Pretraining a language model (LM) on text has been shown to help various downstream NLP tasks.

The Semantic Table Annotation (STA) task, which includes Column Type Annotation (CTA) and Cell Entity Annotation (CEA), maps table contents to ontology entities and plays important roles in various semantic applications. However, complex tables often pose challenges such as semantic loss of column names or cell values, strict ontological hierarchy requirements, homonyms, spelling errors, and abbreviations, which hinder annotation accuracy. To address these issues, this paper proposes an LLM-based agent approach for CTA and CEA. We design and implement five external tools with tailored prompts based on the ReAct framework, enabling the STA agent to dynamically select suitable annotation strategies depending on table characteristics. Experiments are conducted on the Tough Tables and BiodivTab datasets from the SemTab challenge, which contain the aforementioned challenges. Our method outperforms existing approaches across various metrics. Furthermore, by leveraging Levenshtein distance to reduce redundant annotations, we achieve a 70% reduction in time costs and a 60% reduction in LLM token usage, providing an efficient and cost-effective solution for STA.

Effective Question Answering (QA) on large biomedical document collections requires effective document retrieval techniques. The latter remains a challenging task due to the domain-specific vocabulary and semantic ambiguity in user queries. We propose BMQExpander, a novel ontology-aware query expansion pipeline that combines medical knowledge - definitions and relationships - from the UMLS Metathesaurus with the generative capabilities of large language models (LLMs) to enhance retrieval effectiveness. We implemented several state-of-the-art baselines, including sparse and dense retrievers, query expansion methods, and biomedical-specific solutions. We show that BMQExpander has superior retrieval performance on three popular biomedical Information Retrieval (IR) benchmarks: NFCorpus, TREC-COVID, and SciFact - with improvements of up to 22.1% in NDCG@10 over sparse baselines and up to 6.5% over the strongest baseline. Further, BMQExpander generalizes robustly under query perturbation settings, in contrast to supervised baselines, achieving up to 15.7% improvement over the strongest baseline. As a side contribution, we publish our paraphrased benchmarks. Finally, our qualitative analysis shows that BMQExpander has fewer hallucinations compared to other LLM-based query expansion baselines.

We study a fitting problem inspired by ontology-mediated querying: given a collection of positive and negative examples of the form $(\mathcal{A},q)$ with $\mathcal{A}$ an ABox and $q$ a Boolean query, we seek an ontology $\mathcal{O}$ that satisfies $\mathcal{A} \cup \mathcal{O} \vDash q$ for all positive examples and $\mathcal{A} \cup \mathcal{O}\not\vDash q$ for all negative examples. We consider the description logics $\mathcal{ALC}$ and $\mathcal{ALCI}$ as ontology languages and a range of query languages that includes atomic queries (AQs), conjunctive queries (CQs), and unions thereof (UCQs). For all of the resulting fitting problems, we provide effective characterizations and determine the computational complexity of deciding whether a fitting ontology exists. This problem turns out to be ${\scriptsize CO}NP$ for AQs and full CQs and $2E{\scriptsize XP}T{\scriptsize IME}$-complete for CQs and UCQs. These results hold for both $\mathcal{ALC}$ and $\mathcal{ALCI}$.

Metaphorical meaning is not a flat mapping between concepts, but a complex cognitive phenomenon that integrates multiple levels of interpretation. In this paper, we propose a stratified model of metaphor processing that treats meaning as an onion: a multi-layered structure comprising (1) content analysis, (2) conceptual blending, and (3) pragmatic intentionality. This three-dimensional framework allows for a richer and more cognitively grounded approach to metaphor interpretation in computational systems. At the first level, metaphors are annotated through basic conceptual elements. At the second level, we model conceptual combinations, linking components to emergent meanings. Finally, at the third level, we introduce a pragmatic vocabulary to capture speaker intent, communicative function, and contextual effects, aligning metaphor understanding with pragmatic theories. By unifying these layers into a single formal framework, our model lays the groundwork for computational methods capable of representing metaphorical meaning beyond surface associations, toward deeper, more context-sensitive reasoning.

Large Language Models (LLMs) have shown significant potential for ontology engineering. However, it is still unclear to what extent they are applicable to the task of domain-specific ontology generation. In this study, we explore the application of LLMs for automated ontology generation and evaluate their performance across different domains. Specifically, we investigate the generalizability of two state-of-the-art LLMs, DeepSeek and o1-preview, both equipped with reasoning capabilities, by generating ontologies from a set of competency questions (CQs) and related user stories. Our experimental setup comprises six distinct domains carried out in existing ontology engineering projects and a total of 95 curated CQs designed to test the models' reasoning for ontology engineering. Our findings show that with both LLMs, the performance of the experiments is remarkably consistent across all domains, indicating that these methods are capable of generalizing ontology generation tasks irrespective of the domain. These results highlight the potential of LLM-based approaches in achieving scalable and domain-agnostic ontology construction and lay the groundwork for further research into enhancing automated reasoning and knowledge representation techniques.

Medication recommendation is a crucial task for assisting physicians in making timely decisions from longitudinal patient medical records. However, real-world EHR data present significant challenges due to the presence of rarely observed medical entities and incomplete records that may not fully capture the clinical ground truth. While data-driven models trained on longitudinal Electronic Health Records often achieve strong empirical performance, they struggle to generalize under missing or novel conditions, largely due to their reliance on observed co-occurrence patterns. To address these issues, we propose Hierarchical Ontology and Network Refinement for Robust Medication Recommendation (HiRef), a unified framework that combines two complementary structures: (i) the hierarchical semantics encoded in curated medical ontologies, and (ii) refined co-occurrence patterns derived from real-world EHRs. We embed ontology entities in hyperbolic space, which naturally captures tree-like relationships and enables knowledge transfer through shared ancestors, thereby improving generalizability to unseen codes. To further improve robustness, we introduce a prior-guided sparse regularization scheme that refines the EHR co-occurrence graph by suppressing spurious edges while preserving clinically meaningful associations. Our model achieves strong performance on EHR benchmarks (MIMIC-III and MIMIC-IV) and maintains high accuracy under simulated unseen-code settings. Extensive experiments with comprehensive ablation studies demonstrate HiRef's resilience to unseen medical codes, supported by in-depth analyses of the learned sparsified graph structure and medical code embeddings.

Digital Twins (DTs) offer powerful tools for managing complex infrastructure systems, but their effectiveness is often limited by challenges in integrating unstructured knowledge. Recent advances in Large Language Models (LLMs) bring new potential to address this gap, with strong abilities in extracting and organizing diverse textual information. We therefore propose LSDTs (LLM-Augmented Semantic Digital Twins), a framework that helps LLMs extract planning knowledge from unstructured documents like environmental regulations and technical guidelines, and organize it into a formal ontology. This ontology forms a semantic layer that powers a digital twin-a virtual model of the physical system-allowing it to simulate realistic, regulation-aware planning scenarios. We evaluate LSDTs through a case study of offshore wind farm planning in Maryland, including its application during Hurricane Sandy. Results demonstrate that LSDTs support interpretable, regulation-aware layout optimization, enable high-fidelity simulation, and enhance adaptability in infrastructure planning. This work shows the potential of combining generative AI with digital twins to support complex, knowledge-driven planning tasks.