Eden Wu

Eden Wu, Dishita G Turakhia, Guande Wu et al.

Biomedical data harmonization is essential for enabling exploratory analyses and meta-studies, but the process of schema matching - identifying semantic correspondences between elements of disparate datasets (schemas) - remains a labor-intensive and error-prone task. Even state-of-the-art automated methods often yield low accuracy when applied to biomedical schemas due to the large number of attributes and nuanced semantic differences between them. We present BDIViz, a novel visual analytics system designed to streamline the schema matching process for biomedical data. Through formative studies with domain experts, we identified key requirements for an effective solution and developed interactive visualization techniques that address both scalability challenges and semantic ambiguity. BDIViz employs an ensemble approach that combines multiple matching methods with LLM-based validation, summarizes matches through interactive heatmaps, and provides coordinated views that enable users to quickly compare attributes and their values. Our method-agnostic design allows the system to integrate various schema matching algorithms and adapt to application-specific needs. Through two biomedical case studies and a within-subject user study with domain experts, we demonstrate that BDIViz significantly improves matching accuracy while reducing cognitive load and curation time compared to baseline approaches.

Eden Wu, Christos Koutras, Cláudio T. Silva et al.

Schema matching remains fundamental to data integration, yet evaluating and comparing matching methods is hindered by limited benchmark diversity and lack of interactive validation frameworks. BDIViz, recently published at IEEE VIS 2025, is an interactive visualization system for schema matching with LLM-assisted validation. Given source and target datasets, BDIViz applies automatic matching methods and visualizes candidates in an interactive heatmap with hierarchical navigation, zoom, and filtering. Users validate matches directly in the heatmap and inspect ambiguous cases using coordinated views that show attribute descriptions, example values, and distributions. An LLM assistant generates structured explanations for selected candidates to support decision-making. This demonstration showcases a new extension to BDIViz that addresses a critical need in data integration research: human-in-the-loop benchmarking and iterative matcher development. New matchers can be integrated through a standardized interface, while user validations become evolving ground truth for real-time performance evaluation. This enables benchmarking new algorithms, constructing high-quality ground-truth datasets through expert validation, and comparing matcher behavior across diverse schemas and domains. We demonstrate two complementary scenarios: (i) data harmonization, where users map a large tabular dataset to a target schema with value-level inspection and LLM-generated explanations; and (ii) developer-in-the-loop benchmarking, where developers integrate custom matchers, observe performance metrics, and refine their algorithms.

Yurong Liu, Eduardo Pena, Aecio Santos et al.

Recent advances in language models opened new opportunities to address complex schema matching tasks. Schema matching approaches have been proposed that demonstrate the usefulness of language models, but they have also uncovered important limitations: Small language models (SLMs) require training data (which can be both expensive and challenging to obtain), and large language models (LLMs) often incur high computational costs and must deal with constraints imposed by context windows. We present Magneto, a cost-effective and accurate solution for schema matching that combines the advantages of SLMs and LLMs to address their limitations. By structuring the schema matching pipeline in two phases, retrieval and reranking, Magneto can use computationally efficient SLM-based strategies to derive candidate matches which can then be reranked by LLMs, thus making it possible to reduce runtime without compromising matching accuracy. We propose a self-supervised approach to fine-tune SLMs which uses LLMs to generate syntactically diverse training data, and prompting strategies that are effective for reranking. We also introduce a new benchmark, developed in collaboration with domain experts, which includes real biomedical datasets and presents new challenges to schema matching methods. Through a detailed experimental evaluation, using both our new and existing benchmarks, we show that Magneto is scalable and attains high accuracy for datasets from different domains.