In recent years, querying semantic web data using SPARQL has remained challenging, especially for non-expert users, due to the language's complex syntax and the prerequisite of understanding intricate data structures. To address these challenges, we propose InteracSPARQL, an interactive SPARQL query generation and refinement system that leverages natural language explanations (NLEs) to enhance user comprehension and facilitate iterative query refinement. InteracSPARQL integrates LLMs with a rule-based approach to first produce structured explanations directly from SPARQL abstract syntax trees (ASTs), followed by LLM-based linguistic refinements. Users can interactively refine queries through direct feedback or LLM-driven self-refinement, enabling the correction of ambiguous or incorrect query components in real time. We evaluate InteracSPARQL on standard benchmarks, demonstrating significant improvements in query accuracy, explanation clarity, and overall user satisfaction compared to baseline approaches. Our experiments further highlight the effectiveness of combining rule-based methods with LLM-driven refinements to create more accessible and robust SPARQL interfaces.

Documents are a common way to store and share information, with tables being an important part of many documents. However, there is no real common understanding of how to model documents and tables in particular. Because of this lack of standardization, most scientific approaches have their own way of modeling documents and tables, leading to a variety of different data structures and formats that are not directly compatible. Furthermore, most data models focus on either the spatial or the semantic structure of a document, neglecting the other aspect. To address this, we developed S2Doc, a flexible data structure for modeling documents and tables that combines both spatial and semantic information in a single format. It is designed to be easily extendable to new tasks and supports most modeling approaches for documents and tables, including multi-page documents. To the best of our knowledge, it is the first approach of its kind to combine all these aspects in a single format.

Court judgments reveal how legal rules have been interpreted and applied to facts, providing a foundation for understanding structured legal reasoning. However, existing automated approaches for capturing legal reasoning, including large language models, often fail to identify the relevant legal context, do not accurately trace how facts relate to legal norms, and may misrepresent the layered structure of judicial reasoning. These limitations hinder the ability to capture how courts apply the law to facts in practice. In this paper, we address these challenges by constructing a legal knowledge graph from 648 Japanese administrative court decisions. Our method extracts components of legal reasoning using prompt-based large language models, normalizes references to legal provisions, and links facts, norms, and legal applications through an ontology of legal inference. The resulting graph captures the full structure of legal reasoning as it appears in real court decisions, making implicit reasoning explicit and machine-readable. We evaluate our system using expert annotated data, and find that it achieves more accurate retrieval of relevant legal provisions from facts than large language model baselines and retrieval-augmented methods.

Large language models (LLMs) have demonstrated exceptional capabilities across multiple domains by leveraging massive pre-training and curated fine-tuning data. However, in data-sensitive fields such as healthcare, the lack of high-quality, domain-specific training corpus hinders LLMs' adaptation for specialized applications. Meanwhile, domain experts have distilled domain wisdom into ontology rules, which formalize relationships among concepts and ensure the integrity of knowledge management repositories. Viewing LLMs as implicit repositories of human knowledge, we propose Evontree--a novel framework that leverages a small set of high-quality ontology rules to systematically extract, validate, and enhance domain knowledge within LLMs, without requiring extensive external datasets. Specifically, Evontree extracts domain ontology from raw models, detects inconsistencies using two core ontology rules, and reinforces the refined knowledge via self-distilled fine-tuning. Extensive experiments on medical QA benchmarks with Llama3-8B-Instruct and Med42-v2 demonstrate consistent outperformance over both unmodified models and leading supervised baselines, achieving up to a 3.7% improvement in accuracy. These results confirm the effectiveness, efficiency, and robustness of our approach for low-resource domain adaptation of LLMs.

Does vision-and-language (VL) training change the linguistic representations of language models in meaningful ways? Most results in the literature have shown inconsistent or marginal differences, both behaviorally and representationally. In this work, we start from the hypothesis that the domain in which VL training could have a significant effect is lexical-conceptual knowledge, in particular its taxonomic organization. Through comparing minimal pairs of text-only LMs and their VL-trained counterparts, we first show that the VL models often outperform their text-only counterparts on a text-only question-answering task that requires taxonomic understanding of concepts mentioned in the questions. Using an array of targeted behavioral and representational analyses, we show that the LMs and VLMs do not differ significantly in terms of their taxonomic knowledge itself, but they differ in how they represent questions that contain concepts in a taxonomic relation vs. a non-taxonomic relation. This implies that the taxonomic knowledge itself does not change substantially through additional VL training, but VL training does improve the deployment of this knowledge in the context of a specific task, even when the presentation of the task is purely linguistic.

As human machine teaming becomes central to paradigms like Industry 5.0, a critical need arises for machines to safely and effectively interpret complex human behaviors. A research gap currently exists between techno centric robotic frameworks, which often lack nuanced models of human behavior, and descriptive behavioral ontologies, which are not designed for real time, collaborative interpretation. This paper addresses this gap by presenting OntoPret, an ontology for the interpretation of human behavior. Grounded in cognitive science and a modular engineering methodology, OntoPret provides a formal, machine processable framework for classifying behaviors, including task deviations and deceptive actions. We demonstrate its adaptability across two distinct use cases manufacturing and gameplay and establish the semantic foundations necessary for advanced reasoning about human intentions.

