Ontology
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Reconcile Once, Write Anytime: A Trust-Tiered Librarian and a Multi-Agent Writer for Drift-Free, Point-in-Time Research
2026-08-13 09:09:28Xing Zhang, Yanwei Cui, Guanghui Wang, Peiyang HeAbstract
Long-form research reports generated by large language models drift, contradict themselves, and lose provenance: the same metric appears with different values, and rumor is quoted as confidently as an audited filing. We present a two-tier agentic system that separates a maintained, point-in-time knowledge library from report writing. A deterministic "librarian" ingests timestamped sources into a trust-tiered ontology, layering evidence cards, an authoritative metric ledger, and a claim graph into an always-current source of truth, not per-query RAG over raw chunks. A portable multi-agent "writer" runtime then composes a contradiction-free, evidence-grounded report at any knowledge cutoff T, reading only evidence with as_of <= T (no look-ahead); red-team verdicts flow back into the librarian. We evaluate on a self-collected, public corpus of 6,130 sources yielding 555,926 evidence cards (SEC EDGAR filings across 295 issuers and 11 sectors, U.S. Bureau of Labor Statistics releases, and Wikipedia). From the one library we compose four point-in-time reports on distinct theses and run eight reproducible experiments, whose headline metrics come from a deterministic quality-control gate, itself validated by defect-injection meta-evaluation at recall 1.0 and precision 1.0. A shared metric ledger removes 6,845 cross-section contradictions to zero. Tier-first selection is correct on 22/22 gold cases where a popularity-first baseline scores only 9/22; trust tiering leaks zero media-sourced numbers, and no government statistic displaces a company's own filing. A red-team refutation propagates back and self-corrects a later run with zero manual edits. Replay exhibits zero look-ahead violations across seven cutoffs while the library grows from 235,373 to 555,312 cards. Difficulty-tiered model routing exceeds the all-Opus quality ceiling while running 3.7x faster than serial.
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URL
https://arxiv.org/abs/2608.12984
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Moose: Latent concept learning with reasoning-shortcut awareness in $mathcal{EL}^{++}$
2026-08-13 08:44:48Olga Mashkova, Asaad Mohammedsaleh, Fernando Zhapa-Camacho, Robert HoehndorfAbstract
The OWL 2 EL profile is used in some of the largest production ontologies, including the Gene Ontology and SNOMED CT. Existing neuro-symbolic (NeSy) learning methods accept propositional theories or Datalog, and reasoning-shortcut (RS) awareness has not been investigated in ontology settings. We present Moose, a method that compiles an $\mathcal{EL}^{++}$ TBox and finite ABox to a Sentential Decision Diagram (SDD). The SDD acts as a differentiable weighted-model-counting layer, and we add closure clauses outside the $\mathcal{EL}^{++}$ profile on declared exhaustive families to overcome the limited expressivity of $\mathcal{EL}^{++}$ under partial supervision. We show termination, soundness, completeness, and polynomial intermediate sizes, and validate the proofs in Lean. We then define the first formal partial-supervision latent-concept-learning task over an OWL EL ontology, i.e., learning per-individual classifiers for latent concepts from observed ABox literals, and evaluate Moose on MNIST-with-ontology and Pizzaïolo. Moose improves over propositional-NeSy, fuzzy-logic, and ontology embedding baselines, and presents the first reasoning-shortcut analysis in an OWL EL setting.
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URL
https://arxiv.org/abs/2608.12961
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Prompts in the Wild: A Large Analyzed Collection of Transactional Prompts in Code
2026-08-13 07:43:34Victoria Basmov, Yoav Goldberg, Reut TsarfatyAbstract
The behavior of contemporary generative Large Language Models (LLMs) is directly shaped by prompts, unstructured texts that describe the desired output and model behavior. In this paper we argue that prompts are linguistic objects that merit investigation in their own right. To this end, we collect 57.5K unique samples of prompts from GitHub. Specifically, we focus on transactional prompts: reproducible natural language instructions that are integrated into software. To enable the empirical, quantitative study of prompts, we introduce a structured ontology, capturing the properties of prompts as well as their formal and semantic components. Based on this ontology, we transform prompts from unstructured raw texts into richly structured linguistic objects. Analysis of these structured data reveals significant diversity of usage patterns across languages, domains, tasks, and modalities, in a typical Zipf-like distribution where some clearly prevail and others, more diverse, appear in the long tail. To validate the reliability of the ontology-based annotation of the prompts, we perform a comprehensive error analysis across all fields, providing a detailed assessment of annotation quality. We release the dataset together with a browsing and exploration interface (this https URL ).
