Structure-based metabolite function prediction using graph neural networks

Being able to broadly predict the function of novel metabolites based on their structures has applications in systems biology, environmental monitoring and drug discovery. To date, machine learning models aiming to predict functional characteristics of metabolites have largely been limited in scope to predicting single functions, or only a small number of functions simultaneously. Using the Human Metabolome Database as a source for a wider range of functional annotations, we assess the feasibility of predicting metabolite functions more broadly, as defined by four elements, namely location, role, the process it is involved in, and its physiological effect. We evaluated three graph neural network architectures to predict available functional ontology terms. Among the models tested, the Graph Attention Network, incorporating embeddings from the pre-trained ChemBERTa model to predict the process metabolites are involved in, achieved the highest performance with an F1-score of 0.889 and a recall of 0.903. The model identified function-associated structural patterns within metabolite families, demonstrating the potential for interpretably predicting metabolite functions from structural information.