Ontology
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LLM-Assisted Ontology Engineering and Construction of a French Legal Knowledge Graph
2026-07-27 15:26:26G{\'e}nesis Montenegro (WIMMICS), Mokhtar Boumedyen Billami (WIMMICS), Catherine Faron (WIMMICS), Fabien Gandon (WIMMICS), Pierre Monnin (WIMMICS)Abstract
Maintenance regulations are complex legal texts that are difficult to exploit when addressing a specific case and challenging to integrate into operational systems. This paper presents a two-stage LLM-assisted workflow for French maintenance regulations: ontology engineering from a SEMLEG-based core ontology, followed by construction of an ontology-grounded French legal knowledge graph. The first stage consists in the open extraction of typed entities and triples from a stratified corpus sample, the normalization of labels through embedding-based fusion, and the induction of candidate object properties with their signature (domain and range). The second stage uses the resulting ontology to guide the closed extraction of triples and RDF graph construction over the full corpus. Experiments with GPT-4.1 and mistral-large-2512 show robust structured outputs, near-complete class alignment, and a substantial reduction of duplicated entities and predicates after fusion. Fewer than 20% of triples introduce unseen properties, while lower exact signature compliance reveals new domain-range combinations for existing predicates. These results point to predicate normalization and the validation of newly observed relation signatures as key refinement steps for industrial maintenance settings.
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URL
https://arxiv.org/abs/2607.24551
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GraphRareBench: An Auditable Graph-Evidence Benchmark for Phenotype-Driven Rare-Disease Diagnosis
2026-07-27 07:58:29Guiling Guo, Jia Yang, Jiahao Xu, Shuyuan Zheng, Zhonghai Sun, Qiyuan LiAbstract
Phenotype-driven diagnostic benchmarks usually report the rank of the reference disease, but they rarely reveal which plausible alternatives are ranked above it or what evidence a tool-using model examines before making its decision. We introduce GraphRareBench, a provenance-preserving benchmark containing 2,365 ontology-derived cases and 18,093 target-confounder pairs. Each case includes a coarsened HPO query, a fixed candidate pool, graph-defined hard confounders, and source-linked evidence records. On the 237-case gene-component-disjoint test split, supervised rankers using a shared 21-feature interface achieved MRRs ranging from 0.640 to 0.740 and case-averaged target-over-confounder accuracies ranging from 0.898 to 0.916. Agents instantiated with Agents-A1 and DeepSeek-V4-Flash achieved MRRs of 0.746 and 0.718, respectively. Their paired MRR difference was not statistically significant, whereas their target-evidence coverage differed by 0.561. Together with the observation that 22.1% to 43.7% of selected Hit@10 successes still ranked at least one graph-defined hard confounder above the target, these results indicate that full-pool retrieval, hard-confounder discrimination, and observable evidence access capture complementary aspects of model behavior. GraphRareBench therefore provides a foundation for more transparent and evidence-aware evaluation of phenotype-driven diagnostic systems. Code and data are available at this https URL.
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URL
https://arxiv.org/abs/2607.24878
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An Ontology for Machine Learning Interatomic Potentials
2026-07-25 14:16:09Daniel Hern\'andez, Jong Hyun Jung, Yuji Ikeda, Yongliang Ou, Pranav Kumar, Tom Sch\"achtel, Wenchuan Liu, Xin Li, Xi Zhang, Xiang Xu, Lifang Zhu, Fritz K\"ormann, Steffen Staab, Blazej GrabowskiAbstract
Machine learning interatomic potentials (MLIPs) approximate quantum-mechanical energies and forces---conventionally computed by density functional theory (DFT) or wave-function methods---at a fraction of the cost. The field encompasses a growing ecosystem of algorithms, training datasets, hyperparameters, and target materials, yet the metadata needed to systematically compare, reproduce, and build upon MLIP studies remains scattered across papers, scripts, and ad-hoc file formats. We present the MLIPs ontology, an OWL 2 DL ontology that captures the concepts needed to describe MLIP methods, their hyperparameters, training datasets with DFT provenance, and published benchmarks. The ontology is organized into three modules---Method, Training Data, and Benchmark---and connects existing ontologies in materials science (MDO, CMSO/ASMO) and machine learning (ML-Schema), complementing dataset-side schemas such as Croissant. It declares 27 formal axioms enforcing data completeness and consistency, including property chains that link trained models to their methods and training data. We demonstrate the ontology through a running example based on Moment Tensor Potentials and evaluate it through competency-question execution on a 20-paper seeded knowledge graph, OWL reasoning, and comparison with existing ontologies.