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URL
https://arxiv.org/abs/2608.12905
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Compositional Benchmark Synthesis for Hierarchical Human Action Recognition
2026-08-11 10:22:22Farnaz Soleimani (LISSI), Abdelghani Chibani (LISSI), Yacine Amirat (LISSI), Ghazaleh Khodabandelou (LISSI)Abstract
Recognizing human behavior across levels of abstraction, from atomic actions to long-horizon intentions, requires data annotated along a semantic hierarchy. Large corpora provide isolated, atomically labeled clips without temporal composition, whereas recorded composite-activity corpora offer shallow, domain-narrow, fixedhierarchies. A benchmark-generation and evaluation frameworkis proposed that synthesizes a four-level hierarchical-intention benchmark, spanning actions, activities, low-level intentions (LLIs), and high-level intentions (HLIs), from a flat single-label action corpus while retaining real pre-extracted features at the action level. Episodes are assembled by a transition model under a subject-consistency constraint, and a coverage-aware sampler reduces the subject usage Gini from 0.566 to 0.248. Synthesizing such a benchmark raises a circular-supervision risk that recorded datasets avoid: if the rules generating the episodes also govern the evaluation, models can succeed by recovering the generator rather than through genuine reasoning. Validity is addressed by design, holding sequence-generation rules disjoint from the first-order-logic rules used at evaluation. The instantiation yields 15,002 episodes. Four reference baselines from different model families characterize difficulty, not as recognition methods. A compositional held-out gap of 0.13 to 0.17 macro-F1 appears across all baselines, including a graph-aware model that recognizes best yet does not close the gap, indicating a structural property of the benchmark rather than a model artifact. A logic-free baseline still violates the held-out semantic rules above their intrinsic data rate, and the order-destroying control changes macro-F1 within seed variation, serving as a generator-consistency check. Theontology, transition model, and generator are released so the benchmark can beregenerated and extended.
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URL
https://arxiv.org/abs/2608.10765
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Rethinking LLM Verification: Evidence Structure, Uncertainty, and Selective Refinement
2026-08-11 09:43:14Uma Ranjan, Kunal Tilaganji, Aditya Koul, Anurag Mahipal, Dashpreet Singh, Hriday Rana, Manan Jain, Sidharth Gupta, Ajo Babu George, Vineeth Balasubramanian, Nagarajan Natarajan, Amit SharmaAbstract
Large language models (LLMs) often rely on shortcuts rather than systematic reasoning, raising safety concerns in medical applications. Allowing models to abstain when uncertain improves reliability but introduces a coverage accuracy tradeoff. We propose a two-stage framework for medical hypothesis verification in multiple-choice settings that manages this tradeoff through targeted ontology grounding, applied only when the model abstains. We show that abstention is not random but reflects genuine uncertainty, with abstained predictions associated with lower confidence. Across two frontier models (GPT-5.5, accessed via the Azure OpenAI API, and DeepSeek-R1), the proposed framework improves question-level accuracy by 9.6 percentage points (82.9% to 92.5%) and hypothesis-level accuracy by 4.2 percentage points (92.0% to 96.2%). Our experiments conducted on MedReason and MedQA show that abstention can be repurposed as a control signal for selective reasoning refinement, achieving knowledge-graph-level performance without explicit knowledge graph construction.
