论文标题

DDOS:基于图神经网络的药物协同预测算法

DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm

论文作者

Schwarz, Kyriakos, Pliego-Mendieta, Alicia, Mollaysa, Amina, Planas-Paz, Lara, Pauli, Chantal, Allam, Ahmed, Krauthammer, Michael

论文摘要

当两种药物的综合影响超过其个体作用的总和时,就会出现药物协同作用。虽然对细胞系的单毒作用有充分的文献记录,但考虑到大量潜在药物组合的药物协同作用的稀缺性,促使人们对预测未经测试药物对的协同作用的计算方法越来越兴趣。我们介绍了基于药物协同预测的基于图形神经网络(\ textit {gnn})模型,该模型利用药物化学结构和细胞系基因表达数据。我们从最大的可用药物组合数据库(DrugComb)中提取数据,并产生多个协同分数(文献中通常使用),以创建七个具有高信心的可靠基准的数据集。与依靠预计化学特征的常规模型相反,我们的基于GNN的方法直接从药物的图形结构中学习了特定于任务的药物表示,从而在预测药物协同作用方面提供了卓越的性能。我们的工作表明,学习特定于任务的药物表示并利用多样化的数据集是一种有希望的方法,可以促进我们对药物互动和协同作用的理解。

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 (\textit{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.

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