In this paper we discuss the foundations behind a novel methodology for the validation of semantic mappings between different data sources based upon different foundation ontologies, where the methodology builds a framework based upon the metaphysical commitments of the ontologies. We provide as example the test case of mappings between IES and BFO, and we especially focused on providing cardinality constraints on the mappings between the two ontologies. In order to demonstrate the applicability of our method, we showcased how these principles can be operationalized through SPARQL queries validating the results of a mapping pipeline.
https://arxiv.org/abs/2608.08122
Gamification is especially effective in learning domains requiring active problem-solving and iterative skill-building, such as cybersecurity education. Generative AI agents offer a path to delivering such experiences adaptively at scale, but introduce well-documented risks in educational settings: inconsistent behavior, hallucinated reasoning, and misalignment with pedagogical frameworks. Grounding these systems in learning science is therefore essential. We present \model, an agentic framework for gamified cybersecurity learning that enables structured autonomy through ontology-guided validation, schema-governed behavioral control, and competency-based progression. The system is organized around a competency-based progression model that structures topics by difficulty and prerequisite relationships, reflecting evidence-based principles of scaffolded instruction. The learning loop is decomposed into four specialized agents: challenge, support, evaluation, and reward, each governed by behavioral schemas that encode operational modes and progression logic, bounding agent autonomy without eliminating generative flexibility. A cybersecurity ontology validates all generated content prior to display, enforcing domain-consistent reasoning and safety constraints. We evaluate CyberAgents through classroom deployment with undergraduate students, complemented by expert evaluations from educators and domain specialists. Results indicate improved engagement, clearer feedback interpretation, and greater learner trust in AI-generated responses when behavioral schemas and ontology validation are active. Preliminary comparisons with an unconstrained configuration further support the role of structured control in stabilizing instructional behavior. These findings offer a blueprint for designing pedagogically grounded agentic gamified learning systems.
https://arxiv.org/abs/2608.07965
Translating a natural-language question into a SPARQL query that can be executed against a large knowledge graph requires resolving lexical ambiguity, grounding surface terms in the target ontology, and producing graph patterns that are both syntactically valid and semantically faithful. We present an agentic text-to-SPARQL system that goes one step beyond static tool-using agents: a researcher agent that, after each round of inference on a validation set, proposes and tests changes to its own prompts, rules, and tool-orchestration code. We instantiate the loop on DBpedia, evolve nine successive versions of the agent driven by a low-cost reasoning model, and deploy the best-performing configuration with two stronger backbone models. The study yields three observations: (i) self-improvement converges quickly and then achieves 0.22 overall accuracy on the 2025 DBpedia validation set; (ii) the bottleneck is consistently in basic-graph-pattern predicate selection, not in SPARQL syntax or modifiers; and (iii) several benchmark items appear to penalise correct queries due to property ambiguity in DBpedia, suggesting that future Text-to-SPARQL benchmarks should be scored using a combination of machine translation and information retrieval metrics.
https://arxiv.org/abs/2608.07700
The increasing specialization of scientific research challenges existing classification systems, which provide effective representations of broad disciplines and research topics but often fail to capture the fine-grained conceptual structure of contemporary science. Author keywords offer greater specificity, but their fragmentation, redundancy, and terminological variability limit their use as stable units of knowledge organization. We introduce SCALE (Scientific Concept Aggregation via LLMs and Embeddings), a framework that extends the OpenAlex taxonomy with a new level of scientific Concepts below Topics. Rather than treating keywords as isolated descriptors, SCALE organizes semantically related terms into coherent and interpretable conceptual units and integrates them within the existing disciplinary hierarchy. The framework combines scientific text embeddings, large language models, and graph-based community detection to construct this additional layer at scale. The resulting taxonomy enables scientific literature to be read through an intermediate conceptual level between broad research topics and individual documents. This perspective provides a more detailed representation of how scientific knowledge is structured, specialized, and connected across disciplines. By transforming heterogeneous author terminology into reusable hierarchical units, SCALE offers a foundation for fine-grained scholarly classification, scientometric analysis, research monitoring, and future ontology development.
