Ontology
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ScienceBuddy-PV: A Verifier-Governed Recursive Improvement Protocol for Panvascular Intervention Research
2026-10-10 03:35:28Lingsen You, Yujun Guo, Xinyu Zhong, Zijie Feng, Wentong Wang, Li Shen, Junbo GeAbstract
ScienceBuddy-PV adapts the ScienceBuddy recursive-in-recursive design to panvascular intervention research through a structured evidence ledger, device-vessel ontology, abstention contract and retained failure bank. Recursive harness optimization and outer-loop model learning, including reinforcement learning, are specified but not executed. We audit a fixed component, rather than the complete agent system, using separate ARCADE syntax and stenosis tasks (1,000 training, 200 validation and 300 test images per task). A shared task-masked convolutional model was trained once per representation setting; its parameters and the heuristic support gate were then held fixed, with the stenosis threshold selected on validation data. On the locked test sets, syntax Dice was 0.475 (95% CI 0.459-0.490) and stenosis Dice was 0.231 (95% CI 0.214-0.249). Stenosis pixel AUROC was 0.957 and AUPRC was 0.180 at prevalence 0.00975. The gate accepted 76.7% of stenosis-frame outputs versus 100% for a score-only comparator. In a constructed mask audit, it accepted 44.3% of reference candidates and rejected 55.7%, exposing the cost of abstention. Acceptance does not establish correctness or clinical safety. This public-data component audit makes support and abstention measurable and provides a reproducible protocol for future collaborative agent studies. It does not demonstrate recursive improvement, patient-level validity or clinical device recommendations.
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https://arxiv.org/abs/2610.14523
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Speech event detector: Timestamped detection of non-verbal vocalizations and background sounds for rich speech transcription
2026-10-09 18:49:55Ayush Kumar Bar, Promila GhoshAbstract
Automatic speech recognition produces words but drops the non-verbal content of a recording: the breaths, coughs, sighs and laughter of the speaker, and the horns, music or barking around them. We describe Speech Event Detector, a 5.8-million-parameter convolutional-Transformer model that outputs probabilities every 40 ms for 54 event classes (20 speaker vocalizations and 34 background sounds), together with post-processing that converts these probabilities into timestamped events and a procedure for merging the events into a Whisper transcript. The model is trained on material drawn from seven public datasets whose labels come in incompatible forms: single detected regions, free-text tags with timestamps, temporally strong ontology labels, symbols embedded in transcripts, isolated recordings and environmental recordings. We unify them using rule-based label mapping, recover timestamps for transcript-embedded labels through CTC forced alignment, locating 6,360 of 8,620 sounds, and combine about 168 hours of real annotated training recordings with synthetic mixtures and augmentation using real background noise. Per-class thresholds for two operating profiles are tuned on real held-out recordings, and performance is estimated using two-fold cross-validation. On whole held-out recordings from four datasets, considering the 48 classes with at least ten held-out events, the sensitive profile detects an average of 49 percent of a class's events, covering 67 percent of all 9,367 events, at a macro precision of 0.30. The balanced profile achieves a macro recall of 0.37 at a precision of 0.36, with macro event F1 scores of 0.32 and 0.33, respectively. The detector runs about 39 times faster than real time on eight CPU threads.
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https://arxiv.org/abs/2610.14232
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U4RASD at KnowledgeGraphEval-2026: Ontology-Constrained Encoder and LLM Systems for Arabic Relation Extraction
2026-10-08 21:41:29Ahmad Abbas, Hussein Mazeh, Chadi Abou Chakra, Aya Jouni, Mohammad Ballout, Fadi A. ZaraketAbstract
This paper details our submission to KnowledgeGraphEval 2026 Subtask 2 on directed Arabic relation extraction. We explored encoder-based and large language model approaches for predicting one of 40 relations or no_relation from an Arabic sentence and a subject-object pair. Our encoder systems use typed entity markers and separate relation-existence and relation-classification heads, while our LLM systems fine-tune Yehia and Qwen3.5 with QLoRA and ontology-constrained prediction. Our best system, an ensemble of Yehia-RE, Qwen-RE, and TypedPair, achieved a micro-F1 score of 94.06 and ranked 1st in Subtask 2. Yehia-RE (full-vocabulary) achieved 92.98, while the best encoder and Qwen-RE achieved 92.69 and 91.94 respectively. Our results highlight the importance of constrained prediction and complementary modeling approaches for Arabic relation extraction.