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https://arxiv.org/abs/2607.23219
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Toward Automated Detection of Documentation Inconsistencies in Electronic Health Records
2026-07-24 23:43:35Jian Lu, Panyu Chen, Miriam Treggiari, Robert Blessing, Danyang Zhuo, Chunhua Weng, William W. Stead, Anru R. ZhangAbstract
Objective: To characterize the kinds of internal documentation inconsistencies a general-domain large language model (LLM) can surface from real-world discharge summaries, and to identify recurring failure modes that limit reliability at scale. Materials and Methods: We applied a two-stage LLM pipeline---open-ended candidate identification (Gemini 2.5 Pro) followed by context-grounded verification (Gemini 2.5 Flash)---to 3,000 randomly sampled MIMIC-IV-Note discharge summaries. A subset of the pipeline output was then reviewed manually by clinical experts. Results: Our pipeline surfaced 3,460 candidate inconsistencies, affecting 69.7% of admissions. Representative examples spanned demographics, allergies, procedures, diagnoses, laboratory, medications, and care-planning domains, with direct implications for clinical reasoning or patient safety. Expert review also revealed recurring failure modes that arise when verification requires temporal reasoning, evolving-diagnosis context, or knowledge of outpatient-prescribing conventions the model does not natively possess. Discussion: Detection is highly context-dependent: many flagged pairs require anchoring each statement to its source section and clinical domain, then assessing whether the conflict reflects a true contradiction or missing context. We propose a graded ontology spanning strict contradiction and ambiguity, with a schema characterizing each flagged case by category, section, domain, and inconsistency axis. Conclusion: This formative study establishes a methodological foundation and conceptual framework to guide subsequent validated, large-scale EHR-inconsistency analysis.
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https://arxiv.org/abs/2607.22954
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From a Word-Level Dictionary to Sentence-Level Semantics: Multilingual Grievance Labelling with Contextual Models
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Grievance is one of the warning signs analysts look for when assessing threats of violence. It is increasingly measured at scale from online text, most often with word-level lexicons like the Grievance Dictionary that score by matching weighted terms. Such matching is a fast and transparent proxy, but it cannot resolve whether a term is asserted, quoted, negated, or condemned. These lexicons are also often evaluated on pools enriched with the very examples they retrieve, so a high score partly reflects agreement with the lexicon's own selection rule. Examining a five-language, 2{,}000-item evaluation pool, we find its halves separated almost perfectly by the lexicon itself: every item labeled ``random'' is in fact lexicon-negative, so the lexicon's apparent macro-AUROC of 0.686 collapses to a 0.500 floor fixed by construction. We keep the dictionary's 22-construct ontology but replace term matching with context-reading models, evaluated on a non-circular benchmark that separates unconditional-random, lexicon-positive, and lexicon-negative strata across five languages. Reading the full post rather than the target sentence alone helps most where the lexicon is silent, raising average precision on lexicon-negative text from 0.14 to 0.20, with the largest gains on quoted, implicit, and cross-sentence grievance. Together, these results show that grievance is measured more faithfully by reading the surrounding context, and more honestly when tested on text the lexicon did not select. We release our code and benchmark at this https URL.
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URL
https://arxiv.org/abs/2607.20946
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An Ontology-Guided, Deduplication-Aware Extraction Layer for Knowledge Graph Construction from Heterogeneous Documents
2026-07-22 09:45:26Vaibhav Dangaich, Kevin Lewis, Kundeshwar PundalikAbstract
Large language models extract entities and relationships from unstructured documents fluently but inconsistently: type vocabularies fracture across documents, the same person surfaces under several name variants, relationships duplicate, and distinct individuals who share a name risk silent conflation. This paper presents the design, implementation, and empirical refinement of a production extraction layer that converts a live document stream into a validated knowledge graph aligned to a formal ontology. The system consumes document metadata from Kafka, routes PDF, spreadsheet, Office, and image content through handlers built for each format, and extracts entities and relationships in two passes using a locally hosted Qwen3.5-9B model tuned on the ontology. Its distinguishing component is ontology-guided extraction: the relevant slice of a curated ontology is retrieved live from a graph database by embedding similarity and injected into the extraction prompt, reducing catalog overhead by about 94 percent relative to static domain slices. Extracted results then pass through a refinement pipeline of five stages: deterministic cleaning, merging across chunks, a second pass for relationships, six deduplication algorithms that require no model inference, and an embedding resolution subsystem whose conflict guard no similarity score can override. Evaluation on intelligence corpora improved search recall from roughly 70 to 95 percent with no false merges, and corrected seven classes of silent quality defect, ranging from a bug that truncated source text by a single character to the systematic duplication of entities that carried title prefixes.
