Current browse context:
q-bio.QM
Change to browse by:
References & Citations
Quantitative Biology > Quantitative Methods
Title: DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm
(Submitted on 3 Oct 2022 (v1), last revised 26 Apr 2024 (this version, v3))
Abstract: 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.
Submission history
From: Ahmed Allam [view email][v1] Mon, 3 Oct 2022 10:16:29 GMT (320kb,D)
[v2] Mon, 10 Oct 2022 13:49:44 GMT (321kb,D)
[v3] Fri, 26 Apr 2024 07:23:20 GMT (952kb,D)
Link back to: arXiv, form interface, contact.