Ontology
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Ontology-Based Contextual AI Evaluations Methodology
Abstract
The ontology-based contextual AI evaluation (OB-CAIE) methodology was developed to address a lack of scientific rigor that arises from unclear testing coverage, to balance human expertise and automations, and to address a lack of reproducibility of AI evaluation testing environments. OB-CAIE strengthens the current state of AI evaluations by addressing the first step in the scientific method by clearly defining what will be tested. Two ontologies represent the tractable problem space in the OB-CAIE methodology: the Domain-Specific Ontology (DSO) and the Evaluation Process Ontology (EPO). The DSO is the what; the EPO is the how. An OB-CAIE problem space can be used for one or multiple AI evaluations. The OB-CAIE methodology allows for human judgment at specific points, in scientifically grounded ways, and in complex subject areas where human feedback is genuinely irreducible or machine irreplaceable. A key advantage of the OB-CAIE methodology is that failure points can be traced, visualized and analyzed within the canonical OB-CAIE methodology problem space.
Abstract (translated)
URL
https://arxiv.org/abs/2610.00529
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Talk2Agent: Benchmarking Voice Interfaces for Text Agents
2026-09-30 03:19:25Terumi Chiba, Guangzhi Sun, Zheqi Yuan, Chao ZhangAbstract
Large language model (LLM) computer-use agents are typically evaluated with clean written instructions, despite speech being an increasingly popular interface for interacting with such systems. Speech input introduces an additional failure point: transcription errors can alter task-critical entities, constraints, or targets before the agent begins reasoning, while conventional ASR metrics do not directly measure whether the information required for successful execution has been preserved. We introduce Talk2Agent, a benchmark for evaluating how effectively voice interfaces convey human-spoken instructions to LLM-based computer-use agents. Talk2Agent builds human-spoken versions of tasks from WildClawBench and OSWorld and evaluates a range of voice interfaces, including dedicated ASR models, audio-capable LLMs, contextual biasing, and LLM-based ontology repair. Because repeatedly executing long-horizon computer-use tasks is costly and stochastic, we further propose an execution-free, task-conditioned evaluation framework that projects the original task grader onto prompt-addressable intentions and measures how much task-relevant information is retained after the voice interface. On WildClawBench, Talk2Agent's execution-free native projection provides a practical, execution-grounded measure of voice-interface quality, correlating with downstream task completion and improving Pearson correlation by 0.246 over WER/CER on 32 hours of real human speech.
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URL
https://arxiv.org/abs/2609.38867
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RareDx: Controlled Knowledge Integration and Graph-Grounded Policy Optimization for Rare-Disease Diagnosis
2026-09-29 07:14:46Bo Zhang, Yuchen Wang, Dongbai Li, Matthew Yu Heng Wong, Qingkai Zeng, Lijun Wang, Tien-Yin Wong, Peng Cui, Tianyu LiuAbstract
Rare-disease diagnosis is a long-tail reasoning problem: phenotypes are incomplete, individual disorders are sparsely documented, and relevant evidence is distributed across ontologies, gene annotations, and biomedical text. Language models consequently favor common conditions, miss rare candidates, or produce plausible but invalid names. We introduce RareDx, which couples controlled evidence use with knowledge-graph-grounded policy optimization. RareDx-Harness normalizes heterogeneous records into one ranked-diagnosis task and compares direct inference, static retrieval, adaptive tools, and structured phenotype-gene-disease reasoning over a shared knowledge layer. The training pipeline combines Top-10 post-training with RareDx-KGPO, our knowledge-graph-grounded policy optimization method. Its reward projects predictions into a canonical disease graph and integrates curated graded relevance, ontology proximity, biomedical similarity, and phenotype consistency. Vocabulary and output-budget constraints prevent dense partial credit from rewarding fabricated or overlong differentials. Across eight benchmarks, the complete RareDx system centered on Qwen3.5-9B reaches 38.34 macro Hit@10, 1.60 points above GPT-5.5 under the archived protocol; a disjoint validation-selection audit retains a 6.80-point routing gain over Direct on held-out cases. The 27B system reaches 23.53/36.56/40.76 at Hit@1/5/10. Controlled ablations show that retrieval is not uniformly helpful and that controlled routing is central to the gain. These results indicate that structured medical knowledge can turn a compact model into a competitive diagnostic ranker across heterogeneous long-tail settings in clinical practice.
