Predicting Drug Synergy and Discovering New Drug Combinations Based on a Graph Autoencoder and Convolutional Neural Network

Drug synergy is a crucial component in drug reuse since it solves the problem of sluggish drug development and the absence of corresponding drugs for several diseases. Predicting drug synergistic relationships can screen drug combinations in advance and reduce the waste of laboratory resources. In t...

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Bibliographic Details
Published in:Interdisciplinary sciences : computational life sciences 2023-06, Vol.15 (2), p.316-330
Main Authors: Li, Huijun, Zou, Lin, Kowah, Jamal A. H., He, Dongqiong, Wang, Lisheng, Yuan, Mingqing, Liu, Xu
Format: Article
Language:English
Subjects:
Artificial neural networks
Biomedical and Life Sciences
Coders
Computational Biology/Bioinformatics
Computational Science and Engineering
Computer Appl. in Life Sciences
Drug Combinations
Drug development
Graph neural networks
Health Sciences
Life Sciences
Mathematical and Computational Physics
Medicine
Multilayer perceptrons
Neural networks
Neural Networks, Computer
Original
Original Research Article
Statistics for Life Sciences
Theoretical
Theoretical and Computational Chemistry
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Summary:Drug synergy is a crucial component in drug reuse since it solves the problem of sluggish drug development and the absence of corresponding drugs for several diseases. Predicting drug synergistic relationships can screen drug combinations in advance and reduce the waste of laboratory resources. In this research, we proposed a model that utilizes graph autoencoder and convolutional neural networks to predict drug synergy (GAECDS). Our methods include a graph convolutional neural network as an encoder to encode drug features and use a matrix factorization method as a decoder. Multilayer perceptron (MLP) was applied to process cell line features and combine them with drug features. Furthermore, the latent vectors generated during the encoding process are being used to predict drug synergistic scores using a convolutional neural network. By measuring prediction performance using AUC, AUPR, and F1 score, GAECDS superior to other state-of-the-art models. In addition, four pairs of the predicted top 10 drug combinations were found to work well enough for evaluation. The case study shows that the GAECDS approach is useful for identifying potential drug synergy. Graphical Abstract
ISSN:1913-2751
1867-1462
DOI:10.1007/s12539-023-00558-y