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URL
https://arxiv.org/abs/2608.10725
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Curate Before You Connect: Identity and Ontology Tagging in a Production Knowledge Graph
2026-08-11 08:30:37Vaibhav Dangaich, Kevin Lewis, Kundeshwar PundalikAbstract
Extraction produces candidate entities and relationships; writing them into a graph is where identity is decided, and identity decisions are destructive in a way extraction errors are not. A wrong type can be corrected later, but two records merged under one identity cannot be separated once their properties have been combined, and the merge leaves no error behind. This paper describes the ingestion and ontology-tagging layer that turns a validated extraction stream into a knowledge graph of 537,157 entities and 2,198,567 relationships drawn from 98,795 government documents. We describe a record-identity ladder that decides sameness from identifier columns, name columns, display names and type-scoped position rather than from name similarity. The ladder governs de-duplication within parsed tables, while the graph write applies a coarser canonical-name key, so records sharing a canonical name merge automatically on exact equality. We argue rather than demonstrate that this is where the automation line belongs: no identity benchmark is reported, and the over-merges the key permits are undetectable by construction. That policy, under which entity resolution only ever flags candidates, followed an incident in which two surface forms of one name were merged, corrupting a correct record and deleting eight entities from an unrelated document. We then describe multi-class ontology tagging and an evidence asymmetry we did not anticipate: an entity name is an instance label rather than a type assertion, so matching name fragments against a class index invents classifications. Requiring anchored evidence cut role assignments on an enriched sample from 36 to 4, all confirmed correct. We quantify the graph's conformance debt, show secondary classifications compensating for a mis-parented primary class, and describe a curation queue grown to 48,403 pending proposals against 775 human decisions.
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URL
https://arxiv.org/abs/2608.10644
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Defining Decentralization: An Ontological Perspective
2026-08-10 15:41:49Jakub Kacper Szel\k{a}g, Aydin Abadi, Mohammad NaseriAbstract
Decentralization as a concept in computer science has existed for over half a century. Despite its fundamental role across domains such as security, distributed computing, artificial intelligence, cloud infrastructures, and Internet of Things (IoT) architectures, there remains no universally accepted definition of decentralization applicable across computer communication systems. This has become increasingly problematic with the emergence of decentralized AI and machine learning paradigms, including collaborative training, distributed inference, blockchain-based, and agentic AI, where decentralization is often treated as a core design objective. Meanwhile, existing approaches frequently conflate decentralization with related notions such as distribution of trust or specific implementation paradigms. Such ambiguity creates inconsistencies in system analysis, limits comparability between works, and weakens the rigor of formal reasoning surrounding communication architectures and protocol design. In this work, we define this research gap as the Decentralization Problem. We analyze the formal-semantic, epistemological, and pragmatic foundations of decentralization and introduce a graph-based ontology defining it as both relational and subject-specific property of computer communication systems. The framework formally distinguishes decentralization from distribution and supports evaluation through two novel metrics: Void Tolerance and Imperviousness. We also provide a browser-based implementation that enables automated classification and metric computation of arbitrary systems. Instantiations to federated learning and blockchain architectures show consistent, comparable assessments where existing definitions produce incomplete or contradictory conclusions, providing a domain-independent foundation for analysing decentralization across heterogeneous systems.