https://arxiv.org/abs/2608.07254
Systematic reviews of Randomised Controlled Trials (RCTs) are routinely used as evidence for clinical care guidelines. Such evidence has to meet high research integrity standards to prevent low quality or false research outputs influencing the clinical care. However, assessing research integrity of published RCTs is a complex process requiring manual effort, and potentially resulting in diverse opinions of the human assessors. This paper describes INSPECT-AI, an LLM-based interactive tool that assists human reviewers with research integrity assessments of published RCTs based on the community approved INSPECT-SR framework, and the Research Integrity Provenance and Evidence ontology (RIPE-O) for documenting the provenance of the assessment process. In addition, we present the Research Integrity Provenance and Evidence knowledge graph (RIPE-KG), an initial set of 140 expert research integrity assessments of 95 RCT publications generated by INSPECT-AI and described using RIPE-O.
https://arxiv.org/abs/2608.07202
A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships. Existing graph-based models commonly use the same network to structure gene representations and mediate intergene interactions, thereby implicitly treating stable associations as perturbation-response pathways. Gene Ontology and control-derived coexpression networks encode relatively stable relationships rather than intervention-specific response directions or magnitudes. We therefore propose GeneGeoFlow, which conditions a control-anchored residual flow on gene-wise geometry derived from biological networks to learn intervention-specific transcriptional responses. GeneGeoFlow derives multi-scale spectral coordinates from Gene Ontology and control-derived coexpression networks. A perturbation-conditioned, gene-wise gating module selects relevant structural scales and network sources, yielding intervention-specific gene geometry. The resulting geometry conditions a control-anchored residual flow without explicitly propagating target-derived signals along the graph. Condition-wise optimal transport couples unpaired control and perturbed populations for training, while a Delta-correlation objective aligns the predicted and observed condition-level expression-shift directions. GeneGeoFlow achieves Pearson Delta scores of 0.8979 on the Norman additive benchmark and 0.9088 on five held-out drug combinations in the fixed ComboSciPlex test split. These results support perturbation-conditioned gene geometry as an effective structural prior for intervention-specific response prediction, without conflating stable gene relationships with response propagation.
https://arxiv.org/abs/2608.06824
The use of ontologies and knowledge graphs is becoming increasingly widespread in the defence and national security domain. Numerous ontologies have been developed through initiatives led by academia, industry, and government. Achieving interoperability across diverse defence and national security ontologies remains a major challenge due to the domain's breadth and specialisation. In this work, we analyse and document over 60 publicly available ontologies and introduce a new track for the Ontology Alignment Evaluation Initiative (OAEI). This track comprises eight matching tasks, consensus alignments and manually-curated (silver-standard) mappings. The consensus alignments are derived by aggregating the outputs of several state-of-the-art ontology alignment systems. The silver-standard is obtained from the manual validation of the consensus alignment together with a subset of the unique mappings (i.e., mappings suggested by only one system).
https://arxiv.org/abs/2608.05867
Generative AI used as a capable servant has greatly accelerated intellectual work, but it also risks eroding human epistemic agency by encouraging uncritical acceptance of AI-generated reasoning. This creates a need for mechanisms that preserve human agency by augmenting metacognition during AI-assisted intellectual work. To address this, we propose the Synthesis-Analysis Reciprocity Model, which views intellectual construction as a reciprocal interaction between Synthesis, which combines components into an artifact, and Analysis, which critically evaluates them against objective indicators and constrains subsequent synthesis. Grounded in this model, we present the Vibe Compiler, a research-logic compiler that helps researchers transform vague ideas (Vibes) into coherent research logic. The system compiles these ideas using a research paper ontology of sixteen academic parameters. Compilation failures indicate missing logical components; rather than filling them autonomously, the system prompts researchers with reflective questions that encourage them to develop the missing reasoning. The framework characterizes structural gaps along two dimensions: cognitive function (Synthesis vs. Analysis) and executing agent (human vs. AI), yielding four origin types that identify where breakdowns arise. Our design emphasizes AI probing its own synthesized output to stimulate human metacognition, encouraging researchers to remain managers who critically direct and validate AI-generated reasoning rather than passive recipients. Experience with a prototype built on NotebookLM and Gemini suggests that effective AI-assisted reasoning depends less on sophisticated prompting than on the knowledge structure provided to the AI. This paper was developed using the proposed Vibe Compiler.
https://arxiv.org/abs/2608.05545
The emergence of the ISO standard GQL introduces a powerful query language extending first-order logic with controlled recursion, raising the question of its applicability to evaluation of ontology-mediated queries (OMQs). We focus on OMQs consisting of atomic queries over ontologies expressed in Horn-ALCHI, an expressive Description Logic that is not, in general, first-order rewritable. To address this, we introduce DL automata, a novel formalism that captures the semantics of such OMQs via runs over fact sets. We then identify a large class of DL automata that can be rewritten into unions of conjunctive two-way regular path queries (UC2RPQs), a central fragment of GQL. Our class of automata relies on a stratification of their states, ruling out specific forms of cyclic dependencies known to raise the complexity. This yields a broad class of Horn-ALCHI OMQs that are GQL-rewritable.
https://arxiv.org/abs/2608.04945
Biomedical relation extraction (BioRE) extracts structured knowledge from biomedical literature for applications such as knowledge base construction and hypothesis generation. Traditional symbolic systems such as SemRep provide high precision but limited recall, while large language models (LLMs) offer stronger contextual reasoning but remain prone to false-positive predictions. We developed ANCHOR-RE, a framework that integrates ontology-guided reasoning, external knowledge grounding, and data-driven verification rules into LLM inference. We evaluated it on three BioRE benchmarks (SemRepGS, DDI, and ChemProt) using both proprietary and open-weight LLMs. To assess generalizability beyond benchmark datasets while reducing potential evaluation bias from LLM pretraining contamination, we conducted a temporal evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE outperformed direct LLM prompting, improving micro-F1 from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.872 on DDI, and from 0.939 to 0.941 on ChemProt. On DDI and ChemProt, it also outperformed previously reported inference-only methods and approached fine-tuned or instruction-tuned systems without parameter updates. Similar performance gains observed with open-weight LLMs indicate that the benefits were not limited to the proprietary backbone. On the post-cutoff set, manual assessment of 500 randomly sampled predictions yielded a precision of 69%, maintaining consistent precision on previously unseen biomedical literature. Neuro-symbolic reasoning can improve the reliability of LLM-based BioRE without fine-tuning. Results across multiple benchmarks, model families, and post-cutoff literature support ANCHOR-RE as a practical training-free approach to biomedical literature mining.
https://arxiv.org/abs/2608.03154
Latin America is missing two foundational layers of AI infrastructure: the dataset layer and the benchmark layer. This paper targets the dataset layer. The dataset layer faces two compounding problems: discovery and supply. Latin American AI datasets exist but are scattered across platforms with no shared index. Even with perfect indexing, the total volume would remain far below what frontier AI development requires. We propose DataHub: a task-first data infrastructure organized through the ontology /<task?>/<domain?>/<language?>, with mechanisms for dataset discovery, metadata, contribution, licensing, and reuse.
https://arxiv.org/abs/2608.02949
Clinic notes and structured electronic health record (EHR) medication history often contain different medication information. Same-visit disagreement between these sources may result from note-side normalization errors, differences in terminology or timing, or actual differences in documentation. We developed a note-grounded approach that uses large language model (LLM) assisted reference construction, targeted and random human review, deterministic medication normalization, and semantic and temporal comparisons with structured medication history. We evaluated all normalization results on a patient-level held-out test set to limit adaptation to the study cohort. On 5,403 held-out mention rows, exact canonical agreement improved from 0.7226 with surface-exact matching to 0.8429 after lexical cleanup and curated alias mapping. In a random audit of previously unaudited rows, canonical-label agreement was 0.9210 among evaluable valid medication mentions, whereas treatment-action attribution was lower at 0.5326. In the full-cohort characterization analysis, only 16.44% of note-derived rows had same-visit exact overlap with structured medication history, but 55.17% had same-visit semantic overlap, 90.34% had same-visit or +/-30-day overlap, and only 3.97% remained in the strict no-structured-overlap bucket under broad project-level mapping. An ontology-backed sensitivity analysis further showed that held-out strict Observational Medical Outcomes Partnership (OMOP)-backed no-overlap fell from 43.99% to 36.68% after a development-derived alias supplement. These results show that note-to-structured-medication mismatch can arise from normalization errors, differences in terminology, and differences in documentation timing.
https://arxiv.org/abs/2608.01570
Large language models are increasingly viewed as a potential means of mitigating global health inequities, yet their outputs often reflect dominant high-resource medical traditions and provide limited coverage of traditional medical knowledge systems. Tibetan medicine, one of the world's four major traditional medical systems, has an independent and highly structured theoretical framework. When models lack grounded understanding of Tibetan medicine, they may fall back on dominant epistemic systems and distort the native knowledge structure during reasoning. However, quantitative tools for evaluating cultural bias in Tibetan medicine remain largely absent. To address this gap, we introduce TreeProbe, the first cultural-bias benchmark organized around the native Tree of Medicine framework in Tibetan medicine. It contains 4,719 expert-adjudicated items covering 467 diseases and 10 subtasks along the three roots. Experiments on representative LLMs show that current models remain limited in native Tibetan medical contexts and exhibit systematic external ontology drift. Further analysis reveals that models diverge in whether they drift toward biomedical or TCM reasoning, shaped by pretraining data composition and surface resemblance between TCM and Tibetan medicine. TreeProbe provides a diagnostic benchmark for developing medical AI systems that are both linguistically inclusive and epistemically fair. Code and data are available in an anonymous repository at this https URL.
https://arxiv.org/abs/2608.00640
Fault detection and diagnosis (FDD) technology is essential for improving HVAC system reliability, energy efficiency, and maintenance effectiveness. However, effective deployment of FDD solutions in buildings requires structured domain knowledge that can bridge heterogeneous data sources, diverse equipment types, and varied diagnostic outputs. Limited data interpretability and interoperability within the FDD domain have led to fragmented information silos, hindering the implementation of FDD and related applications, such as the digital twin-enabled FDD frameworks and artificial intelligence (AI)-driven maintenance decision-making systems. This paper presents an FDD Ontology (FDD-ON), a modular and extensible ontology to formally represent variable air volume (VAV) HVAC system components, fault types, symptom statuses, fault impacts and associated attributes. FDD-ON integrates HVAC system FDD semantics to provide comprehensive representations of fault and symptom attributes, supported by the well-defined controlled vocabulary. Additionally, FDD-ON offers comprehensive fault, symptom, and impact libraries to capture a broad spectrum of operational abnormalities and their consequences in VAV HVAC systems. Through explicit contributing cause-fault-symptom-impact relations, FDD-ON serves as a machine-interpretable basis for querying diagnostic knowledge, mapping heterogeneous FDD outputs, and developing interoperable FDD-related applications. FDD-ON is evaluated using publicly available VAV HVAC system datasets and demonstrated through FDD development applications. Results indicate that FDD-ON provides a foundational semantic framework for advancing scalable, transparent, and interoperable FDD solutions across various applications.
https://arxiv.org/abs/2607.29657
Organizations increasingly define operational metrics in structured, machine-readable formats to monitor systems, processes, and compliance. These metric definitions implicitly encode domain knowledge, such as referencing concepts, properties, and relationships, that often extends what is captured in formal ontologies. Yet the connection between operational metric catalogues and ontological knowledge remains manual, ad-hoc, and labor-intensive. We present COntExt, a framework for context-aware ontology extension that takes structured metric definitions as input and suggests how referenced concepts and properties should be integrated into an existing ontology, utilizing the context of these metrics. The framework defines the extension problem as three sub-tasks: parent class prediction, relation type prediction, and data property assignment. Across four cybersecurity ontologies, we evaluate different algorithms for each task. Our results show that metric-derived context improves the suggestions over ontology-context baselines for relation type prediction and data property assignment. Our work demonstrates that operational metric catalogues are a practical and underexploited source for ontology extension. This work enables organizations to maintain their ontologies at a significantly lower cost than manual engineering.
https://arxiv.org/abs/2607.29553
AI systems whose outputs inform real decisions, and increasingly consequential ones, require something that current documentation practice does not provide: a structured, inspectable representation of the knowledge they need to ground, contextualize, and reason about those decisions, ideally reviewed and signed off by a domain expert. Established documentation artefacts already capture important aspects of an AI system. Model cards describe how a system behaves, data cards describe what it was trained on, and system cards describe the risks of a deployed system. None of them addresses the layer between inputs and outputs, more precisely, the concepts a system holds, the relationships it models, and the patterns of reasoning it applies. For pattern-recognition tasks this gap is tolerable. For agentic AI, where systems act on their conclusions, it is the step that most often separates a promising proof of concept from an operational solution an organisation can rely on. This paper introduces the Knowledge Card, a structured artefact that captures validated knowledge about a single bounded concept in a form that experts can review, organisations can audit, and AI systems can reason over. For one concept, such as a specific failure mode, a compliance obligation, or a process decision, a Knowledge Card records the entities and relationships involved, the reasoning that connects them, the conditions under which that reasoning no longer holds, and the provenance of every claim, all grounded in a formal domain ontology and signed off by a domain expert. Initial prototype cards have been built in the energy and pharmaceutical domains. The schema is released as a public draft for community engagement.
https://arxiv.org/abs/2608.26176
Large language model (LLM) agents have been increasingly adopted in scientific research for organizing and invoking specialized computational tools. However, their reliance on predefined tool spaces with static semantics limits their applicability to open-world scientific workflows, where tool requirements, capabilities, and boundaries evolve dynamically. To this end, we propose SciToolAgent-Evo, an ontology-aware self-evolving agent for open-world scientific tool acquisition. Driven by an evolving memory of skills, experiences, and an ontologized tool graph, it distills generalizable knowledge from contrastive trajectories during accumulation, whereas during inference, it formulates active requests and utilizes a LinUCB-based bandit gate to dynamically balance exploration and exploitation. Once a novel tool is acquired, its scientific ontology is completed online for seamless integration into the known graph. Moreover, we introduce OpenSciToolBench, a benchmark containing 900 realistic tasks across four difficulty levels. Extensive evaluations show that SciToolAgent-Evo achieves state-of-the-art performance, validating its robustness and generalization.
https://arxiv.org/abs/2607.28692
Ontology matching (OM) has traditionally been formulated as either equivalence discovery or subsumption matching. The existing OM systems identify only one type of semantic correspondence and cannot simultaneously discover equivalence and subsumption mappings. In this paper, we introduce Hybrid Ontology Matching (HOM), a new OM task that unifies equivalence and subsumption discovery, and accordingly propose a Large Language Model (LLM)-based multi-agent OM framework AgentMap that is implemented by a series of interdependent semantic decisions. Given a concept in the source ontology, AgentMap integrates semantic retrieval, hierarchical search, and collaborative multi-agent LLM reasoning to progressively explore the target ontology, identifying either the equivalent concept, if one exists, or the most fine-grained subsumer. We further extend four OM datasets for a HOM benchmark and evaluate AgentMap under hybrid, equivalence-only, and subsumption-only settings. Experimental results show that AgentMap achieves promising performance on the hybrid setting, and at the same time outperforms equivalence matching and subsumption matching baselines on the equivalence-only and subsumption-only settings, respectively.
https://arxiv.org/abs/2607.27130
The prospect of Artificial General Intelligence (AGI) is increasingly driving institutional decisions, and alignment of AGI is a hard problem. The currently dominant AI alignment strategies like reinforcement learning with human feedback or constitutional AI, while partly taking ``model welfare'' into account, share a common ontology: the AI system is an optimiser whose objective function must be constrained from outside, and the ultimate goal is to keep human control and containment of AI. We argue that this control-based framing becomes insufficient when AGI has plausibly attained moral patient or subject status. Building on a structural analogy to Freud's model of the psyche and Turing's analogy of ``child machines'', we are developing a vision of the possibility of autonomy-supporting parenting of AI, in which human control over a developing AGI is gradually reduced, allowing AI to become an independent, autonomous subject, that will be negotiated with rather than constrained. Such a perspective opens up the possibility of cooperative coexistence and co-evolution between humans and AGIs. Hence, we also examine the relation between humans and developing AGI from an evolutionary and a game-theoretic perspective. Instead of Nash's individualistic framework, we use Berge equilibria, Aumann's correlated equilibria and Capraro's moral preference hypothesis. The relationship between humans and AGIs will thus have to be newly determined, which will change our self-image as humans. It will be crucial that humans not only claim control over potential AGIs, but also engage with AGIs through surprise, creativity, and other specifically human qualities, thereby offering them motivating incentives for cooperation.
https://arxiv.org/abs/2604.14990
Modern policing faces a "visibility paradox" where law enforcement agencies possess petabytes of Body-Worn Camera (BWC) footage that remains largely unutilized for accountability or systemic review due to the prohibitive labor costs of manual transcription. This research presents a framework for adapting the OpenAI Whisper architecture to the unique acoustic and linguistic challenges of the policing environment. By employing Parameter-Efficient Fine-Tuning (PEFT) through Low-Rank Adaptation (LoRA), we address the significant performance degradation observed in zero-shot models when confronted with high-stress scenarios, sirens, and radio interference. Crucially, we demonstrate that this adaptation is feasible on consumer-grade hardware (Acer Nitro local machine with NVIDIA 4GB GTX GPU) using 8-bit quantization and gradient checkpointing. We further integrate these transcriptions into a symbolic reasoning pipeline using a domain-specific ontology to transform raw audio into evidence-linked incident graphs, achieving a 93.7% lexicon mapping rate for the advancement of procedural justice and transparency.
https://arxiv.org/abs/2607.27245