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URL
https://arxiv.org/abs/2607.28662
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Skillware: A Software Ontology and Engineering Lifecycle for Persistent Behavioral Artifacts
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Agent Skills have become persistent behavioral artifacts across independent AI agent systems. They combine natural-language task specifications with metadata and optional references, scripts, assets, hooks, package manifests, tests, and companion interfaces. Existing studies explain how Skills are specified, executed, maintained, and evolved, but lack an ontology that defines these artifacts as independent software objects. This paper introduces Skillware as the software abstraction that extends software engineering to persistent Behavioral Artifacts in agent systems. A Skill Artifact specifies reusable task behavior; a Skillware Unit manages that artifact as software through an independent identity and lifecycle. A compatible Agent Host activates the unit for runtime interpretation. Three necessary conditions operationalize category membership: behavioral primacy, independent software identity, and an Agent Host execution relationship. Lifecycle Continuity records whether the same unit identity persists through update, maintenance, rollback, and removal as a separate software-grade property. Evidence combines the Agent Skills specification, a frozen corpus of 138,133 content-deduplicated this http URL records associated with 20,556 repository identifiers, independent empirical studies, 15 category-boundary cases, and 13 fixed-revision engineering implementations. The evidence establishes a recurring artifact envelope, separable software identities, compatible execution paths, and lifecycle engineering pressure. Skillware provides the software ontology and engineering lifecycle through which agent capabilities can become identifiable, composable, maintainable, and evolvable software artifacts.
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URL
https://arxiv.org/abs/2607.18970
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OntoBook: Ontology-Grounded Synthetic Textbooks for Medical Encoder Pretraining
2026-07-21 10:11:10Rian Touchent (ALMAnaCH), \'Eric de la Clergerie (ALMAnaCH)Abstract
We present OntoBook, a method that converts medical ontology structure into pretraining signal for encoder language models. Our approach has three stages: random walks through ontology graphs capture hierarchical and causal relations between medical codes, a large language model reformulates these walks into fluent textbook-style prose, and the resulting text is used to train ModernCamemBERT, a 149M-parameter French encoder, with two objectives on the same data: masked language modeling and relation prediction between code pairs. On three French medical coding benchmarks (FRACCO, Cantemist-FR, Distemist-FR), OntoBook achieves significant improvements over MLM-only pretraining, with +2.5 micro-F1 on FRACCO and +8.0 micro-F1 on Distemist. We find that alignment between objectives is necessary: misaligned training, where each task uses different data, causes a 30-point degradation. We release 1.3 million LLM-reformulated medical textbooks across three French ontologies (CIM-10, CCAM, ATC) and pretrained model checkpoints.
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https://arxiv.org/abs/2607.18927
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Temporal-Causal Unity as an Operational Framework for Collective Dynamics: Causal-Progress Clocks, Synchronization, and Polarization
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This paper develops temporal-causal unity (TCU), a framework connecting a process-philosophical thesis -- time is the ordered unfolding of causal change -- to an operational model of cognitive and social dynamics. The framework deliberately separates three claims: an interpretive thesis about becoming, a measurable causal-progress coordinate, and a stochastic network model. Causal progress is defined by $\tau(t)=\int_0^t\lambda(s\mid\mathcal H_s)\,{\rm d}s$, where the nonnegative event intensity $\lambda$ must be specified independently of the outcome. Agents carry an orientation phase and an activation amplitude; weighted interaction, heterogeneous drift, external input, anchoring, and diffusion govern their evolution in $\tau$. First- and second-harmonic order parameters separate consensus from bipolar polarization. For the all-to-all noisy Kuramoto special case with Lorentzian drift width $\Delta$, synchronization begins at the conditional threshold $K_c = 2(\Delta + D)$, not at a universal constant. Reproducible numerical illustrations illustrate (not empirically demonstrate) this threshold, causal-clock curve collapse, and the consensus-polarization distinction. Six historical episodes are treated as scope probes rather than validation data. The paper derives falsifiable hypotheses and an out-of-sample protocol for comparing causal-progress and chronological-time models. TCU is therefore offered as a disciplined bridge between process ontology and complex-systems modeling, not as a replacement for spacetime physics or as an empirically established identity between time and causation.
