across four datasets, as they require deep analogical reasoning capabilities. The results show that this integrated approach surpasses current baselines, performs better than humans in understanding visual metaphors, and enables more explainable reasoning processes, though still has inherent limitations in metaphor understanding, especially for domain-specific metaphors. Furthermore, we propose a thorough error analysis, discussing issues with metaphorical annotations and current evaluation methods.

How can the complexity of ML-enabled systems be managed effectively? The goal of this research is to investigate how complexity affects ML-Enabled Systems (MLES). To address this question, this research aims to introduce a metrics-based architectural model to characterize the complexity of MLES. The goal is to support architectural decisions, providing a guideline for the inception and growth of these systems. This paper brings, side-by-side, the architecture representation of two systems that can be used as case studies for creating the metrics-based architectural model: the SPIRA and the Ocean Guard MLES.

AutomationML (AML) enables standardized data exchange in engineering, yet existing recommendations for proper AML modeling are typically formulated as informal and textual constraints. These constraints cannot be validated automatically within AML itself. This work-in-progress paper introduces a pipeline to formalize and verify such constraints. First, AML models are mapped to OWL ontologies via RML and SPARQL. In addition, a Large Language Model translates textual rules into SHACL constraints, which are then validated against the previously generated AML ontology. Finally, SHACL validation results are automatically interpreted in natural language. The approach is demonstrated on a sample AML recommendation. Results show that even complex modeling rules can be semi-automatically checked -- without requiring users to understand formal methods or ontology technologies.

Having a unified, coherent taxonomy is essential for effective knowledge representation in domain-specific applications as diverse terminologies need to be mapped to underlying concepts. Traditional manual approaches to taxonomy alignment rely on expert review of concept pairs, but this becomes prohibitively expensive and time-consuming at scale, while subjective interpretations often lead to expert disagreements. Existing automated methods for taxonomy alignment have shown promise but face limitations in handling nuanced semantic relationships and maintaining consistency across different domains. These approaches often struggle with context-dependent concept mappings and lack transparent reasoning processes. We propose a novel framework that combines large language models (LLMs) with expert calibration and iterative prompt optimization to automate taxonomy alignment. Our method integrates expert-labeled examples, multi-stage prompt engineering, and human validation to guide LLMs in generating both taxonomy linkages and supporting rationales. In evaluating our framework on a domain-specific mapping task of concept essentiality, we achieved an F1-score of 0.97, substantially exceeding the human benchmark of 0.68. These results demonstrate the effectiveness of our approach in scaling taxonomy alignment while maintaining high-quality mappings and preserving expert oversight for ambiguous cases.