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URL
https://arxiv.org/abs/2608.09748
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PolicyKG: An Agentic LLM Pipeline for Translating Institutional Policies into SHACL Knowledge Graphs
2026-08-10 02:28:57Ponkrit Kaewsawee, Chaklam Silpasuwanchai, Chutiporn AnutariyaAbstract
Institutional policies stay in natural language while the systems that check compliance demand machine-readable constraints. Bridging that gap is still done by hand. PolicyKG closes the loop. It is an LLM pipeline that reads a policy PDF, classifies each sentence as an obligation, permission, or prohibition, lifts the label into first-order deontic logic, and emits SHACL constraints. Four stages run on a LangGraph state machine with per-stage validators. The piece that matters most is the Corpus Adapter: a YAML vocabulary registry that grounds LLM predicates in a target ontology. Retargeting to a new domain means swapping the registry, not retraining a model. On the Asian Institute of Technology Policies and Procedures corpus (1,663 sentences, 443 rules), PolicyKG reaches 86.9% deontic classification accuracy (Cohen's kappa = .709). Three annotators independently re-label a 50-item sample and agree at Fleiss' kappa = .844. SHACL shape correctness on a 69-shape subset is F1 = .866. The FOL path handles 79.2% of rules; the rest go through a direct NL-to-SHACL fallback. We audited every one of the 443 rules for second- or higher-order constructs. An automated regex checklist flagged none, and a first-author pass on the 92 FOL-fallback cases confirmed the same. The exact upper 95% Clopper-Pearson bound on the true HOL rate is 0.67%. This is an audit finding for one corpus, not a proof of FOL sufficiency for institutional policy. Swapping the AIT registry for a GDPR registry raises exact property alignment from 1/15 to 11/15 (Fisher's exact p < .001; Cohen's h = 1.53). On the LexDeMod lease-contract benchmark (N = 200), Macro F1 drops to .370 because lease English uses "shall be entitled" for permission -- exactly the vocabulary mismatch registry swap is meant to fix. Repeated runs produce hash-identical SHACL outputs.
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URL
https://arxiv.org/abs/2608.09028
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How Far Do Foundation Models Transfer to Infant Signals? A Cross-Dataset Transfer Audit with a Unified Need Ontology
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Public infant cry corpora are small, label-incompatible, and almost always evaluated one corpus at a time. We ask what this practice hides and what fixes it. Across four cry corpora screened by a multi-level leakage audit (byte-level and embedding-level deduplication plus a within-corpus train-test near-duplicate audit), we probe four frozen encoders and a handcrafted baseline under a unified five-class need ontology and shared task formulations. The audit exposes what single-corpus evaluation conceals: within-domain macro-F1 swings by 0.57-0.80 for the same encoder, cross-corpus transfer is negative on average (negative-transfer ratio 0.19-0.35, significant in 18 of 30 directed cells, BH-FDR), and 349 content-identical clip groups carry conflicting metadata labels across corpus distributions. The same audit, however, reveals a consistent way forward. Transfer into the noisiest corpus is consistently positive in effect size at matched training size and after near-duplicate removal, offering a practical recipe for small, noisy corpora. Frozen probes saturate at modest label budgets, while stabilized fine-tuning wins with full labels; domain-adaptive pretraining significantly beats stabilized fine-tuning at 5-10-shot (the 1-shot advantage is not robust to optimization-seed variance) but shows no significant advantage at 50-shot or beyond. In the tested binary, shared-label settings, ontology-mapped joint training wins in all four encoder-by-target combinations, whereas naively merging unmapped labels costs up to 37 F1 points. We release the ontology, mapping code, and audit pipeline, turning incompatible cry corpora into a usable joint-training resource.
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URL
https://arxiv.org/abs/2608.08989
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RAG-Based Auto-Configuration for Industrial Fieldbus Devices
2026-08-09 10:07:13Aadil Gani Ganie, Saad Ezzini, Naveed Farooz MaraziAbstract
Industrial device commissioning requires engineers to manually extract hundreds of protocol-specific parameters from heterogeneous PDF manuals and transcribe them into supervisory control systems, a time-intensive, error-prone workflow. This paper presents SysName, a production-oriented pipeline that automates device configuration end-to-end for Modbus RTU, OPC-UA, Profibus DP, and CANopen. It builds a hybrid dense-sparse retrieval index augmented by an ontology graph derived from ECLASS, AAS, and SOSA/SSN, using a BGE-M3 encoder with a cross-encoder reranker to surface relevant manual passages. A local LLM (T=0.1) generates ontology-aligned JSON-LD configurations via protocol-specific prompts and a four-step repair pipeline. A two-stage abstention gate, combining a reranker-score threshold and an IRI resolution ratio, blocks unsafe LLM invocations and filters low-coverage configurations before SHACL validation. On a gold set of 28 field-level queries, the hybrid retriever reaches 0.96 HitRate@10, and the reranker raises MRR@10 from 0.56 to 0.63 with perfect score separation for abstention. The generator attains field-level F1=0.87 with exact match on 9 of 12 runs. End-to-end runs on an H100 GPU complete in 2.6-6.6s per device with zero unsafe writes and zero silent failures on a five-device benchmark; every unsuccessful run is flagged by abstention or deployment verification. Component-wise evaluation localises the single systematic failure to OPC-UA generation, invisible to end-to-end metrics alone. A case study commissions a physics-simulated Universal Robots UR5e robot from unmodified vendor documentation (254-page manual, 8-page register list, 496 chunks), reaching field-level F1=1.0 over three runs with read-back and joint-consistency verification. An ablation study and comparison with five industrial-LLM systems complete the analysis.