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https://arxiv.org/abs/2607.18620
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Natural Language Access to Domain-Specific Metadata: A Reusable Framework for LLM Query Generation
2026-07-20 14:59:33Blake G. Fitch, Cato Elia KurtzAbstract
Researchers need to answer ad-hoc questions about the contents of domain-specific archives but often lack the expertise to write structured queries on the metadata. We show that when domain vocabulary and semantics are captured in a well-designed Web Ontology Language (OWL) ontology, Large Language Models (LLMs) can generate accurate structured queries zero-shot, without fine-tuning, retrieval augmentation, or multi-agent orchestration. We present the Natural Language Knowledge Graph Query (NLKGQ) system, a framework and development process that enables natural language access to metadata in such archives. The framework includes a web interface that helps researchers pose natural language questions, which a domain-agnostic harness translates to SPARQL via an LLM and executes against a knowledge graph. The development process begins with capturing domain vocabulary and semantics in a formal OWL ontology. Domain-specific code then extracts metadata from archive sources and imports it into a knowledge graph defined by the ontology. Both are designed for reuse across domains. We demonstrate the system on metadata derived from a large-scale neuroimaging research archive, evaluating multiple LLMs and ontology representations. The best configurations achieve 100% accuracy on a competence and regression question set developed with domain experts. An ablation study across eight ontology representations reveals that readable entity names and semantic annotations are the dominant factors in accuracy, more significant than model choice or prompt engineering. We also compare SPARQL to an auto-generated SQL database as query backends, showing that OWL's structural features provide a substantial advantage over SQL DDL for LLM-driven query generation. Our demonstration domain also requires local LLMs on modest institutional hardware to address privacy concerns for human subject data.
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URL
https://arxiv.org/abs/2607.18029
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OntoExtend: A Framework for Requirement-driven and Scalable Ontology Extension with LLMs
2026-07-20 14:04:01Anna Sofia Lippolis, Mohammad Javad Saeedizade, Stefan Schmid, Simon Blattner, Robin Keskis\"arkk\"a, Aldo Gangemi, Eva Blomqvist, Andrea Giovanni NuzzoleseAbstract
Ontology extension refers to the process of enriching an existing ontology in response to emerging requirements, making it more complete. This task is a resource-intensive and error-prone process. Large Language Models (LLMs) have shown promising performance on generating ontologies from scratch, but current approaches rarely tie ontology extension explicitly to requirements or reusable core models, and offer limited, systematic evaluation of LLM outputs. This paper introduces OntoExtend, a requirements-driven framework for ontology extension with LLMs. It uses retrieval-augmented generation (RAG) over relevant input ontologies and requirements in the form of competency questions to propose grounded extensions. We evaluate OntoExtend on 39 CQs from two use cases: a public EU-project ontology, Onto-DESIDE, and an industrial ontology from Bosch. The generated fragments show few structural issues, satisfy all functional evaluation tests, and are rated by ontology engineers as requiring minor to moderate revision before integration. These results suggest that OntoExtend is useful as a drafting assistant for requirement-driven ontology extension in real world scenarios, while remaining sensitive to CQ specificity and modelling profile.
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URL
https://arxiv.org/abs/2607.17963
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Benchmarking Resource-Efficient LLMs for Research Topic Ontology Generation in the Biomedical Field
2026-07-20 12:48:41Tanay Aggarwal, Angelo Salatino, Francesco Osborne, Enrico MottaAbstract
Knowledge Organization Systems like Ontologies and taxonomies are fundamental for structuring scientific knowledge, yet their manual curation presents a persistent bottleneck in knowledge management. While Large Language Models (LLMs) offer a scalable mechanism for automated ontology generation, their capacity to classify complex, domain-specific semantics requires systematic evaluation. In this paper, we assess the performance of five small, open-source LLMs (up to 9 billion parameters) in identifying semantic relationships between biomedical concepts. To support this evaluation, we introduce MeSH-Rel-4K, a dataset comprising 4K semantic relationships extracted from the Medical Subject Headings (MeSH). We analyse three adaptation strategies: standard prompting, Chain-of-Thought prompting, and fine-tuning. While parameter-constrained models traditionally struggle with the nuances of in-context logic, our results reveal that targeted fine-tuning increases the average F1-score by 34.1 percentage points. These results confirm that direct fine-tuning effectively exceeds the reasoning bottlenecks of smaller LLMs, providing an accurate, automated methodology for the construction and evolution of specialised biomedical ontologies.