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https://arxiv.org/abs/2610.12742
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CLUE: A Contrastive Learning Framework for Unsupervised Event Type Induction and Annotation
2026-10-08 18:05:16Pratik Maitra, Lauren Kwon, Qi LiAbstract
Event ontology is the foundational framework for defining events in a dataset. Event type induction generally involves domain experts who define guidelines for creating event types and their names based on the dataset's domain and scope. However, this process is resource-intensive in terms of annotation costs and is prone to human biases. To alleviate the need for manual event ontology creation, we propose the CLUE framework for event type induction, naming, and annotation. Our main contributions in this work are: 1) designing a novel joint embedding representation for expressing both the verb-centric view and the semantic view of events; 2) event type induction using contrastive loss guided clustering; 3) event naming and refinement. Experiments demonstrate the effectiveness of our method. Our code is available at this https URL.
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https://arxiv.org/abs/2610.12580
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Natural Language to First-Order Logic LLM-based Autoformalization
2026-10-08 14:24:12Andrea Brunello, Cristian Curaba, Luca Geatti, Michele Mignani, Angelo Montanari, Nicola SaccomannoAbstract
Large Language Models (LLMs) have renewed interest in autoformalization. Yet, when First-Order Logic (FOL) is considered as the target formalism, the field still lacks a unified task formulation and a systematic survey. This paper addresses this gap: we first provide a principled definition for the FOL-autoformalization task by distinguishing Ontology Extraction from Logical Translation, showing how their conflation obscures (cross-study) evaluation; we review existing datasets, evaluation metrics, and LLM-based methods, including fine-tuning, prompting, and verification-based refinement; we identify open challenges in benchmarking, semantic evaluation, ontology-aware methods, and end-to-end applications.
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https://arxiv.org/abs/2610.12030
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Narrow and Deep: An Ontology Tower as the Knowledge of an LLM Agent for an Industrial Equipment System
2026-10-08 11:50:51Younghwan Joo, Sung-il KimAbstract
Large language model (LLM) agents are beginning to operate industrial energy equipment, and what they get right depends on what they are told about the plant. Established building ontologies name many kinds of points across many sites, whereas an industrial equipment system needs few entities with much knowledge about each. This study proposes the ontology tower, a narrow-and-deep ontology of a single equipment system whose knowledge deepens in two ways: through quantities derived from the measured points by physical relations, and through lessons from the operating journal incorporated as knowledge nodes. On a real low-humidity air-handling test plant operated daily through a programmable logic controller, agents received a text projected from its tower in a preregistered evaluation of nine tasks replayed from the plant's records, using four open-weight models from 9 to about 750 billion parameters. This knowledge raised the rate at which the agents avoided the most plausible misjudgment of each task by about 20 percentage points, and the overall task score of the 9-billion-parameter model as much as that of the largest. Operating lessons were used when incorporated into the tower or placed in the prompt as records, but seldom when left in the journal behind a search tool. In live runs through an invariant safety layer, the agents brought the controlled variable into its target band in 12 of 14 runs. An ontology narrow in entities but deep in what is known about them can thus supply the knowledge that an agent for an industrial equipment system needs.
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https://arxiv.org/abs/2610.11768
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Coverage-Aware Reasoning with Medical Tokens for Diagnosis Prediction
2026-10-07 14:39:18Kaisong Zhang, Haotian Fang, Junmeng Zhou, Hang Lv, Yulan Pan, Yanchao TanAbstract
Large language models (LLMs) offer promising potential for next-visit diagnosis prediction, owing to their ability to integrate longitudinal clinical evidence and reason over it in natural language. However, reinforcement learning for LLM reasoning commonly rewards each trajectory according to the correctness of its final answer. In next-visit diagnosis prediction, multiple diagnoses can be simultaneously valid, but independently rewarding one diagnosis per trajectory does not distinguish repeated hits from coverage of different diagnoses. The policy can therefore concentrate on a few correct diagnoses, leaving others uncovered. Meanwhile, LLM tokenizers can split ICD codes into several generic tokens with limited clinical meaning, requiring multiple decoding steps to predict each diagnosis and hindering reasoning over a large disease vocabulary. To address both challenges, we propose CARing, a framework that represents diagnoses with compositional Semantic IDs (SIDs) and optimizes reasoning trajectories for multi-label coverage. Concretely, we first encode ontology-enriched disease semantics into compact SIDs through residual quantization, and ground the resulting SID tokens in natural language and longitudinal EHR contexts through multi-task alignment and reasoning-enriched training to unlock transferable LLM reasoning. CARing further improves unordered multi-label prediction through a coverage reward for reinforcement learning and multi-positive supervision. At inference time, the model supports both efficient direct constrained decoding and multi-chain reasoning with rank fusion. On MIMIC-III and MIMIC-IV, CARing exceeds all EHR-trained baselines in weighted F1 and attains the highest top-k recall at every reported cutoff, including R@30 of 46.04% and 46.52% in reasoning mode. Our codes and logs are available at this https URL.
