Abstract
Subcellular localization prediction is crucial for understanding protein functions and cellular processes. Subcellular localization is dependent on tissue and cell lines derived from different cell types. Predicting cell line-specific subcellular localization using the information of protein-protein interactions (PPIs) offers deeper insights into dynamic cellular organization and molecular mechanisms. However, many existing PPI networks contain systematic errors that limit prediction accuracy. In this study, we propose a reinforcement learning approach, ProtLoc-GRPO, to enhance subcellular localization prediction by optimizing the structure of the underlying PPI network. ProtLoc-GRPO learns to rank and retain the most informative PPI edges to maximize the macro-F1 score for cell line-specific subcellular localization. Our approach yields a 7% improvement in macro-F1 score over the baseline. We further evaluate its robustness across various edge pruning rates and benchmark it against conventional pruning strategies. Results show that our proposed method consistently outperforms existing approaches. To our knowledge, this work represents the first study to predict cell line-specific protein subcellular localization and the first application of the Group Relative Policy Optimization (GRPO) framework to a graph-based model for bioinformatics tasks.