GraphGDel: Constructing and Learning Graph Representations of Genome-Scale Metabolic Models for Growth-Coupled Gene Deletion Prediction

In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked nature of genome-scale metabolic models, existing computational approaches rely primarily on sequential data and lack graph representations that capture their complex relationships, as both well-defined graph constructions and learning frameworks capable of exploiting them remain largely unexplored. To address this gap, we present a twofold solution. First, we introduce a systematic pipeline for constructing graph representations from constraint-based metabolic models. Second, we develop a deep learning framework that integrates these graph representations with gene and metabolite sequence data to predict growth-coupled gene deletion strategies. Across three metabolic models, our approach consistently outperforms established baselines, with improvements in overall accuracy of 14.04%, 16.26%, and 13.18% over a deep feedforward neural network baseline, 6.17%, 4.96%, and 5.31% over a sequence-learning baseline, and 5.10%, 4.36%, and 4.70% over a topology-aware graph aggregation baseline on the same metabolite graph, respectively. The source code and example datasets are available at: https://github.com/MetNetComp/GraphGDel.