Daily Papers

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new BioML track at OAEI 2022.

Self-consistency detects hallucinations by generating multiple sampled answers to a question and measuring agreement, but this requires repeated decoding and can be sensitive to lexical variation. Semantic self-consistency improves this by clustering sampled answers by meaning using natural language inference, but it adds both sampling cost and external inference overhead. We show that first-token confidence, phi_first, computed from the normalized entropy of the top-K logits at the first content-bearing answer token of a single greedy decode, matches or modestly exceeds semantic self-consistency on closed-book short-answer factual question answering. Across three 7-8B instruction-tuned models and two benchmarks, phi_first achieves a mean AUROC of 0.820, compared with 0.793 for semantic agreement and 0.791 for standard surface-form self-consistency. A subsumption test shows that phi_first is moderately to strongly correlated with semantic agreement, and combining the two signals yields only a small AUROC improvement over phi_first alone. These results suggest that much of the uncertainty information captured by multi-sample agreement is already available in the model's initial token distribution. We argue that phi_first should be reported as a default low-cost baseline before invoking sampling-based uncertainty estimation.

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.

Security policy enforcement in contemporary agentic systems predominantly consists of embedding natural-language policies within an agent's system prompt and delegating compliance to the agent's reasoning. This approach admits no formal enforcement guarantee and cannot express policies whose satisfaction depends on the causal history of an execution, a gap that becomes acute in multi-agent systems, where enforcement must reason across agents. We argue that policy enforcement in agentic systems is most naturally understood as a cross-cutting concern, and propose a framework grounded in aspect-oriented programming that specifies policies independent of the agent's reasoning and enforces them at every policy-relevant decision. Policies are written in Datalog over a set of abstract predicates describing the execution context, an observability service governed by a formal assume/guarantee contract maintains these predicates, and a reference monitor consults the policy at each action to produce an enforcement decision. When the environment contract holds, enforcement decisions coincide with the policy's intended semantics. We adopt Datalog as the policy language, a natural fit because it supports declarative rule specification, admits recursion for policies over transitive relationships, and yields deterministic enforcement. Datalog further admits tractable static analyses for contradiction, redundancy, subsumption, and conditional reachability, enabling authors to verify policy intent and surface ambiguities inherent in natural-language specifications. We realize the framework in FORGE, which enforces policies over agentic deployments without modification to the underlying agents. We evaluate FORGE on three case studies: information flow policies for prompt injection defense, approval workflows in a multi-agent pharmacovigilance system, and organizational policies for customer service.

Interpreting hierarchical structures latent in language is a key limitation of current language models (LMs). While previous research has implicitly leveraged these hierarchies to enhance LMs, approaches for their explicit encoding are yet to be explored. To address this, we introduce a novel approach to re-train transformer encoder-based LMs as Hierarchy Transformer encoders (HiTs), harnessing the expansive nature of hyperbolic space. Our method situates the output embedding space of pre-trained LMs within a Poincar\'e ball with a curvature that adapts to the embedding dimension, followed by re-training on hyperbolic cluster and centripetal losses. These losses are designed to effectively cluster related entities (input as texts) and organise them hierarchically. We evaluate HiTs against pre-trained and fine-tuned LMs, focusing on their capabilities in simulating transitive inference, predicting subsumptions, and transferring knowledge across hierarchies. The results demonstrate that HiTs consistently outperform both pre-trained and fine-tuned LMs in these tasks, underscoring the effectiveness and transferability of our re-trained hierarchy encoders.

The iMet 2020 dataset is a valuable resource in the space of fine-grained art attribution recognition, but we believe it has yet to reach its true potential. We document the unique properties of the dataset and observe that many of the attribute labels are noisy, more than is implied by the dataset description. Oftentimes, there are also semantic relationships between the labels (e.g., identical, mutual exclusion, subsumption, overlap with uncertainty) which we believe are underutilized. We propose an approach to cleaning and structuring the iMet 2020 labels, and discuss the implications and value of doing so. Further, we demonstrate the benefits of our proposed approach through several experiments. Our code and cleaned labels are available at https://github.com/sunniesuhyoung/iMet2020cleaned.

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

We present a machine-checked formalization of structurally governed AI workflow architectures and prove that effect-level governance can be imposed without reducing internal computational expressivity. Using Interaction Trees in Rocq 8.19, we define a governance operator G that mediates all effectful directives, including memory access, external calls, and oracle (LLM) queries. Our development compiles with 0 admitted lemmas and consists of 36 modules, ~12,000 lines of Rocq, and 454 theorems. We establishseven properties: (P1) governed Turing completeness, (P2) governed oracle expressivity, (P3) a decidability boundary in which governance predicates are total and closed under Boolean composition while semantic program properties remain non-trivial and undecidable by governance, (P4) goal preservation for permitted executions, (P5) expressive minimality of primitive capabilities (compute, memory, reasoning, external call, observability), (P6) subsumption asymmetry showing structural governance strictly subsumes content-level filtering, and (P7) semantic transparency: on all executions where governance permits, the governed interpretation is observationally equivalent (modulo governance-only events) to the ungoverned interpretation. Together, these results show that governance and computational expressivity are orthogonal dimensions: governance constrains the effect boundary of programs while remaining semantically transparent to internal computation.