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URL
https://arxiv.org/abs/2609.35549
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GeoOutageBench: Benchmarking Ambiguity-aware, Ontology-grounded Geospatiotemporal KGQA for Multimodal Power Outage and Resilience Analysis
2026-09-28 18:26:22Ethan D. Frakes, Amy Kvien, Rishabh Kundu, Redad Mehdi, Van D. Tran, Vibha S. Mandayam, Kristopher O. Davis, Erika I. Barcelos, Roger H. French, Yinghui Wu, Mengjie LiAbstract
We introduce GeoOutageBench, a benchmark for assessing LLM-based geospatiotemporal KGQA for multimodal outage and resilience analysis. Unlike existing KGQA benchmarks for Web knowledge, GeoOutageBench considers a spatiotemporal KG that integrates visual, textual, and structured data from outage records, remote sensing, weather observations, storm and power events, geographic entities, and domain ontologies. It provides a competency query taxonomy at different difficulty levels from spatiotemporal containment and proximity, spatiotemporal co-occurrence analysis, multimodal evidence, to hypothetical evaluation. Over multimodal KG and query classes, GeoOutageBench provides user-configurable evaluation of three important, highly coherent yet less studied tasks: (1) LLMs' understanding for ambiguous geospatiotemporal questions in terms of NL to SPARQL interpretation, (2) query-driven assessment of ontology utility, and (3) answer accuracy of multimodal KGQA retrieval. GeoOutageBench provides a design principle and foundation for assessing LLM-KG systems that support real-world infrastructure resilience analysis. Our benchmark, source code, data, results, and other documentation are available at this https URL.
Abstract (translated)
URL
https://arxiv.org/abs/2609.36082
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HCOE: Hyperbolic Clinical Ontology Embeddings from Biomedical Language Models
2026-09-25 03:39:25Yixuan Li, Weihao Li, Ziyang SongAbstract
Biomedical language models (LMs) encode textual semantics but do not explicitly preserve medical code hierarchies. We present Hyperbolic Clinical Ontology Embeddings (HCOE) for hierarchy-aware clinical concept representation. HCOE maps frozen BioBERT embeddings into a Poincare ball, combining parent-side and child-side ontology-guided contrastive learning with coarse-to-fine ontology-path aggregation. It uses International Classification of Diseases (ICD) codes organized by Clinical Classifications Software (CCS) and Anatomical Therapeutic Chemical (ATC) medication hierarchies. Evaluations show that HCOE performs best on ICD/ATC clinical relation prediction and CCS-to-PheCode hierarchy transfer. On the MIMIC-IV dataset, HCOE also achieves the best performance on mortality prediction, readmission prediction, medication recommendation, and rare drug prediction.
Abstract (translated)
URL
https://arxiv.org/abs/2609.30763
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Benchy: towards a universal language for task-oriented AI benchmarks
2026-09-24 20:57:44Francis F Daniel, Mauro Iba\~nez, Francis Perelman, Marian BastiAbstract
Benchy is a semantic language and execution engine for benchmarking AI programs. A benchmark is completely specified by a program, a scoring function, and a dataset, B=(P,S,D), and is separate from the AI-system taking it; a run binds the two, R=(B,AI). Benchmarks are authored as canonical YAML in which each semantic concept has one valid syntax, classified by a shared task/domain/language ontology, and deterministically compiled into a canonical JSON intermediate representation that the engine executes. Compilation changes representation, not meaning: it does not repair invalid definitions or inject hidden defaults. Programs use fixed schemas of named input and output fields, the leaf output fields are the scoring dimensions, and the engine exposes one universal runtime contract --- a named-field input object in, a named-field output object out --- to which external AI-systems adapt at the boundary, so integration mechanics never propagate into benchmark semantics. This paper gives the semantic object model, the ontology and task-to-program validation rule, the scoring and failure semantics, the compilation and execution architecture, and the scope of the current language. An appendix fixes the normative engineering contract for the first engine implementation.