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https://arxiv.org/abs/2610.10641
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FaceKit: a Toolkit for Interpretable Facial Phenotyping, Synthetic Image Generation and Privacy Analysis in Rare Diseases
2026-10-07 01:43:49Hongzhuo Chen, Zhanliang Wang, Florent Pollet, Mian Umair Ahsan, Joshua Bie, Tzung-Chien Hsieh, Peter Krawitz, Cong Liu, Wendy K Chung, Chunhua Weng, Gamze G\"ursoy, Kai WangAbstract
Many rare genetic diseases are associated with recognizable craniofacial features. However, traditional approaches for describing facial morphology rely largely on qualitative clinical observation and free-text descriptions, which are often subjective, non-standardized, and difficult to reproduce across observers and institutions. Although the Human Phenotype Ontology (HPO) provides controlled terms for describing facial features, these terms are typically categorical rather than quantitative and may vary depending on examiner experience and interpretation. Here, we present FaceKit, a computational framework for quantitative facial phenotyping from frontal facial photographs. FaceKit extracts standardized measurements of facial landmarks and derived 120 morphological features, then reports feature-level z-scores representing deviation from population reference distributions. The reference distributions are built from the FairFace dataset spanning diverse ancestral groups. We evaluated FaceKit on a curated subset of the GestaltMatcher Database covering 50 rare-disease cohorts. In addition to quantitative facial analysis, FaceKit includes synthetic facial image generation to support rare disease model development and data augmentation. We also performed privacy evaluation to assess whether synthetic images reveal identifiable information from real patient photographs and could compromise patient privacy. Across disease case studies, FaceKit-derived quantitative measurements captured known facial features associated with rare genetic disorders and provided objective support for clinical phenotyping. Together, these results establish FaceKit as a useful tool for quantitative phenotyping, and has the potential to improve rare disease diagnosis, support genotype-phenotype studies, and enable more reproducible clinical characterization across diverse patient populations.
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https://arxiv.org/abs/2610.09288
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BEACON-SP: Ontology-Grounded GraphRAG Framework for Clinical Suicide Risk Assessment
2026-10-06 19:23:51Kemal Davaslioglu, Nathan Conger, Sastry Kompella, Yalin E. Sagduyu, Nathaniel D. BastianAbstract
We present BEACON-SP, an ontology-grounded Graph Retrieval-Augmented Generation (GraphRAG) framework for clinician-facing decision support in behavioral health settings such as suicide prevention, where effective assessment requires integrating heterogeneous clinical, behavioral, social, and temporal evidence. BEACON-SP combines patient knowledge graphs with ontology-guided retrieval to support multi-hop reasoning across diagnoses, medications, risk and protective factors, life events, and temporal relationships. The framework is enabled by a comprehensive suicide prevention ontology that integrates the Three-Step Theory, the Integrated Motivational-Volitional Model, and the Suicide Social Determinants of Health Ontology into a unified representation of patient risk factors. We construct ontology-grounded patient knowledge graphs and evaluate BEACON-SP for clinician-facing question answering. Compared with a vector-based retrieval-augmented generation (RAG) baseline on a 1,500-query benchmark spanning 15 clinical categories and 100 patients, BEACON-SP improves completeness, clinical relevance, and evidence grounding under a corrected comparative evaluation protocol, with a small gain on factual accuracy. In paired criterion-level comparisons, GraphRAG is preferred in 76.4% of cases. These results demonstrate the potential of ontology-guided GraphRAG to provide structured, contextualized patient evidence for clinical decision support.
