Journal
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 1, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbab464
Keywords
miRNA-disease associations; subgraph; graph convolutional network; signed network
Funding
- National Natural Science Foundation of China [62072206, 61772381]
- Huazhong Agricultural University Scientific & Technological Self-innovation Foundation
- Fundamental Research Funds for the Central Universities [2662021JC008]
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MiRNAs, small non-coding RNA molecules, play a significant role in biological processes. This paper proposes a signed graph neural network method (SGNNMD) to predict the deregulation types of miRNA-disease associations, which have potential applications in drug development and clinical diagnosis. Experimental results demonstrate the competitive performance of SGNNMD.
MiRNAs are a class of small non-coding RNA molecules that play an important role in many biological processes, and determining miRNA-disease associations can benefit drug development and clinical diagnosis. