Large Language Models (LLMs) exhibit representational and syntactic biases that are difficult to evaluate due to the stochastic nature of text generation. Standard auditing methods rely on a single output inspection or static automated metrics. These approaches obscure the underlying probability distributions and fail to capture biases hidden in lower-probability generation branches. This paper introduces TreeTracer, a visual analytics tool designed to evaluate LLM bias through aggregated comparison. Using a systematic perturbation analysis pipeline, the tool replaces ontology-defined terms in each input prompt, aggregates hundreds of stochastic generations into a syntax-aligned hierarchical structure, and then performs classification-aware node merging with an auxiliary language model. The resulting structure is visualized through a custom Sankey diagram. By juxtaposing two ontology-driven trees, the workspace enables direct comparison between semantic contexts and supports systematic bias detection. Because any visualization reflects only a subset of the model's learned behavior, the system further applies contrastive inference to compute and directly display counterfactual token probabilities across contexts, reducing the risk of misinterpreting the presence of bias. We validate the workspace through case studies comparing an unaligned baseline model GPT-2 XL against the constitutionally aligned Apertus models. The visual aggregation successfully exposes hidden representational harms, such as counterfactual pronoun suppression and conversational marginalization of individuals. A preliminary user study confirms that the aggregated comparative interface reduces cognitive load and effectively supports analysts in detecting systemic biases.
https://arxiv.org/abs/2606.19344
We consider the following fundamental problem: given a database D, Boolean conjunctive query (CQ) q, and fact f in D, decide whether f is relevant to q wrt. D, i.e., does f belong to a minimal subset S of D such that S |= q. Despite being of central importance to query answer explanation, the combined complexity of deciding query relevance has not been studied in detail, leaving open what makes this problem hard, and which restrictions can yield lower complexity. Relevance has already been shown to be harder than query evaluation: namely, $\Sigma^p_2$-complete for CQs, even over a binary signature. We further observe that NP-hardness applies already to (acyclic) chain CQs. Our work identifies self-joins (multiple atoms with the same relation) as the culprit. Indeed, we prove that if we forbid or bound the occurrence of self-joins, then relevance has the same complexity as query evaluation, namely, NP (without structural restrictions) and LogCFL (for bounded hypertreewidth classes). In the ontology setting, we establish an analogous result for ontology-mediated queries consisting of a CQ and DL-Lite_R ontology, namely that relevance is no harder than query answering provided that we bound the interaction width (which generalizes both self-join width and a recently introduced 'interaction-free' condition). Our results thus pinpoint what makes relevance harder than query evaluation and identify natural classes of queries which admit efficient relevance computation.
https://arxiv.org/abs/2604.22422
Time introduces fundamental challenges in model development and deployment: models are usually trained on historical data while deployed on future data where semantic distributions and domain knowledge may evolve. Unfortunately, existing studies either overlook temporal shifts or hardly capture rich shifting patterns of both semantic and knowledge. We develop Knowledge-driven Augmentation and Retrieval for Integrative Temporal Adaptation (KARITA) to capture diverse temporal shifts (e.g., uncertainty and feature shift), construct and integrate rich knowledge sources (e.g., medical ontology like MeSH), and leverage shifting insights for selecting-retrieval augmented learning. We evaluate KARITA on classification tasks across multiple domains, clinical, legal, and scientific corpora, demonstrating consistent improvements across multiple domains with temporal adaptation. Our results show that knowledge integration can be more critical and effective in temporal augmentation and learning.
https://arxiv.org/abs/2604.22098
Biomedical findings often seem to conflict across studies, but many of these differences are context-dependent rather than true contradictions. Variations in cohort, geography, assay protocol, disease subtype, and clinical setting can make both claims locally valid. Existing NLI and scientific claim-verification benchmarks reduce such cases to entailment, contradiction, or neutral, failing to capture the contextual structure behind divergence. To address this, we introduce BioDivergence, an evaluation framework with a six-class conflict taxonomy, a 13-axis divergence ontology, and four structured outputs per claim pair: conflict type, divergence axes, dominant confounder, and reconciliation explanation. We release BioDivergence-Silver-v1.0, an article-disjoint silver benchmark of 11,865 claim pairs across five biomedical domains, alongside a legacy deduplicated variant for comparison. Results show notable ranking differences between the two variants, with the fine-tuned reference model dropping about 12 points under the article-disjoint setting, while Mistral-7B-Instruct-v0.3 achieves 0.5523 accuracy and 0.3894 contextual-F1 on the 842-example primary test set. BioDivergence offers a more faithful way to distinguish contextual divergence from direct contradiction and to separate article-level memorization from genuine task learning.
https://arxiv.org/abs/2606.11208
Electronic health record (EHR) question answering is often handled by LLM-based pipelines that are costly to deploy and do not explicitly leverage the hierarchical structure of clinical data. Motivated by evidence that medical ontologies and patient trajectories exhibit hyperbolic geometry, we propose HypEHR, a compact Lorentzian model that embeds codes, visits, and questions in hyperbolic space and answers queries via geometry-consistent cross-attention with type-specific pointer heads. HypEHR is pretrained with next-visit diagnosis prediction and hierarchy-aware regularization to align representations with the ICD ontology. On two MIMIC-IV-based EHR-QA benchmarks, HypEHR approaches LLM-based methods while using far fewer parameters. Our code is publicly available at this https URL.
https://arxiv.org/abs/2604.21027
This paper presents a hybrid architecture for intelligent systems in which large language models (LLMs) are extended with an external ontological memory layer. Instead of relying solely on parametric knowledge and vector-based retrieval (RAG), the proposed approach constructs and maintains a structured knowledge graph using RDF/OWL representations, enabling persistent, verifiable, and semantically grounded reasoning. The core contribution is an automated pipeline for ontology construction from heterogeneous data sources, including documents, APIs, and dialogue logs. The system performs entity recognition, relation extraction, normalization, and triple generation, followed by validation using SHACL and OWL constraints, and continuous graph updates. During inference, LLMs operate over a combined context that integrates vector-based retrieval with graph-based reasoning and external tool interaction. Experimental observations on planning tasks, including the Tower of Hanoi benchmark, indicate that ontology augmentation improves performance in multi-step reasoning scenarios compared to baseline LLM systems. In addition, the ontology layer enables formal validation of generated outputs, transforming the system into a generation-verification-correction pipeline. The proposed architecture addresses key limitations of current LLM-based systems, including lack of long-term memory, weak structural understanding, and limited reasoning capabilities. It provides a foundation for building agent-based systems, robotics applications, and enterprise AI solutions that require persistent knowledge, explainability, and reliable decision-making.
https://arxiv.org/abs/2604.20795
Persistent memory is the bottleneck separating stateless chatbots from long-running agentic systems. Retrieval-augmented generation (RAG) over flat vector stores fragments facts into chunks, loses cross-session identity, and has no first-class notion of supersession or contradiction. Recent bitemporal knowledge-graph systems (Graphiti, Memento, Hydra DB) add typed edges and valid-time metadata, but the graph itself remains flat: no recursive composition, no content-addressed invariants on nodes, and edge types carry no behavior beyond a label. We present WorldDB, a memory engine built on three commitments: (i) every node is a world -- a container with its own interior subgraph, ontology scope, and composed embedding, recursive to arbitrary depth; (ii) nodes are content-addressed and immutable, so any edit produces a new hash at the node and every ancestor, giving a Merkle-style audit trail for free; (iii) edges are write-time programs -- each edge type ships on_insert/on_delete/on_query_rewrite handlers (supersession closes validity, contradicts preserves both sides, same_as stages a merge proposal), so no raw append path exists. On LongMemEval-s (500 questions, ~115k-token conversational stacks), WorldDB with Claude Opus 4.7 as answerer achieves 96.40% overall / 97.11% task-averaged accuracy, a +5.61pp improvement over the previously reported Hydra DB state-of-the-art (90.79%) and +11.20pp over Supermemory (85.20%), with perfect single-session-assistant recall and robust performance on temporal reasoning (96.24%), knowledge update (98.72%), and preference synthesis (96.67%). Ablations show that the engine's graph layer -- resolver-unified entities and typed refers_to edges -- contributes +7.0pp task-averaged independently of the underlying answerer.
https://arxiv.org/abs/2604.18478
Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often display inaccuracies, while the comparative performance of specialized biomedical LLMs in this domain remains unknown. Methods: This study evaluated general-purpose LLMs (GPT-4o and DeepSeek-R1) versus biomedically fine-tuned LLMs (QuantFactory/Bio-Medical-Llama-3-8B-GGUF and Irathernotsay/qwen2-1.5B-medical_qa-Finetune) using 46 protocols (2018-2024) from the HMA-EMA Catalogue and Sentinel System. Performance was assessed across relevance, logic of justification, and ontology-code agreement across multiple coding systems using Least-to-Most (LTM) and Active Prompting strategies. Results: GPT-4o and DeepSeek-R1 paired with LTM prompting achieved the highest relevance and logic of justification scores, with GPT-4o-LTM reaching a median relevance score of 4 in 8 of 9 questions for HMA-EMA protocols. Biomedical LLMs showed lower relevance overall and frequently generated insufficient justification. All LLMs demonstrated limited proficiency in ontology-code mapping, although LTM provided the most consistent improvements in reasoning stability. Conclusion: Off-the-shelf general-purpose LLMs currently offer superior support for pharmacoepidemiologic design compared to biomedical LLMs. Prompt strategy strongly influenced LLM performance.
https://arxiv.org/abs/2604.17988
This article examines the enduring epistemic and methodological crisis of traditional legal practice in light of the opportunities and constraints introduced by artificial intelligence. It proposes an ontologically grounded framework termed the Mecellem semantic protocol as a response to this crisis. The analysis focuses on the structural tension within law between maintaining normative coherence and adapting to evolving social and institutional conditions, and shows why approaches based solely on codification, positivist systematization, or quantitative methods such as jurimetrics are insufficient. The article argues that legal reasoning cannot be reduced to data retrieval or statistical pattern recognition. Instead, it is grounded in the premise that meaning is context-dependent and must be dynamically reconstructed through ontologically defined entity categories and differentiated layers of knowledge. Within this perspective, Mecellem reconceptualizes law not as a fixed system of rules, but as an ontodynamic architecture structured along the interconnected axes of ontology, epistemology, and methodology. The transition from jurimetrics to a semantic protocol is presented not merely as a technical shift, but as a transformation in the foundations of legal knowledge. The article further argues that neurosymbolic systems, knowledge graphs, and agentic artificial intelligence can effectively address persistent legal challenges only when embedded within such an ontodynamic framework. By understanding law as a domain of ongoing formation rather than a completed rational totality, Mecellem advances a context-sensitive, auditable, and coherent model for legal meaning production at both human and machine levels, offering a comprehensive framework for rethinking legal reasoning in the age of artificial intelligence.
https://arxiv.org/abs/2608.04011
Skills are a natural unit for describing what a language model can do and how its behavior can be changed. However, existing characterizations rely on human-written taxonomies, textual descriptions, or manual profiling pipelines--all external hypotheses about what matters that need not align with the model's internal representations. We argue that when the goal is to intervene on model behavior, skill characterization should be *model-native*: grounded in the model's own representations rather than imposed through external ontologies. We instantiate this view by recovering a compact orthogonal basis from sequence-level activations. The resulting basis is semantically interpretable but need not correspond to any predefined human ontology; instead, it captures axes of behavioral variation that the model itself organizes around. We validate this characterization on reasoning post-training, using the recovered basis for both SFT data selection and inference-time steering. We develop lightweight proxy interventions to identify which directions are most useful for a given model. Across Llama3-8B and Qwen2.5-3B, selecting data along those directions improves Pass@1 by up to 20% on MATH and 41% on AMC, outperforming data selection based on human-characterized skills. Because the basis lives in activation space, the same directions also serve as steering vectors at inference time, improving Pass@8 by up to 4.8% on MATH--an intervention that human-characterized skills cannot support. We further validate the characterization on safety alignment, where selecting adversarial training data for model-native skill coverage rather than textual diversity yields more sample-efficient learning. These results suggest that recovering skills from the model's own representations, rather than imposing them externally, provides a more effective foundation for intervening on model behavior. Codes are open-sourced.
https://arxiv.org/abs/2604.17614
Current agent evaluations largely reward execution on fully specified tasks, while recent work studies clarification [11, 22, 2], capability awareness [9, 1], abstention [8, 14], and search termination [20, 5] mostly in isolation. This leaves open whether agents can diagnose why a task is blocked before acting. We introduce the Support-State Triage Audit (SSTA-32), a matched-item diagnostic framework in which minimal counterfactual edits flip the same base request across four support states: Complete (ANSWER), Clarifiable (CLARIFY), Support-Blocked (REQUEST SUPPORT), and Unsupported-Now (ABSTAIN). We evaluate a frontier model under four prompting conditions - Direct, Action-Only, Confidence-Only, and a typed Preflight Support Check (PSC) - using Dual-Persona Auto-Auditing (DPAA) with deterministic heuristic scoring. Default execution overcommits heavily on non-complete tasks (41.7% overcommitment rate). Scalar confidence mapping avoids overcommitment but collapses the three-way deferral space (58.3% typed deferral accuracy). Conversely, both Action-Only and PSC achieve 91.7% typed deferral accuracy by surfacing the categorical ontology in the prompt. Targeted ablations confirm that removing the support-sufficiency dimension selectively degrades REQUEST SUPPORT accuracy, while removing the evidence-sufficiency dimension triggers systematic overcommitment on unsupported items. Because DPAA operates within a single context window, these results represent upper-bound capability estimates; nonetheless, the structural findings indicate that frontier models possess strong latent triage capabilities that require explicit categorical decision paths to activate safely.
https://arxiv.org/abs/2604.16752
We present a framework for evaluating adaptive personalization of educational reading materials with theory-grounded simulated learners. The system builds a learning-objective and knowledge-component ontology from open textbooks, curates it in a browser-based Ontology Atlas, labels textbook chunks with ontology entities, and generates aligned reading-assessment pairs. Simulated readers learn from passages through a Construction-Integration-inspired memory model with DIME-style reader factors, KREC-style misconception revision, and an open New Dale-Chall readability signal. Answers are produced by score-based option selection over the learner's explicit memory state, while BKT drives adaptation. Across three sampled subject ontologies and matched cohorts of 50 simulated learners per condition, adaptive reading significantly improved outcomes in computer science, yielded smaller positive but inconclusive gains in inorganic chemistry, and was neutral to slightly negative in general biology.
https://arxiv.org/abs/2604.16744
In active learning, membership queries (MQs) allow a learner to pose questions to a teacher, such as ''Is every apple a fruit?'', to which the teacher responds correctly with yes or no. These MQs can be viewed as subsumption tests with respect to the target ontology. Inspired by the standard reduction of subsumption to satisfiability in description logics, we reformulate each candidate axiom into its corresponding counter-concept and verbalise it in controlled natural language before presenting it to Large Language Models (LLMs). We introduce LLMs as a third component that provides real-world examples approximating an instance of the counter-concept. This design property ensures that only Type II errors may occur in ontology modelling; in the worst case, these errors merely delay the construction process without introducing inconsistencies. Experimental results on 13 commercial LLMs show that recall, corresponding to Type II errors in our framework, remains stable across several well-established ontologies.
https://arxiv.org/abs/2604.16672
Competency Questions (CQs) are a cornerstone of requirement elicitation in ontology engineering. CQs represent requirements as a set of natural language questions that an ontology should satisfy; they are traditionally modelled by ontology engineers together with domain experts as part of a human-centred, manual elicitation process. The use of Generative AI automates CQ creation at scale, therefore democratising the process of generation, widening stakeholder engagement, and ultimately broadening access to ontology engineering. However, given the large and heterogeneous landscape of LLMs, varying in dimensions such as parameter scale, task and domain specialisation, and accessibility, it is crucial to characterise and understand the intrinsic, observable properties of the CQs they produce (e.g., readability, structural complexity) through a systematic, cross-domain analysis. This paper introduces a set of quantitative measures for the systematic comparison of CQs across multiple dimensions. Using CQs generated from well defined use cases and scenarios, we identify their salient properties, including readability, relevance with respect to the input text and structural complexity of the generated questions. We conduct our experiments over a set of use cases and requirements using a range of LLMs, including both open (KimiK2-1T, LLama3.1-8B, LLama3.2-3B) and closed models (Gemini 2.5 Pro, GPT 4.1). Our analysis demonstrates that LLM performance reflects distinct generation profiles shaped by the use case.
https://arxiv.org/abs/2604.16258
In November 2025, the Government of Canada operationalized its commitment to transparency by releasing its first Federal AI Register. In this paper, we argue that such registers are not neutral mirrors of government activity, but active instruments of ontological design that configure the boundaries of accountability. We analyzed the Register's complete dataset of 409 systems using the Algorithmic Decision-Making Adapted for the Public Sector (ADMAPS) framework, combining quantitative mapping with deductive qualitative coding. Our findings reveal a sharp divergence between the rhetoric of "sovereign AI" and the reality of bureaucratic practice: while 86\% of systems are deployed internally for efficiency, the Register systematically obscures the human discretion, training, and uncertainty management required to operate them. By privileging technical descriptions over sociotechnical context, the Register constructs an ontology of AI as "reliable tooling" rather than "contestable decision-making." We conclude that without a shift in design, such transparency artifacts risk automating accountability into a performative compliance exercise, offering visibility without contestability.
https://arxiv.org/abs/2604.15514
Which tasks inside an enterprise workflow can a large-language-model agent reliably handle, and under what conditions? Most business process modeling frameworks still answer this at the activity level, even though a single activity can bundle work of radically different difficulty. This paper takes the analysis a step smaller. We describe two design artifacts developed in a financial-services IT setting: T-IPO, which represents each task as an eight-element tuple, and LARA (LLM Agent Readiness Assessment), a five-dimension rubric that scores a task's readiness for agent substitution. Compliance Sensitivity carries $1.5\times$ weight, a value we fixed through a three-round Delphi study and cross-checked with AHP. The rubric produces four levels, L1 to L4, and applies a floor rule so that a task with maximum compliance load cannot be classified below L3 no matter what the other scores say. Both artifacts sit inside a larger methodology (PARTIS) that we map onto BWW ontology in Section 3. We evaluate the instruments across 127 tasks. Inter-rater agreement reaches Fleiss' $\kappa = 0.80$; a replication at three further institutions returns $\kappa = 0.73$. A controlled comparison against activity-level assessment suggests, though does not prove, an improvement in predictive utility at the task level. Pilot deployment of 120 task instances confirms that auto-completion decays monotonically from $95\%$ at L1 through about $70\%$ at L2 to about $40\%$ at L3. Exploratory factor analysis points to a two-factor structure: task readiness seems to be determined jointly by cognitive-execution complexity and governance-compliance intensity. We close with a recalibration procedure (LARA-TCA) so the rubric can keep pace with evolving LLM capabilities.
https://arxiv.org/abs/2605.16297
Large language models still struggle with reliable long-term conversational memory: simply enlarging context windows or applying naive retrieval often introduces noise and destabilizes responses. We present APEX-MEM, a conversational memory system that combines three key innovations: (1) a property graph which uses domain-agnostic ontology to structure conversations as temporally grounded events in an entity-centric framework, (2) append-only storage that preserves the full temporal evolution of information, and (3) a multi-tool retrieval agent that understands and resolves conflicting or evolving information at query time, producing a compact and contextually relevant memory summary. This retrieval-time resolution preserves the full interaction history while suppressing irrelevant details. APEX-MEM achieves 88.88% accuracy on LOCOMO's Question Answering task and 86.2% on LongMemEval, outperforming state-of-the-art session-aware approaches and demonstrating that structured property graphs enable more temporally coherent long-term conversational reasoning.
https://arxiv.org/abs/2604.14362
Large Language Models (LLMs) and Vision-Language Models (VLMs) increasingly generate indoor scenes through intermediate structures such as layouts and scene graphs, yet evaluation still relies on LLM or VLM judges that score rendered views, making judgments sensitive to viewpoint, prompt phrasing, and hallucination. When the evaluator is unstable, it becomes difficult to determine whether a model has produced a spatially plausible scene or whether the output score reflects the choice of viewpoint, rendering, or prompt. We introduce SceneCritic, a symbolic evaluator for floor-plan-level layouts. SceneCritic's constraints are grounded in SceneOnto, a structured spatial ontology we construct by aggregating indoor scene priors from 3D-FRONT, ScanNet, and Visual Genome. SceneOnto traverses this ontology to jointly verify semantic, orientation, and geometric coherence across object relationships, providing object-level and relationship-level assessments that identify specific violations and successful placements. Furthermore, we pair SceneCritic with an iterative refinement test bed that probes how models build and revise spatial structure under different critic modalities: a rule-based critic using collision constraints as feedback, an LLM critic operating on the layout as text, and a VLM critic operating on rendered observations. Through extensive experiments, we show that (a) SceneCritic aligns substantially better with human judgments than VLM-based evaluators, (b) text-only LLMs can outperform VLMs on semantic layout quality, and (c) image-based VLM refinement is the most effective critic modality for semantic and orientation correction.
https://arxiv.org/abs/2604.13035
The Semantic Web standardizes concept meaning for humans and machines, enabling machine-operable content and consistent interpretation that improves advanced analytics. Reusing ontologies speeds development and enforces consistency, yet selecting the optimal choice is challenging because authors lack systematic selection criteria and often rely on intuition that is difficult to justify, limiting reuse. To solve this, WiseOWL is proposed, a methodology with scoring and guidance to select ontologies for reuse. It scores four metrics: (i) Well-Described, measuring documentation coverage; (ii) Well-Defined, using state-of-the-art embeddings to assess label-definition alignment; (iii) Connection, capturing structural interconnectedness; and (iv) Hierarchical Breadth, reflecting hierarchical balance. WiseOWL outputs normalized 0-10 scores with actionable feedback. Implemented as a Streamlit app, it ingests OWL format, converts to RDF Turtle, and provides interactive visualizations. Evaluation across six ontologies, including the Plant Ontology (PO), Gene Ontology (GO), Semanticscience Integrated Ontology (SIO), Food Ontology (FoodON), Dublin Core (DC), and GoodRelations, demonstrates promising effectiveness.
https://arxiv.org/abs/2604.12025
While the shortage of explicit action data limits Vision-Language-Action (VLA) models, human action videos offer a scalable yet unlabeled data source. A critical challenge in utilizing large-scale human video datasets lies in transforming visual signals into ontology-independent representations, known as latent actions. However, the capacity of latent action representation to derive robust control from visual observations has yet to be rigorously evaluated. We introduce the Latent Action Representation Yielding (LARY) Benchmark, a unified framework for evaluating latent action representations on both high-level semantic actions (what to do) and low-level robotic control (how to do). The comprehensively curated dataset encompasses over one million videos (1,000 hours) spanning 151 action categories, alongside 620K image pairs and 595K motion trajectories across diverse embodiments and environments. Our experiments reveal two crucial insights: (i) General visual foundation models, trained without any action supervision, consistently outperform specialized embodied latent action models. (ii) Latent-based visual space is fundamentally better aligned to physical action space than pixel-based space. These results suggest that general visual representations inherently encode action-relevant knowledge for physical control, and that semantic-level abstraction serves as a fundamentally more effective pathway from vision to action than pixel-level reconstruction.
https://arxiv.org/abs/2604.11689