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https://arxiv.org/abs/2610.09026
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Natural Language Questions as an Interface for Knowledge Graphs: QRAKEN Graph Distillation and Semantic Self-Healing
2026-10-06 10:24:26Remo Grillo, Lukas Klic, Giovanni ColavizzaAbstract
Natural-language access to RDF knowledge graphs is a core Semantic Web ambition. Large language models (LLMs) have advanced Text-to-SPARQL, yet on unfamiliar graphs they often generate valid queries that misrepresent the populated data model. QRAKEN is a training-free, ontology-agnostic neurosymbolic pipeline grounding generation in empirical graph evidence rather than schema expectations. An offline distiller produces TTQL, a compact description of populated multi-hop patterns, conditional frequencies and path-conditioned literal examples, plus a class-property co-occurrence matrix. Online, TTQL guides the LLM, while deterministic syntax, vocabulary and data-model checks provide diagnostics for iterative refinement. On CK25 (First International Text2SPARQL Challenge), under matched-condition recomputation on a QLever snapshot, QRAKEN achieves strict F1 of 0.643 $\pm$ 0.026 with GPT-4.1 mini and 0.652 $\pm$ 0.012 with GPT-5.4: relative gains of 30% and 32% over the strongest recomputed participant, outperforming systems using the same base model family. Ablations identify TTQL patterns as the dominant driver (+0.31 strict F1 over a shape-only baseline); the refinement loop provides a cheap safety net, rejecting triple patterns unsupported by the co-occurrence matrix. Compared with auto-derived SHACL, TTQL yields 64% higher strict F1, supporting the value of empirical patterns beyond schema exposure. With two local 35B 4-bit open-weight models at zero marginal cost, the same pipeline matches the strongest recomputed participant, and TTQL advantages over shape-only and SHACL baselines persist. Results on a single, relatively small benchmark provide an initial empirical signal; monolithic TTQL injection on very open cross-domain graphs remains the main limitation.
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URL
https://arxiv.org/abs/2610.08095
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POLAR: Ontology-Guided Risk Prevention for Tool-Calling LLM Agents
2026-10-06 10:14:16Yunju Kang, Seonghyeon Cho, Irene Li, Yeo-Chan Yoon, Chanjun ParkAbstract
LLM tool-use agents operate in dynamic environments where many actions carry operational risk. However, most safety mechanisms react only after errors manifest. Existing pre-emptive approaches either fine-tune the agent on chain-of-thought deliberation or compile natural-language guardrails into runtime checks, but they do so without exposing a structural, auditable verdict. We propose POLAR, a guardrail framework for small tool-calling agents that assesses reversibility through a structured two-layer ontology. POLAR assigns each action a graded reversibility score by deriving a candidate inverse sequence; calls failing a threshold are pruned before execution. Evaluated on $\tau^2$-bench across six agent models, POLAR improves mean task reward by 0.11 to 0.18 points on airline for four of six agents, but only eight of eighteen model--domain cells improve overall; retail and stronger agents often regress. POLAR provides an auditable structural check and characterizes its task-utility trade-offs. Reward is not a direct measure of prevented harm.
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https://arxiv.org/abs/2610.08082
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OMIT the Action: Measuring Framing-Invariant Omission Bias under Philosophical Disagreement
2026-10-06 06:54:19Sihyeon Lee, Jihun Song, Chanwoo Kim, Jiwoo Kum, Chanjun ParkAbstract
As LLMs increasingly assist in moral reasoning, omission bias, the tendency to prefer inaction even when equivalent framings reverse substantive outcomes, poses a significant risk of skewed decision-making. Yet omission bias remains underexplored in LLM evaluation, with the few existing studies limited in scale and focused largely on utilitarian-deontological conflicts. To address this gap, we introduce OMIT, a benchmark consisting of 218 paired-frame scenarios across 10 conflict types, constructed by leveraging disagreement patterns from an LLM-based, five-perspective philosophical persona panel (utilitarianism, deontology, virtue ethics, care ethics, and contractualism). Evaluating eight LLMs, we find that omission bias is pervasive but inversely correlates with model size within families. We further evaluate four inference-time interventions and find that interventions encouraging models to consider moral principles before committing to a yes/no answer reduce omission bias and increase frame-consistent responses, although lower omission bias rates can also coincide with shifts toward action-biased responses. Ultimately, this work contributes not only the OMIT benchmark, but also a methodology for using diverse philosophical disagreement signals to evaluate framing-sensitive inaction preferences and the distributional effects of mitigation attempts in LLMs under complex moral conflicts.
