Ontology
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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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URL
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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URL
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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URL
https://arxiv.org/abs/2610.00682
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Ontology-Based Contextual AI Evaluations Methodology
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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.
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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.
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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.
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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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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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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.
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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
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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
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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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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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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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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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https://arxiv.org/abs/2609.23381
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