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https://arxiv.org/abs/2607.17902
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An Explicit World Model Based on Data-First Ontology: DaoQL Multimodal Storage Validation and Counterfactual Reasoning Evaluation
2026-07-19 14:20:22Zhanbo Li, Shifeng Wu, Xiangjin Meng, Wenjie CaiAbstract
Large language models encode world models implicitly in neural weights, which exposes four structural risks in high-precision domains such as medicine and finance: hallucination, frozen knowledge, poor explainability, and poor modifiability. This paper proposes data-first ontology: LLMs are treated as reasoning and language engines, while deterministic knowledge is moved into an explicit multimodal database, DaoQL. We formalize an explicit world model and show that, under rule independence, deterministic evaluation, and fixed conflict resolution, explicit models provide a sufficient condition for composable counterfactual decomposability; implicit models lack atomic read/delta semantics and therefore provide no comparable architectural guarantee. The implemented system focuses on DaoQL's verified storage layer and explicit Eval path, integrating graph, column, vector, and full-text engines within one process. KVCache graph nodes, expert hot updates, and the DaoQL-Agent runtime remain future work. On an embedded same-machine setup, DaoQL reports graph BFS at 1.20 ms, HNSW at 83.1 us, and a Fluent hybrid query at 105.8 us; these results indicate engineering potential but must be interpreted with deployment-shape differences from client-server systems. Exploratory measurements on LDBC SNB SF1 and ANN-Benchmarks further show 34/34 query coverage with interactive-class queries mostly in the sub-millisecond to millisecond range, but only 1.8 QPS overall due to long-tail BI/IC queries; ANN-Benchmarks reaches Recall@10 >= 99% at thousand-level QPS after a bridge-edge protection fix. In a five-domain counterfactual experiment (n = 1250), DaoQL+GPT-4o achieves 94% composable counterfactual decomposability, 49 percentage points above GPT-4o alone. The paper explicitly separates provable structure, preliminary empirical evidence, and architectural roadmap claims.
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URL
https://arxiv.org/abs/2607.17269
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PriorProof: A Point-in-Time Measure of Technique Novelty for Formal Proofs
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Mathematicians distinguish proofs that explain, simplify, or introduce a nonstandard route, but these judgments are difficult to operationalize. We study a deliberately narrower construct: time-relative proof-route nonstandardness in formal mathematics. For a Lean theorem, PriorProof extracts the dependency footprint of its elaborated proof term and scores the weighted surprisal of that footprint under a retrieval-conditioned, hierarchically smoothed prior built only from an earlier quarterly snapshot of Mathlib. The method requires no hand-built technique ontology and no human labels: statement retrieval is learned from proof-derived contrastive pairs, while the scored object is read mechanically from proof terms. In a blinded topology study, 100 presentations collapse to 76 distinct underlying pairs: 12 canonical contrasts shown three times for consistency screening and 64 distinct stratified pairs. Against the majority of three retained domain raters, PriorProof agrees on 53/76 pairs (69.7%, Wilson 95% CI 58.7-78.9%), including 11/12 canonical pairs (91.7%, 64.6-98.5%) and 42/64 stratified pairs (65.6%, 53.4-76.1%). Score-gap quartiles are nonmonotone after repeat collapse; the endpoints are 12/19 (63.2%, 41.0-80.9%) in the smallest-gap bin and 16/19 (84.2%, 62.4-94.5%) in the largest, supporting an endpoint-calibration tendency rather than a resolved staircase. The best language-model condition agrees on 60/76 pairs (78.9%, 68.5-86.6%); on paired outcomes, PriorProof alone is correct on 8 pairs and the model alone on 15 (exact two-sided McNemar p = 0.210), so the difference is not established at this sample size. We therefore present PriorProof not as a replacement for expert or model judgment, but as a decomposable, time-anchored signal whose score gap provides an interpretable reliability indicator.