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URL
https://arxiv.org/abs/2609.30550
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Ontology-Mediated Neurosymbolic Constraint Acquisition from Multiple Stakeholders
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Neurosymbolic research typically assumes a pre-existing symbolic specification, leaving the upstream challenge of acquiring and formalizing requirements and constraints largely unaddressed. We present an architecture that fills this gap by using an OWL configuration ontology to mediate between neural constraint sources and downstream consumers. In this framework, LLM assistants elicit soft stakeholder preferences, while hardware specifications define hard physical and engineering limits. The ontology unifies these heterogeneous inputs, leverages description logic to identify unsatisfiability, and generates symbolic explanations that enable LLMs to interactively renegotiate terms with users. Any remaining conflicts are resolved downstream via priority-based relaxation. We illustrate our approach on a microgrid use case from the FLEXI project and argue its generalizability to multi-stakeholder domains where constraint acquisition is distributed across human and automated sources of unequal authority.
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URL
https://arxiv.org/abs/2609.29876
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UniDataAgent: An Ontology-Grounded Agent for Enterprise Question-to-Report Automation
2026-09-23 02:42:34Yutai Duan, Yahui Zhao, Zhangti Li, Yu Ma, Zhenfeng Qi, Shaoyang Yuan, Jing Fan, Jie LiuAbstract
Enterprise data agents must preserve organization specific semantics, not just translate questions into queries. We present ChinaUnicom DataAgent (UniDataAgent), an ontology grounded system for reusable question-to-report analysis that separates semantic acquisition from online execution. Ontology Acquisition and Validation stage (OAV) builds versioned enterprise ontologies from metadata, business knowledge, and supporting materials through expert authored business skills, constrained generation, question verification, and selected expert review. Question-to-Report Execution (QRE) stage retrieves semantic contracts for each question, coordinates skills and data tools, validates results, and produces evidence linked reports. Across 27 enterprise tables and roughly thousands of metric types, ontology construction took a few hours instead of about one week manually. It took just a few minutes to generate the reports, instead of several working days. Ontology grounding achieved 95.0\% strict accuracy on real business questions, versus 72.5\% for document RAG, especially on structured and compositional tasks. The system has already been deployed to generate cost savings and has the potential to be replicated in other enterprises.
Abstract (translated)
URL
https://arxiv.org/abs/2609.27257
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Towards Systematic Qualification of Vision-Language Models for Automotive Perception Systems
2026-09-22 09:51:12Malsha Ashani Mahawatta Dona, Konstantinos Rokanas, Alexander S\"afstr\"om, Krishna Ronanki, Christian BergerAbstract
The field of Artificial Intelligence has been adopted for many application domains. Vision Language Models are one of the recently advanced AI techniques that have been explored to support automotive features such as vehicle perception, and safety assurance. However, such language models are prone to hallucinations, posing a potential threat to the safety of automotive systems that may incorporate them. Within the automotive domain, VLMs could not only hallucinate traffic objects, but could also fail to identify traffic objects that are actually present, which may potentially lead to dangerous situations. Though we have observed a growing body of literature that proposes verification and validation techniques for safe and trustworthy AI, these methods are often studied in isolation, focusing either on run-time or design-time phases. Such isolated techniques could be insufficient in safety-critical, realistic contexts such as automotive perception systems. In this paper, we analyze design-time and run-time verification and validation techniques based on a taxonomy presented by Huang et al. We present an automotive study in which a design-time qualification workflow is proposed to complement run-time monitoring. This workflow combines a fixed safety-relevant ontology-based structured annotation system together with a synonym-based evaluation process to statistically evaluate three state-of-the-art VLMs against data from the nuScenes dataset. We observed that the proposed technique enables deterministic and repeatable quantification of the hallucinations VLMs generate in automotive perception-related tasks. The proposed workflow supports model comparison and deployment-oriented engineering decisions within the design-time verification and validation process and will contribute to a holistic verification strategy that strives towards trustworthy automotive perception systems
Abstract (translated)
URL
https://arxiv.org/abs/2609.25945