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https://arxiv.org/abs/2610.07847
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EIO-Agents: The Missing Semantic Layer for AI Agent Evaluation
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AI agents are entering production in increasingly consequential environments without a shared semantic standard for what their evaluations actually mean. Scores, traces, judge outputs, and multi juror findings are increasingly used to justify readiness and release decisions, yet they often do not specify what evidence supports a claim, what that evidence can establish, or how the claim leads to a decision. We introduce EIO-Agents, an open specification for interoperable AI agent evaluation built on two layers. The Evaluation Intelligence Ontology (EIO) provides the semantic layer through typed evidence, versioned behavioral predicates, evidence contracts, claims, witness rules, proof status, recurrence, and computable derivations for metrics, findings, controls, and PASS, REVIEW, or BLOCK decisions. The Portable Evaluation Record (PER) provides the system of record: a canonical, content addressed representation of one evaluation that preserves the evidence to decision chain and can be re derived, explained, and verified. Scores summarize, juries interpret, and traces record, but none of them define what the evidence means or what it can prove. EIO provides that missing semantic contract, while PER preserves the resulting evaluation as a portable and verifiable system of record. As AI agents assume greater operational responsibility, evaluation must become more than a collection of scores and verdicts; it must become an accountable artifact whose meaning, evidence, limitations, and decisions can be independently checked.
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https://arxiv.org/abs/2610.07675
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OntoPlan: An Ontology-Grounded Scene Representation and Agentic Framework for Scalable Robot Task Planning
2026-10-06 02:45:03Hyeongwoo Nam, Woongje Cho, Juwon Kim, Jongeun ChoiAbstract
Large language model (LLM)-based robot task planning is promising for open-ended instruction following, but degrades on long-horizon tasks in large environments. When spatial information is conveyed to the LLM through text, the model can fail to capture spatial context, and token cost grows with environment size. Generating action sequences directly with an LLM also makes it difficult to satisfy the current world state and action preconditions. We address this with an ontology-grounded scene representation that aligns objects, spaces, relations, and states in a shared symbolic vocabulary for spatial reasoning and task planning, and with OntoPlan, an agentic framework that interprets instructions, selectively retrieves task-relevant information, formalizes goals and constraints, and produces executable plans. Across 150 general tasks spanning five indoor environments and three scene scales, OntoPlan achieves 0.89 average task success, compared with 0.27 for the strongest baseline, while using 18.1k total tokens per task on average, about 5.6$\times$ fewer than the most efficient baseline. These advantages persist as scene scale increases, whereas prior methods degrade more sharply in success and remain far more costly in tokens. OntoPlan also responds appropriately to ambiguous or infeasible instructions by asking follow-up questions or reporting insufficient information rather than committing to invalid plans. Code available at this https URL.
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https://arxiv.org/abs/2610.07649
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SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotation
2026-10-02 09:07:55Drew Ross, Arya Hadizadeh Moghaddam, Dongjie Wang, Xiaoyu Zhang, Zijun YaoAbstract
Gene set analysis is a cornerstone of functional genomics, yet it remains labor-intensive and heavily dependent on manual curation and expert biological interpretation. While Large Language Models (LLMs) have emerged as powerful tools for genomic reasoning and annotation, most existing approaches rely on symbolic gene names and fail to capture domain-specific biological structure, particularly protein sequence information that governs molecular activity, interactions, and downstream gene function. In this work, we propose SoftGene, a novel framework for LLM-based gene set annotation that leverages the hierarchical structure of gene sets. First, we use a hierarchical attention-based encoder built on ESM, a protein language model, to represent each gene set using protein-level amino acid sequence information. Second, we construct a hybrid prompting scheme that combines soft prompts derived from gene set embeddings with hard prompts containing auxiliary context generated by an LLM, and feed the resulting prompt into a local LLM for annotation. We evaluate our framework on two benchmark datasets: Gene Ontology (GO) and the Molecular Signatures Database (MSigDB). Our results show that integrating protein-sequence representations with textual context improves gene set annotation overall, while per-domain analyses reveal that the contribution of protein embeddings varies across biological domains.
