MetaboliteChat: A Unified Multimodal Large Language Model for Interactive Metabolite Analysis and Functional Insights

Abstract

Accurately characterizing the mechanisms and properties of metabolite molecules is essential for advancing metabolomics and systems biology. Yet most existing approaches are narrow, task-specific models that do not transfer across tasks and cannot express the richer, multimodal biological context of a metabolite in natural language. To address these challenges, we introduce MetaboliteChat, a multimodal ChatGPT-like large language model (LLM) that provides a unified and interactive framework for metabolite analysis. MetaboliteChat integrates molecular-graph and image reasoning with natural language understanding to generate comprehensive, free-form predictions about metabolite mechanisms and properties. The MetaboliteChat architecture consists of a graph neural network (GNN), a convolutional neural network (CNN), a large language model (LLM), and adapters, all trained end to end. This unified, multimodal design enables interactive reasoning over unseen metabolites, allowing the model to integrate structural and contextual cues and support discovery and translational insights across diverse biological systems.