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The Copy Ceiling: An Input-Exposure Control for Ontology-Grounded Generation over Curated Corpora
Abstract
When a language model answers from a curated corpus via graph-based retrieval, a large grounding uplift does not establish reasoning over the retrieved structure: the context may already expose the gold answers. We propose exposure accounting, which classifies each gold item by whether the shown context exposes it and whether the answer recovers it. Its scalar reference is the copy ceiling, the recall a verbatim copy of the context achieves; signed gain over copy measures the model's recall relative to this deterministic, judge-free baseline. Across ten models, unaided recall averages 0.26 and grounded recall 0.92, yet gain over copy is uniformly negative (-0.067 to -0.022). Of 11,360 gold-item observations, representing 1,136 target instances evaluated under ten models, only three unexposed items receive lexical credit. A stratified model-judged audit of 423 observations, with a symmetric quotation-verification policy, estimates that 97.1% of credited items assert the requested relation; all three unexposed credits fail relational adjudication. On targets the scaffold does not expose, lexical recovery falls from 0.121 unaided to 0.004 grounded; adjudication validates 71 of the 92 unaided credits and none of the three grounded credits, without establishing full-frame relational recovery rates. Rephrasing questions outside the graph's title vocabulary reduces exposure from 0.964 to 0.328, while an absence-triggered fallback activates on only 2 of 506 questions. A paired production study improves judged quality by +0.27 pooled, but negative controls do not establish content specificity beyond a well-formed on-corpus block. These results support exposure accounting as a standing control for corpus-derived evaluations. The accounting distinguishes exposed-item omissions from beyond-exposure recoveries; it does not determine whether reasoning occurred.
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URL
https://arxiv.org/abs/2609.24885
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QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation
2026-09-21 13:09:59Demian Pavlyshenko, Bohdan PavlyshenkoAbstract
Functional annotation of newly sequenced proteins remains a bottleneck in molecular biology: the number of sequences in public repositories grows far faster than the capacity for manual curation. Most computational approaches consider annotation as multi-label classification over a fixed ontology, which constrains predictions to a predefined label set. In this work we study the the protein annotation as a sequence-to-text generation problem. We fine-tune the 3B-parameter Ministral 3 base model with QLoRA (4-bit NF4 quantization with low-rank adapters) on sequence annotation pairs. We assess predictions with an LLM-as-expert protocol: a GPT model prompted as a senior molecular-biology curator scores organism identification as binary and function annotation quality. We conclude that QLoRA-fine-tuned compact LLMs can generate curator-style annotations with genuine biological value for a substantial subset of proteins. We also discuss future directions in data quality, model scaling, and evidence grounding that are needed to make the approach sufficiently reliable for practical use.
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URL
https://arxiv.org/abs/2609.24538
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Blind Thermodynamic Ontology Discovery from Anonymous Experiments
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Before a machine learning model can learn a thermodynamic equation of state, it must discover what its measurements represent: which channels scale with system size, which are intensive conjugates, how sectors pair through contact, and which potential governs stability. When sensors expose only an unknown linear mixture of extensive states and intensive responses, passive observations cannot disentangle physical quantities from coordinate artifacts. We formulate the problem of discovering this hidden thermodynamic ontology directly from anonymous controlled experiments. We present an operational identifiability theory and a constructive polynomial-time algorithm that extracts extensive and intensive scaling sectors from replication contrasts, recovers their dual cotangent pairing from thermal contact and reciprocity, verifies a globally admissible concave potential via discrete cyclic concavity, and determines an invariant matroid of reservoir ensembles. We prove that the residual observational equivalence is strictly (x, lambda) ~ (A x, a A^{-T} lambda + beta), establishing the sharp observational limit that no permitted experiment can break. Blind evaluations on van der Waals fluids and Curie-Weiss magnets confirm robust recovery under ill-conditioned mixing, correctly resolving anonymous Maxwell tie-lines while rejecting non-equilibrium continuations. External validation across six real fluids from the NIST WebBook demonstrates that operational ontology discovery transfers across real physical substances without coordinate leakage.
