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Retrieval-Augmented Language Models Enable Scalable Chemical Source Classification in Metabolomics Workflows

Дата публикации: 27-08-2026 00:00:00

There is a growing need for scalable chemical classification to support the interpretation of exposomics and metabolomics data. While structural categorization has been largely automated, functional and exposure-based labeling of chemicals remains a manual and time-consuming process. Here, we present chemsource, a flexible framework that integrates large language models (LLMs) with retrieval-augmented generation (RAG) to automate chemical classification. chemsource retrieves descriptive text from Wikipedia or PubMed abstracts based on chemical names and prompts LLMs to assign user-defined categories based on the retrieved content. We demonstrate classification into five exposure categories: endogenous metabolites, food molecules, drugs, personal care products, industrial chemicals, and combinations of these possibilities. Benchmarking against manually curated labels for 4,953 compounds showed 75% overall agreement, with category-level recall exceeding 75% across...

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