MetaboT: An LLM-based Multi-Agent Frameworkfor Interactive Analysis of Mass SpectrometryMetabolomics Knowledge Graphs

Madina Bekbergenova; Lucas Pradi; Benjamin Navet; Emma Tysinger; Franck Michel; Matthieu Feraud; Yousouf Taghzouti; Yan Zhou Chen; Olivier Kirchhoffer; Florence Mehl; Martin Legrand; Tao Jiang; Marco Pagni; Soha Hassoun; Jean-Luc Wolfender; Wout Bittremieux; Fabien Gandon; Louis-Félix Nothias

arXiv · 2510.01724

MetaboT: An LLM-based Multi-Agent Frameworkfor Interactive Analysis of Mass SpectrometryMetabolomics Knowledge Graphs

Madina Bekbergenova·Lucas Pradi·Benjamin Navet·Emma Tysinger·Franck Michel·Matthieu Feraud·Yousouf Taghzouti·Yan Zhou Chen·Olivier Kirchhoffer·Florence Mehl·Martin Legrand·Tao Jiang·Marco Pagni·Soha Hassoun·Jean-Luc Wolfender·Wout Bittremieux·Fabien Gandon·Louis-Félix Nothias

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Abstract

Mass spectrometry-based metabolomics generates complex, high-dimensional data that holds vast potential for biological discovery but remains difficult to integrate and interpret. Knowledge graphs (KGs) unify this heterogeneous information by representing spectra, annotations, taxa, chemical classes, and biological activities as a single interoperable network; however, their practical use is limited by the steep learning curve of corresponding specialized representation and query languages. Here we introduce MetaboT, an open-source multi-agent Large Language Model (LLM) framework that translates natural-language questions into executable SPARQL queries over metabolomics knowledge graphs. MetaboT mitigates the hallucination and schema-compliance limitations of single-model approaches through a modular architecture in which specialised agents handle scope validation, entity resolution against authoritative resources, schema-aware query generation, iterative refinement, and result interpretation. We validated MetaboT on the Experimental Natural Products Knowledge Graph (ENPKG), using an expert-authored benchmark of natural-language questions paired with reference SPARQL queries, and demonstrate its ability to answer complex questions about plant--metabolite relationships and biological activities. MetaboT lowers the technical barrier for metabolomics researchers and enables semantic data mining without specialised programming expertise.

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Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Emma Tysinger, Franck Michel, Matthieu Feraud, Yousouf Taghzouti, Yan Zhou Chen, Olivier Kirchhoffer, Florence Mehl, Martin Legrand, Tao Jiang, Marco Pagni, Soha Hassoun, Jean-Luc Wolfender, Wout Bittremieux, Fabien Gandon, Louis-Félix Nothias. 2025-10-02. MetaboT: An LLM-based Multi-Agent Frameworkfor Interactive Analysis of Mass SpectrometryMetabolomics Knowledge Graphs. https://arxiv.org/abs/2510.01724

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