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URL
https://arxiv.org/abs/2609.23387
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Discovering Physical Representation Languages
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Before a machine can discover a physical law, it must discover what its measurements are: which observations live on cells, which are intensive or extensive, which sectors are dual, and which distinctions are merely gauge. We introduce physical representation-language discovery, the problem of recovering this hidden ontology directly from anonymous controlled experiments. We give an identifiability theory and constructive polynomial-time procedure that recovers a carrier and differential sequence, measurement types and orientation twist, noninvertible refinement semantics, primal-dual Maxwell diagrams, and the residual equivalences that no permitted experiment can break. The theory turns material nuisance into a commutant, uses refinement to separate quantities from coordinates, and selects physics only after its representation has been recovered. For a certified finite experiment family, we prove an end-to-end two-stage measurement bound and a matching minimax rate in dimension, accuracy, and confidence. Blind Maxwell experiments recover complete primal/relative-dual ontologies on regular and unstructured carriers under jointly corrupted observations; an independent unstructured RLC system demonstrates that the result is not specific to Maxwell. The framework scales to tens of thousands of cells per carrier, while stress audits demonstrate robustness across severe physical regimes - including non-Markovian memory, nonlinearities, nonlocality, and complex constitutive hysteresis. A public FDTD audit demonstrates the emergence of anonymous curl structure from incomplete field data, while characterizing the informational prerequisites for complete recovery. The goal is to move scientific ML from learning laws in a human-supplied language to discovering the language in which laws become expressible, establishing exact theoretical limits on observational identifiability.
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URL
https://arxiv.org/abs/2609.23381
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Graph Memory for LLM Agents: At What Cost? A Comparative Evaluation of Query, Ingest, and Update Performance Across Graph Database Engines
2026-09-20 03:04:30Donald Nguyen, Gurbinder Gill, Hadi Ahmadi, Christopher J. RossbachAbstract
Graph databases are frequently positioned as categorically necessary for connected-data workloads, yet the systems dimension along which they actually differ - query planning, indexing, and data-readiness cost - is rarely isolated from vendor framing. We construct a synthetic, biomedical-shaped property graph (1.02 million nodes, 5.34 million total node and edge rows) and a twenty-query workload spanning neighborhood lookups, bounded paths, set intersections, anti-joins, grouped aggregation, top-k ranking, temporal filters, full scans, and relational joins. We benchmark Corvic AI - a purpose-built columnar query engine underlying Corvic's ontology management layer ("memories")- against seven purpose-built or graph-extension database systems (LoraDB, Ladybug, DuckPGQ, Memgraph, Neo4j, HugeGraph, and FalkorDB) at three graph scales spanning three orders of magnitude. We report query latency geomeans, bulk-ingest throughput, point-update latency, and answer correctness for each system, and we derive a simple total-cost-of-ownership model that expresses the ingest/query trade-off as a function of query volume. Our central finding is that no system in this sample is categorically fastest: a native graph engine (Ladybug) outperforms Corvic AI on narrow, bounded-neighborhood shapes, while Corvic AI is faster on shapes that scan or join a large fraction of the graph, and a system implementing graph query syntax via SQL/PGQ (DuckPGQ) is measurably slower purely due to query-plan choice. The dominant cost differential in our data is not query latency but the cost of making data queryable at all: bulk-ingest throughput varies by three orders of magnitude across engines (5.0k-4.3M rows/s), a gap that a simple crossover-point calculation shows dominates total cost for any workload with fewer than roughly 105 queries per data refresh.