Neuroscience research publications encompass a vast wealth of knowledge. Accurately retrieving existing information and discovering new insights from this extensive literature is essential for advancing the field. However, when knowledge is dispersed across multiple sources, current state-of-the-art retrieval methods often struggle to extract the necessary information. A knowledge graph (KG) can integrate and link knowledge from multiple sources. However, existing methods for constructing KGs in neuroscience often rely on labeled data and require domain expertise. Acquiring large-scale, labeled data for a specialized area like neuroscience presents significant challenges. This work proposes novel methods for constructing KG from unlabeled large-scale neuroscience research corpus utilizing large language models (LLM), neuroscience ontology, and text embeddings. We analyze the semantic relevance of neuroscience text segments identified by LLM for building the knowledge graph. We also introduce an entity-augmented information retrieval algorithm to extract knowledge from the KG. Several experiments were conducted to evaluate the proposed approaches. The results demonstrate that our methods significantly enhance knowledge discovery from the unlabeled neuroscience research corpus. The performance of the proposed entity and relation extraction method is comparable to the existing supervised method. It achieves an F1 score of 0.84 for entity extraction from the unlabeled data. The knowledge obtained from the KG improves answers to over 52% of neuroscience questions from the PubMedQA dataset and questions generated using selected neuroscience entities.

Background: Evidence synthesis facilitates evidence-based medicine. This task becomes increasingly difficult to accomplished with applying computational solutions, since the medical literature grows at astonishing rates. Objective: This study evaluates an information retrieval-driven workflow, CASMA, to enhance the efficiency, transparency, and reproducibility of systematic reviews. Endometriosis recurrence serves as the ideal case due to its complex and ambiguous literature. Methods: The hybrid approach integrates PRISMA guidelines with fuzzy matching and regular expression (regex) to facilitate semi-automated deduplication and filtered records before manual screening. The workflow synthesised evidence from randomised controlled trials on the efficacy of a subclass of gonadotropin-releasing hormone agonists (GnRH-a). A modified splitting method addressed unit-of-analysis errors in multi-arm trials. Results: The workflow sharply reduced the screening workload, taking only 11 days to fetch and filter 33,444 records. Seven eligible RCTs were synthesized (841 patients). The pooled random-effects model yielded a Risk Ratio (RR) of $0.64$ ($95\%$ CI $0.48$ to $0.86$), demonstrating a $36\%$ reduction in recurrence, with non-significant heterogeneity ($I^2=0.00\%$, $τ^2=0.00$). The findings were robust and stable, as they were backed by sensitivity analyses. Conclusion: This study demonstrates an application of an information-retrieval-driven workflow for medical evidence synthesis. The approach yields valuable clinical results and a generalisable framework to scale up the evidence synthesis, bridging the gap between clinical research and computer science.

Relation extraction between drugs plays a crucial role in identifying drug drug interactions and predicting side effects. The advancement of machine learning methods in relation extraction, along with the development of large medical text databases, has enabled the low cost extraction of such relations compared to other approaches that typically require expert knowledge. However, to the best of our knowledge, there are limited datasets specifically designed for drug drug relation extraction currently available. Therefore, employing transfer learning becomes necessary to apply machine learning methods in this domain. In this study, we propose DREAM, a method that first employs a trained relation extraction model to discover relations between entities and then applies this model to a corpus of medical texts to construct an ontology of drug relationships. The extracted relations are subsequently validated using a large language model. Quantitative results indicate that the LLM agreed with 71 of the relations extracted from a subset of PubMed abstracts. Furthermore, our qualitative analysis indicates that this approach can uncover ambiguities in the medical domain, highlighting the challenges inherent in relation extraction in this field.

Constructing comprehensive knowledge graphs requires the use of multiple ontologies in order to fully contextualize data into a domain. Ontology matching finds equivalences between concepts interconnecting ontologies and creating a cohesive semantic layer. While the simple pairwise state of the art is well established, simple equivalence mappings cannot provide full semantic integration of related but disjoint ontologies. Complex multi-ontology matching (CMOM) aligns one source entity to composite logical expressions of multiple target entities, establishing more nuanced equivalences and provenance along the ontological hierarchy. We present CMOMgen, the first end-to-end CMOM strategy that generates complete and semantically sound mappings, without establishing any restrictions on the number of target ontologies or entities. Retrieval-Augmented Generation selects relevant classes to compose the mapping and filters matching reference mappings to serve as examples, enhancing In-Context Learning. The strategy was evaluated in three biomedical tasks with partial reference alignments. CMOMgen outperforms baselines in class selection, demonstrating the impact of having a dedicated strategy. Our strategy also achieves a minimum of 63% in F1-score, outperforming all baselines and ablated versions in two out of three tasks and placing second in the third. Furthermore, a manual evaluation of non-reference mappings showed that 46% of the mappings achieve the maximum score, further substantiating its ability to construct semantically sound mappings.