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URL
https://arxiv.org/abs/2607.16997
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NeurOWL: An LLM-Based Neural-symbolic Framework for Incomplete OWL Ontology Reasoning
2026-07-17 09:12:10Hui Yang, Jiaoyan Chen, Yiping Song, Renate Schmidt, Wen ZhangAbstract
OWL ontologies provide a formal knowledge representation framework that enables semantic reasoning, and have been widely adopted across domains such as healthcare and bioinformatics. In practice, however, real-world ontologies are often incomplete, which pose challenges for reasoning. In this work, we focus on a fundamental subsumption reasoning problem: given an incomplete ontology and a candidate (non-entailed) subsumption, determine whether the subsumption is semantically plausible and, if so, providing a logically sound explanation containing potential missing axioms. This task unifies subsumption verification with ontology abduction, and generalizes the latter by removing the need for a predefined candidate set of missing axioms. To address this subsumption reasoning problem, we propose NeurOWL, an end-to-end neuro-symbolic framework that jointly performs verification and abduction, leveraging both formally defined semantics and textual semantics through Large Language Models and ontology embeddings. We evaluate NeurOWL on real-world ontologies across multiple domains, demonstrating strong and robust performance across different domains.
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URL
https://arxiv.org/abs/2607.15776
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JEEVHITAA -- An HCAI Ecosystem to Support Collective Care
2026-07-16 07:37:48Shyama Sastha Krishnamoorthy Srinivasan, Harsh Pala, Mohan Kumar, Pushpendra SinghAbstract
Current mobile health platforms are predominantly individual-centric and lack the support for coordinated, auditable multi-actor workflows. However, in many settings worldwide, health decisions are enacted through multi-actor coordination rather than individual users. We present JEEVHITAA, a cross-platform mobile system enabling role-aware sharing and verifiable information flows within permissioned care circles. JEEVHITAA ingests platform and device data, builds layered profiles from sensors and tiered onboarding, and enforces fine-grained, time-bounded access control across care graphs. Data stays secure both within the application and the cloud. Integrated retrieval-augmented Large Language Models produce structured, role-targeted summaries and action plans, offer evidence-grounded verification with provenance and confidence scores, and support advanced insights on reports. We describe the architecture, connector abstractions, and security primitives, and report robustness evaluations using synthetic, ontology-driven data and findings from a feasibility study with real-life care circles across 9-14 weeks. We outline plans for larger multi-site evaluations focusing on operational alignment, longitudinal trust & literacy impact, and relational friction & efforts to sink into the daily infrastructure.
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URL
https://arxiv.org/abs/2512.06364
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Towards an Intention Abstraction Layer for Autonomous Industrial Systems
2026-07-16 04:31:20Artan Markaj, Raphael H\"ofer, Felix GehlhoffAbstract
Modern industrial environments increasingly run many autonomous subsystems at once - schedulers, energy managers, vehicle fleets - each pursuing its own goals while sharing the same physical resources. Because high-level human intentions are translated into low-level control logic and then discarded, no running component can tell whether it is still doing what was actually intended, and goal conflicts surface only after they have caused a missed target or a shutdown. We propose the Intention Abstraction Layer (IAL), a domainagnostic middleware that represents intentions as first-class, persistent, and explainable runtime objects: a large language model grounded in a formal OWL ontology parses naturallanguage goals into structured intentions, a consistency monitor detects conflicts at registration time, before execution, and a transparency module explains them in natural language. We report a first proof of concept in which two autonomous agents register conflicting production and energy intentions, and the IAL flags and explains the conflict before it reaches the execution layer. The result is a mechanism that shifts behavioral assurance for cooperating autonomous systems from post-hoc failure analysis to pre-execution, intention-level checking.