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URL
https://arxiv.org/abs/2609.23315
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Integrating knowledge from case reports: a medical ontology based multimodal information system with structured summary
2026-09-17 06:41:18Shuyu Guo, Lan Huang, Yichen Liu, Hanbin Ma, Tian BaiAbstract
Published medical case reports serve as a crucial medical information carrier, documenting discoveries in rare diseases, diagnostic methods, and innovative treatments. Despite the wealth of clinical knowledge in millions of case reports in the public medicine literature database (PubMed), accessing relevant information efficiently is hindered by the limitations of traditional keyword-based retrieval tools on unstructured and diverse case reports. To address the above issues, we introduce a comprehensive multimodal information system for case reports integrating structured clinical summaries of patients including medical images and biomedical named entities from 52949 open-access case reports published from 2000 to 2021. The multimodal essential information is organized in a well-structured medical ontology. Also, a powerful interface for searching and browsing case reports is designed to assist junior clinicians in retrieving cases effectively and improving the identification and diagnosis of rare diseases.
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URL
https://arxiv.org/abs/2609.19775
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Large Language Model Agents for Evidence Based Genetic Disease Severity Classification
2026-09-17 01:56:38Tohid Ghasemnejad, Ahmadreza Argha, Mark Grosser, John Wang, Min Yang, Thantrira Porntaveetus, Tony Roscioli, Nigel H. Lovell, Mahmoud Aarabi, Hamid Alinejad-RoknyAbstract
Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap. We developed an autonomous AI agent integrating Reasoning and Acting (ReAct) with Retrieval-Augmented Generation (RAG) to classify 10,211 Human Phenotype Ontology terms. It uses American College of Medical Genetics (ACMG)-endorsed severity guidelines and American College of Obstetricians and Gynecologists (ACOG) quality-of-life criteria to retrieve PubMed literature, generate interpretable reasoning chains, and independently verify claims. At the phenotype level, using expert-curated cohorts, the agent achieved 93.55% accuracy (MCC 0.9237) with 82.6% to 91.4% of claims supported by direct evidence or valid inferences. Gene-level severity was aggregated across 8,738 pairs, identifying 3,283 autosomal recessive pairs with severe or profound presentations. External validation showed 95.2% concordance with Mackenzie's Mission gene list. This system enables standardized panel design by providing reliable, automated classification supported by direct evidence.
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URL
https://arxiv.org/abs/2609.19569
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Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs
2026-09-16 11:11:46Pietro Miotto, Lucia Mellini, Tommaso Marzi, Cesare Alippi, Elena Casiraghi, Alberto Paccanaro, Giorgio Valentini, Mauricio Soto-GomezAbstract
Biomedical knowledge graphs combine ontology-derived hierarchies with transversal associations among heterogeneous entities such as phenotypes, diseases, genes, proteins, and patients. This hybrid structure raises the question of whether hyperbolic embeddings, which naturally capture tree-like organization, remain useful beyond purely hierarchical graphs. We present a preliminary study of hyperbolic graph representation learning for Mendelian-disease differential diagnosis on a patient-integrated biomedical graph. Experiments on isolated ontology subgraphs show that hyperbolic models achieve strong performance in substantially lower dimensions than Euclidean baselines. We then evaluate the models on a link-prediction task that ranks candidate diseases for each patient. Results suggest that hyperbolic embeddings can exploit biomedical hierarchical structure while supporting diagnostic reasoning over heterogeneous patient-level graphs.
