GraFSyn: An Interpretable Deep Learning Framework for Anticancer Drug Synergy via Graphlet Fingerprints

Predicting drug synergy is important for accelerating the discovery of effective anticancer combination therapies. Synergy intrinsically depends on the precise interactions of key chemical substructures within specific cellular environments. However, current molecular graph-based computational methods typically rely on implicit atom-level feature aggregation, which may obscure the topological representation of critical chemical substructures and limit structural traceability. Therefore, we present Graphlet Fingerprint-based Synergy prediction (GraFSyn), a deep learning framework for anticancer drug synergy prediction that uses graphlet fingerprints to encode drugs as explicit connected substructure units, preserving predefined chemical substructures and their topological identity. We further introduce a Dynamic Multi-Scale Convolution (DMSC) module to learn informative representations from high-dimensional and sparse graphlet features. The framework also includes an interaction module to capture context-dependent interactions between drug substructures and cell line gene expression. On the Merck and AstraZeneca benchmark data sets, GraFSyn achieved ROC-AUC/PR-AUC values of 0.972/0.912 and 0.823/0.906, respectively, outperforming representative baseline methods. In addition, attributed signals can be mapped back to specific pharmacophoric regions, supporting substructure-level analysis of synergistic interactions. In general, GraFSyn provides an accurate and structurally traceable approach for anticancer drug combination screening.