Large Language Models (LLMs) are increasingly being integrated into various components of Ontology Matching pipelines. This paper investigates the capability of LLMs to perform ontology matching directly on ontology modules and generate the corresponding alignments. Furthermore, it is explored how a dedicated fine-tuning strategy can enhance the model's matching performance in a zero-shot setting. The proposed method incorporates a search space reduction technique to select relevant subsets from both source and target ontologies, which are then used to automatically construct prompts. Recognizing the scarcity of reference alignments for training, a novel LLM-based approach is introduced for generating a synthetic dataset. This process creates a corpus of ontology submodule pairs and their corresponding reference alignments, specifically designed to fine-tune an LLM for the ontology matching task. The proposed approach was evaluated on the Conference, Geolink, Enslaved, Taxon, and Hydrography datasets from the OAEI complex track. The results demonstrate that the LLM fine-tuned on the synthetically generated data exhibits superior performance compared to the non-fine-tuned base model. The key contribution is a strategy that combines automatic dataset generation with fine-tuning to effectively adapt LLMs for ontology matching tasks.

Ontology Matching (OM) is a cornerstone task of semantic interoperability, yet existing systems often rely on handcrafted rules or specialized models with limited adaptability. We present KROMA, a novel OM framework that harnesses Large Language Models (LLMs) within a Retrieval-Augmented Generation (RAG) pipeline, to dynamically enrich the semantic context of OM tasks with structural, lexical, and definitional knowledge. To optimize both performance and efficiency, KROMA integrates a bisimilarity-based concept matching and a lightweight ontology refinement step, which prune candidate concepts and substantially reduce the communication overhead from invoking LLMs. Through experiments on multiple benchmark datasets, we show that integrating knowledge retrieval with context-augmented LLMs significantly enhances ontology matching--outperforming both classic OM systems and cutting-edge LLM-based approaches--while keeping communication overhead comparable. Our study highlights the feasibility and benefit of the proposed optimization techniques (targeted knowledge retrieval, prompt enrichment, and ontology refinement) for ontology matching at scale. Our code and experimental dataset has been made available at: https://github.com/lamng3/kroma

Ontology alignment plays a crucial role in integrating diverse data sources across domains. There is a large plethora of systems that tackle the ontology alignment problem, yet challenges persist in producing highly quality correspondences among a set of input ontologies. Human-in-the-loop during the alignment process is essential in applications requiring very accurate mappings. User involvement is, however, expensive when dealing with large ontologies. In this paper, we explore the feasibility of using Large Language Models (LLM) as an alternative to the domain expert. The use of the LLM focuses only on the validation of the subset of correspondences where an ontology alignment system is very uncertain. We have conducted an extensive evaluation over several matching tasks of the Ontology Alignment Evaluation Initiative (OAEI), analysing the performance of several state-of-the-art LLMs using different ontology-driven prompt templates. The LLM results are also compared against simulated Oracles with variable error rates.

Hallucinations are inevitable in downstream tasks using large language models (LLMs). While addressing hallucinations becomes a substantial challenge for LLM-based ontology matching (OM) systems, we introduce a new benchmark dataset called OAEI-LLM-T. The dataset evolves from the TBox (i.e. schema-matching) datasets in the Ontology Alignment Evaluation Initiative (OAEI), capturing hallucinations of different LLMs performing OM tasks. These OM-specific hallucinations are carefully classified into two primary categories and six sub-categories. We showcase the usefulness of the dataset in constructing the LLM leaderboard and fine-tuning foundational LLMs for LLM-based OM systems.

Hallucinations of large language models (LLMs) commonly occur in domain-specific downstream tasks, with no exception in ontology matching (OM). The prevalence of using LLMs for OM raises the need for benchmarks to better understand LLM hallucinations. The OAEI-LLM dataset is an extended version of the Ontology Alignment Evaluation Initiative (OAEI) datasets that evaluate LLM-specific hallucinations in OM tasks. We outline the methodology used in dataset construction and schema extension, and provide examples of potential use cases.

Ontology matching is defined as finding a relationship or correspondence between two or more entities in two or more ontologies. To solve the interoperability problem of the domain ontologies, semantically similar entities in these ontologies must be found and aligned before merging them. GraphMatcher, developed in this study, is an ontology matching system using a graph attention approach to compute higher-level representation of a class together with its surrounding terms. The GraphMatcher has obtained remarkable results in in the Ontology Alignment Evaluation Initiative (OAEI) 2022 conference track.

Ontology matching (OM) enables semantic interoperability between different ontologies and resolves their conceptual heterogeneity by aligning related entities. OM systems currently have two prevailing design paradigms: conventional knowledge-based expert systems and newer machine learning-based predictive systems. While large language models (LLMs) and LLM-based agents have become revolutionary in data engineering and have been applied creatively in various domains, their potential for OM remains underexplored. This study introduces a novel agent-powered LLM-based design paradigm for OM systems. With thoughtful consideration of several specific challenges to leverage LLMs for OM, we propose a generic framework, namely Agent-OM, consisting of two Siamese agents for retrieval and matching, with a set of simple prompt-based OM tools. Our framework is implemented in a proof-of-concept system. Evaluations of three Ontology Alignment Evaluation Initiative (OAEI) tracks over state-of-the-art OM systems show that our system can achieve very close results to the best long-standing performance on simple OM tasks and significantly improve the performance on complex and few-shot OM tasks.

Ontology (and more generally: Knowledge Graph) Matching is a challenging task where information in natural language is one of the most important signals to process. With the rise of Large Language Models, it is possible to incorporate this knowledge in a better way into the matching pipeline. A number of decisions still need to be taken, e.g., how to generate a prompt that is useful to the model, how information in the KG can be formulated in prompts, which Large Language Model to choose, how to provide existing correspondences to the model, how to generate candidates, etc. In this paper, we present a prototype that explores these questions by applying zero-shot and few-shot prompting with multiple open Large Language Models to different tasks of the Ontology Alignment Evaluation Initiative (OAEI). We show that with only a handful of examples and a well-designed prompt, it is possible to achieve results that are en par with supervised matching systems which use a much larger portion of the ground truth.

Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM models have harnessed the power of transformer-based language models and the advantages of knowledge graph embedding. Nevertheless, these OM models still face persistent challenges, such as a lack of reference alignments, runtime latency, and unexplored different graph structures within an end-to-end framework. In this study, we introduce a novel self-supervised learning OM framework with input ontologies, called LaKERMap. This framework capitalizes on the contextual and structural information of concepts by integrating implicit knowledge into transformers. Specifically, we aim to capture multiple structural contexts, encompassing both local and global interactions, by employing distinct training objectives. To assess our methods, we utilize the Bio-ML datasets and tasks. The findings from our innovative approach reveal that LaKERMap surpasses state-of-the-art systems in terms of alignment quality and inference time. Our models and codes are available here: https://github.com/ellenzhuwang/lakermap.

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 Bio-ML track at OAEI 2022.