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URL
https://arxiv.org/abs/2609.18481
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Too Good to Be Real? Diagnosing and Reducing the Gap Between AI Preference and Real User Engagement
2026-09-16 08:04:14Xinglang Zhang, Yuanmeng Xiang, Yunyao Zhang, Zeliang Chen, Junqing Yu, Zikai SongAbstract
Large language models are increasingly used to generate and evaluate online content, yet it remains unclear whether the qualities they associate with higher engagement match what real users respond to. We study this question using 1.17 million answers to 25,978 questions from Zhihu, Quora, and Reddit, comparing real platform answers and AI-generated answers across four within-question engagement levels. We introduce Ontological Preference Measurement, which represents answers along three dimensions: logic, affect, and expression. We find a systematic gap between AI preference and real user engagement: as target engagement increases, LLMs add more explicit logical structure, while real user engagement is more strongly associated with affective and expressive salience. We call this tendency logic overbinding. Based on this diagnosis, we propose Ontology-Masked Reasoning Autoencoding (OMRA), a controlled intervention that masks and reconstructs over-explained spans while preserving stance, factual content, and coherence. Across four LLM families, OMRA reduces the measured gap by an average of 54.4%. In human evaluation, OMRA wins 62.4% of pairwise preference judgments against matched real platform answers, even though the real answers are more often judged to be human-written.
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URL
https://arxiv.org/abs/2609.18282
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SNOMED CT Concept Recommendation from Masked Clinical Context
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Standardizing clinical language to SNOMED CT supports interoperability, analytics, and reusable phenotyping, but concept recommendation remains difficult when relevant concepts are rare or absent from training data. We present a masked-concept recommendation benchmark using the SNOMED CT Entity Linking Challenge v1.2.1 data derived from MIMIC-IV-Note. The dataset contains 75,491 annotations across 272 discharge summaries, with 204 notes used for training and 68 for historical testing. For each unique note-concept pair, the target mention is masked from a local clinical context and the system ranks SNOMED CT concepts observed during training. We compare a popularity baseline, sparse TF-IDF concept prototypes, dense latent semantic analysis embeddings, sparse-dense fusion, retrieved-note evidence, and a retrieval-augmented hybrid. Sparse TF-IDF performs best, achieving Recall@1 of 14.81%, Recall@10 of 33.43%, MRR of 0.2114, and nDCG@10 of 0.2297. Retrieval augmentation does not improve this baseline, with Recall@10 of 31.99% and MRR of 0.1937. Performance is strongly affected by concept frequency: Recall@10 is 7.74% for concepts appearing in only one or two training notes versus 43.90% for concepts appearing in more than ten. In addition, 9.66% of test note-concept pairs contain concepts unseen during training. These findings show that local lexical context and terminology coverage are major determinants of recommendation quality in low-resource settings and provide a reproducible baseline for future ontology-grounded and biomedical-encoder retrieval systems.
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URL
https://arxiv.org/abs/2609.17855
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Extracting ontology-compliant knowledge from scientific text describing irradiated materials using large language models
2026-09-15 15:05:57Marco Luca Sbodio, Marcos Mart\'inez Galindo, Vanessa Lopez, Blanca Biel, Pablo Canca, Pedro Delgado, Jes\'us I. Mendieta-Moreno, Raphael Tack, Maria J. CaturlaAbstract
The quest for new materials increasingly relies on predictive models and comprehensive simulations that span scales from atomic to macroscopic levels. However, essential data necessary for these models and simulations are often embedded in scientific literature as unstructured text, limiting reusability and posing challenges for researchers seeking to leverage existing knowledge effectively. While extracting structured data from unstructured text using large language models is gaining popularity, traditional methods typically generate key-value pairs data with straightforward schemas. In contrast, we introduce eolas, a modular pipeline that uses large language models to automatically transform scientific documents into knowledge graphs aligned with a specified ontology. We demonstrate eolas effectiveness in extracting useful information for scientists studying materials designed to endure the extreme temperatures and radiation levels found in fusion reactors. While a human expert might spend between thirty to ninety minutes extracting relevant data from an article, eolas can generate high-quality knowledge graphs in just a few minutes. These are presented in a tabular format with faceted navigation for easy human validation. Additionally, we introduce the first benchmark dataset designed to assess large language models capabilities in constructing knowledge graphs within the domain of irradiated materials. The analysis of 168 experiments using our dataset, various large language models and prompting techniques provides key insights that we summarize into practical guidelines for effectively extracting knowledge graphs aligned with an input ontology.
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URL
https://arxiv.org/abs/2609.17291
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