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URL
https://arxiv.org/abs/2608.08618
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Constraining ontology mappings using metaphysical choices
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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.
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https://arxiv.org/abs/2608.08122
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CyberAGENTS: Structured Autonomy for Agentic Gamified Learning in Cybersecurity
2026-08-08 06:59:45Ivan Hornung, Deepthi Marasinghe Arachchige, Tharindu Kumarage, Garima Agrawal, Yuli Deng, Ying-Chih Chen, Huan LiuAbstract
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.
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URL
https://arxiv.org/abs/2608.07965
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Towards Researcher Agents for Knowledge-Graph Question Answering
2026-08-07 18:42:53Tommaso Soru, Abdulsobur OyewaleAbstract
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.
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URL
https://arxiv.org/abs/2608.07700
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SCALE: Scientific Concept Aggregation via LLMs and Embeddings for Fine-Grained Taxonomy Extension
2026-08-07 14:12:15Daniele Raimondi, Feichi Lu, Oliver Grun, Mariia Eremina, Andrea PerlatoAbstract
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.
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URL
https://arxiv.org/abs/2608.07254
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Authoring and Management of Transparent Research Integrity Assessments of Randomised Clinical Trial Publications Using LLM-assisted Tools and Provenance Knowledge Graphs
2026-08-07 13:17:56Milan Markovic, Goutham Indukuri, Somayajulu Sripada, Colby J. Vorland, Jack Wilkinson, Clare Robertson, Mark Bolland, Andrew Grey, Miriam Brazzelli, Alison AvenellAbstract
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.
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URL
https://arxiv.org/abs/2608.07202
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Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling
2026-08-07 05:29:00Quanquan Li, Yihe Chi, Liuyang Song, Hongbo Zhang, Jingyu Li, Xidong Xi, Conghua Wei, Yijie Sun, Yu Chen, Xin Liu, Qi Hu, Jing Ke, Guitao CaoAbstract
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.
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URL
https://arxiv.org/abs/2608.06824
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Improving Interoperability among Defence and National Security Ontologies: Analysis and Evaluation Tasks
2026-08-06 10:47:02Jonathon Dilworth, Pedro Giesteira Cotovio, David Herron, Paul Cripps, Nigel Dewdney, Catia Pesquita, Ernesto Jim\'enez-RuizAbstract
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).
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URL
https://arxiv.org/abs/2608.05867
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Vibe Compiler: A Research-Logic Synthesis Tool That Runs without Prompt Engineering -Toward Enhancing Metacognition for Sustaining Agency in the Age of Generative AI-
2026-08-06 02:51:03Riichiro Mizoguchi, Tomoki Aburatani, Kento Koike, Machi ShimmeiAbstract
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.
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URL
https://arxiv.org/abs/2608.05545
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A General Sufficient Condition for Rewriting Horn-ALCHI Atomic Queries into GQL
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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.
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URL
https://arxiv.org/abs/2608.04945
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ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extraction
2026-08-04 05:36:19Shufan Ming, Yikun Han, Gibong Hong, Rui Zhang, Halil KilicogluAbstract
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.
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URL
https://arxiv.org/abs/2608.03154
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