2022/10/03 by Kyriakos Schwarz, Schwarz, Kyriakos, Alicia Pliego‐Mendieta +10
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Gene Regulatory Network Analysis #Machine Learning (cs.LG) #Quantitative Methods (q-bio.QM) #Receptor Mechanisms and Signaling
paper · pdf · doi:10.48550/arxiv.2210.00802
openalex publication_date 2022/10/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Drug synergy arises when the combined impact of two drugs exceeds the sum of their individual effects. While single-drug effects on cell lines are well-documented, the scarcity of data on drug synergy, considering the vast array of potential drug combinations, prompts a growing interest in computational approaches for predicting synergies in untested drug pairs. We introduce a Graph Neural Network (GNN) based model for drug synergy prediction, which utilizes drug chemical structures and cell line gene expression data. We extract data from the largest available drug combination database (DrugComb) and generate multiple synergy scores (commonly used in the literature) to create seven datasets that serve as a reliable benchmark with high confidence. In contrast to conventional models relying on pre-computed chemical features, our GNN-based approach learns task-specific drug representations directly from the graph structure of the drugs, providing superior performance in predicting drug synergies. Our work suggests that learning task-specific drug representations and leveraging a diverse dataset is a promising approach to advancing our understanding of drug-drug interaction and synergy.