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https://arxiv.org/abs/2610.03029
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Asterism: Exploring and Synthesizing Scattered Observations into Literature-Grounded Hypotheses and Theories
2026-10-02 01:55:14Joseph Chee Chang, Michael D'Arcy, Amy X. Zhang, Pao Siangliulue, Sangho Suh, Aakanksha Naik, Jena D. Hwang, Javier Ramos Benitez, Stella Wroblewski, Matt Latzke, Michael Cuoco, Ruben Lozano-Aguilera, Kris Ganjam, Joel Chan, Doug Downey, Peter Jansen, Kyle J. Travaglini, Daniel S. WeldAbstract
A theory draws many independent observations into one framework with novel hypotheses. A researcher building such a theory must synthesize observations scattered across many papers, each describing related concepts but often in different terms. Which concepts matter most also depends on their preferences and research questions. Recent approaches scale theory synthesis with LLMs, but automate away choices and intuitions from researchers. We present Asterism, which extracts observations from hundreds of papers as concept-relation triples, with concepts unified in a hierarchical ontology. Researchers curate an evidence graph using the ontology and aggregate observations at different levels of granularity to focus theory formation on specific phenomena of interest. In a field deployment (n=10), researchers worked from observations to theories, and kept concepts and hypotheses fitting their preferences. In two case studies, teams of immunology and agriculture researchers discovered mechanisms outside their standard analyses and constructed hypotheses worth follow-up experiments.
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https://arxiv.org/abs/2610.02673
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Can LLMs Reliably Annotate Bioassay Metadata to Improve Data Readiness?
2026-10-01 12:54:29Laura van Weesep, Riccardo Tedoldi, Jens Sj\"olund, Hossein Azizpour, Susanne Winiwarter, Ola Engkvist, Jon Paul Janet, Samuel Genheden, Juan Viguera DiezAbstract
The emergence of foundation models for molecular property prediction requires a high degree of AI data readiness, including reliable metadata annotation. However, both public repositories and industrial screening databases suffer from missing, inconsistent, or conflated assay annotations. In this work, we quantify the extent of missing annotations in PubChem for the BioAssay Ontology (BAO) assay format and physical detection method fields and investigate whether open-source and proprietary large language models (LLMs) can reliably predict and audit metadata annotations directly from the assay text. In our assessment, we found that the annotation coverage across PubChem's $\sim$2 million bioassays is critically sparse, 36\% lacking an assay format, 89\% a BioAssay type, and >99.9\% any BAO-mapped assay format or detection technology term. This motivates the need for automated test-metadata curation. Using evaluation sets derived from PubChem and ChEMBL, we assess the agreement of seven open-source and proprietary LLMs with existing silver labels. Recall is at least 0.96 for biochemical and cell-based assay formats, with a similar pattern for detection technology, although disagreements increase on under-represented classes. Manual inspection shows that many of these disagreements trace back to inconsistencies between silver sources rather than to LLM error. Moreover, in a qualitative study with a senior industrial curator, LLM-generated evidence prompted the expert to revise some of their own labels, showing LLMs can flag potentially mislabeled assays. Across the study, performance differences between proprietary and open-source models were small. Together, these results suggest LLMs can support the large-scale annotation and auditing of assay metadata, though per-class reliability estimates and targeted human review remain necessary before such labels enter downstream ML pipelines.
