BMC Bioinformatics | |
AttentionDDI: Siamese attention-based deep learning method for drug–drug interaction predictions | |
Kyriakos Schwarz1  Nicolas Andres Perez Gonzalez1  Ahmed Allam1  Michael Krauthammer1  | |
[1] Department of Quantitative Biomedicine, University of Zurich, Schmelzbergstrasse 26, 8006, Zurich, Switzerland;Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland; | |
关键词: Drug–drug interactions; Side effects; Prediction; Deep learning; Attention; | |
DOI : 10.1186/s12859-021-04325-y | |
来源: Springer | |
【 摘 要 】
BackgroundDrug–drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible drug pairs, it is nearly impossible to experimentally test all combinations and discover previously unobserved side effects. Therefore, machine learning based methods are being used to address this issue.MethodsWe propose a Siamese self-attention multi-modal neural network for DDI prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles.ResultsOur proposed DDI prediction model provides multiple advantages: (1) It is trained end-to-end, overcoming limitations of models composed of multiple separate steps, (2) it offers model explainability via an Attention mechanism for identifying salient input features and (3) it achieves similar or better prediction performance (AUPR scores ranging from 0.77 to 0.92) compared to state-of-the-art DDI models when tested on various benchmark datasets. Novel DDI predictions are further validated using independent data resources.ConclusionsWe find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid in DDI model explainability.
【 授权许可】
CC BY
【 预 览 】
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