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URL
https://arxiv.org/abs/2607.14553
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FAIR GraphRAG: A Retrieval-Augmented Generation Approach for Semantic Data Analysis
2026-07-13 12:15:27Marlena Fl\"uh, Soo-Yon Kim, Carolin Victoria Schneider, Sandra GeislerAbstract
Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions. Graph-based RAG approaches, such as GraphRAG, enhance retrieval by capturing semantic relationships within knowledge graphs (KGs). While the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) are becoming prevalent for scientific data management, especially in complex domains such as medicine, existing RAG approaches lack a structured FAIRification of the underlying knowledge resources. This lack limits their potential for FAIR information retrieval in these domains. To address this gap, we introduce FAIR GraphRAG, a novel framework that integrates FAIR Digital Objects (FDOs) as the fundamental units of a graph-based retrieval system. Each graph node represents an FDO that incorporates core data, metadata, persistent identifiers, and semantic links. We leverage LLMs to support schema construction and automated extraction of content and metadata from data sources. The framework was co-designed by physicians and computer scientists to ensure technical and clinical relevance. We apply FAIR GraphRAG to a biomedical dataset in gastroenterology, demonstrating its applicability to RNA-sequencing data. Beyond ensuring adherence to the FAIR principles, FAIR GraphRAG significantly improves question answering accuracy, coverage, and explainability, particularly for complex queries involving metadata and ontology links. This work shows the feasibility of combining FAIR data practices with graph-based retrieval techniques. We see potential for applying our approach to other specialized fields such as education and business.
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https://arxiv.org/abs/2607.11464
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A Task-Centric Ontology and Deterministic Domain Rules as a Verifiable Core for AI-Assisted Chemistry Problem Solving
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Large language models can interpret natural-language chemistry questions, but their internal reasoning is difficult to inspect, constrain, and validate. This paper presents ChemOntoRule, a proof-of-concept symbolic core for AI-assisted school-level chemistry problem solving. The central design choice is task-centric ontology engineering: the ontology is constructed around the concepts, properties, relations, and executable procedures required by a defined collection of chemistry problems, rather than as a universal representation of chemistry. The implemented artifact combines a lightweight ontology serialized in JSON and RDF/Turtle with deterministic Python rules for electronic structure, periodic trends, oxidation states, oxide and hydride behavior, and related school-level reasoning patterns. A separate expert-coded fallback handles problem families not yet represented by general rules. The system was examined on 300 human-authored and manually validated chemistry problems. The complete system matched 296 of 300 reference answers (98.67%). The ontology-driven rule subset covered 269 problems and matched 266 references (98.88%); 31 problems were handled by task-specific expert-coded fallbacks, with 30 matches. Because the same collection informed ontology construction and evaluation, these results measure implemented coverage and internal consistency, not independent generalization. We analyze the four mismatches, distinguish structural validation from chemical correctness, and define a future architecture in which a language model acts primarily as a translator from user language into a normalized ontological task frame. Token efficiency is presented as a testable hypothesis for future controlled studies, not as a result of the current work.
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URL
https://arxiv.org/abs/2608.26164
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Ontology-Amplified Distillation and Contextuality Auditing for Sovereign Enterprise Language Models: A Combined Proof-of-Mechanism and Negative-Results Method Study
2026-07-11 15:42:40Thanh Luong TuanAbstract
Regulated financial institutions operating under data-residency rules need tenant-owned language models that can run inside the institution's perimeter. This paper combines two related FAOS studies into one mechanism-and-control article. First, it reports a reduced-power proof-of-mechanism study of ontology-amplified distillation: a Qwen3.6-27B student is adapted to the Foundation AgenticOS ontology through supervised fine-tuning on frontier-teacher trajectories and ontology-grounded direct preference optimization (DPO), trained locally on a single Apple M5 Max from 47 synthetic, English-language, cross-domain preference pairs. On 40 held-out Vietnamese financial-domain tasks, the distilled student grounds 36 of 40 tasks (grounded rate 0.90; mean ontology term-coverage r_onto = 0.95 on a metric floored at 0.50), equal to the GPT-5 frontier baseline, which also grounds 36 of 40. The outcome is underpowered to establish equivalence: the paired-difference 95% confidence interval spans +/-4 tasks, and the run does not test or show the pre-registered amplification prediction that the student should exceed the frontier. Second, the paper consolidates a contextuality-audit method for enterprise-agent routing. In a separate negative-results pilot, the corrected canonical Contextuality-by-Default degree is zero for all Phase 1.3 groups in both the local-Qwen run and an explicitly labeled Gemma replication check; the useful signal is direct influence and construct coupling, not surviving residual contextuality. Together, the studies pair an ontology-grounded model-building mechanism with a governance diagnostic for deciding when apparent disagreement should trigger prompt standardization, multi-agent synthesis, or human review. The evidence supports neither deployability, safety, superiority, statistical equivalence, nor a contextuality-positive routing rule.
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URL
https://arxiv.org/abs/2607.11948
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