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https://arxiv.org/abs/2610.01616
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LLM-Assisted Discovery of Typed Semantic Links for Ontology Network Construction
2026-10-01 09:59:00Nouha Hayouni, Sheeba Samuel, Alsayed AlgergawyAbstract
Constructing typed, justified semantic links between ontologies is essential for enabling interoperability across heterogeneous and interdisciplinary knowledge domains. However, manually curating such links is difficult to scale. To address this challenge, we propose an end-to-end framework for ontology network construction that automates the discovery and generation of both intra-domain and inter-domain relationships. Our approach combines domain-adapted DistilBERT embeddings for dense contextual representation, clustering-based pre-filtering to reduce the candidate search space, and GPT-4o-driven relationship generation via iterative prompt engineering to produce semantically rich, interpretable links. Applied to ReproduceMeON - a network of 33 ontologies spanning machine learning, microscopy, computational science, and experimental workflow - the pipeline reduces approximately 800k raw concept pairs to 95k high-quality candidates. Human expert validation of 429 generated relationships by two independent annotators yields an overall precision of 80.19% (91.49% on high-certainty annotations) and an F1 of 0.890, with substantial inter-annotator agreement. Comparative experiments against five similarity-based baselines, including Sentence-BERT, show a substantial performance gap (best baseline F1 = 0.581), while an ablation study demonstrates that similarity-based methods alone fail to discriminate valid from invalid relationships (AUC approx 0.5) on the filtered candidate set. These findings highlight the necessity of LLM-based reasoning over concept roles and domain semantics for accurate relationship construction.
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https://arxiv.org/abs/2610.01393
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An ontology for cross-sectoral crisis management: core and public health modules
2026-10-01 08:52:29Aldo Gangemi, Rita T. Sousa, Luigi Asprino, Giorgia Lodi, Andrea G. Nuzzolese, Valentina Presutti, Johannes Gysen, Diana F. Sousa, Luigi SpagnoloAbstract
This paper presents the European Crisis Management Ontology (ECMO), a modular OWL-based ontology intended as a cross-sectoral reference for disaster risk reduction and response. ECMO is designed to be organised as a network of ontological modules. Among the modules, ECMO-CORE captures fundamental crisis management concepts such as hazard, event, exposure, impact, and response measure and uses ontology design patterns and the OWL2 punning technique to resolve ambiguities between hazard types and event manifestations. In addition, domain-specific modules are defined as in the case of the public health module aligned with SNOMED CT and ICD-11. To demonstrate the resource's utility, we used ECMO to represent the data of the Epidemic Intelligence from Open Sources system of the Joint Research Centre to generate an end-to-end pipeline that populates an ECMO-compliant knowledge graph from unstructured epidemiological news. Initial results demonstrate that ECMO provides the formal guardrails necessary for consistent and unified knowledge representation and integration. The ontology is publicly available at this https URL and is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
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https://arxiv.org/abs/2610.01326
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Ontology-Grounded, Reasoner-Verified Benchmarks for Evaluating LLM Reasoning in Scientific AI
2026-09-30 20:23:55Nishtha N. Vaidya, Stephan Grimm, Thomas Hubauer, Thomas A. RunklerAbstract
Large language models (LLMs) increasingly underpin scientific AI applications that reason over structured knowledge, from biomedical question answering to materials informatics. However, their logical reasoning often falls short, producing factual inaccuracies unacceptable in these settings. Reliable evaluation remains challenging: manual dataset construction scales poorly, and LLM-based generation risks embedding the very flaws it aims to measure. High-quality benchmarks must ground both correct and incorrect labelled examples in explicit background knowledge, formally verifiable by a standard reasoner. We propose a pipeline that automatically generates ontology-grounded multiple-choice question (MCQ) benchmarks from any sufficiently axiomatised OWL 2 ontology, with correct answers grounded in the ontology by design. Distractors are generated by perturbing the right-hand-side class expressions of class definition axioms, and their incorrectness is formally verified by an OWL reasoner via entailment checks. We evaluate the pipeline on three ontologies: Pizza (small, academic), PMDco (complex, materials science), and DOID (large, biomedical), generating 112, 2,491, and 15,216 MCQs respectively. Distractors span four semantic categories from class unsatisfiability to weakened subsumptions, enabling diagnostic evaluation of specific reasoning failures. Items meet natural language quality standards: mean LLM judge scores of 4.02, 4.36, and 3.36 out of 5 confirm fluency, and correct-answer-to-distractor similarity above 0.8 shows that wrong options cannot be dismissed on surface form alone. Six LLMs evaluated zero-shot achieve 41.1-76.8% accuracy, well above the 25% random-guessing baseline, indicating the benchmarks are challenging and discriminative. This work is a step towards more reliable benchmarks for assessing logical reasoning in scientific AI.
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https://arxiv.org/abs/2610.00682
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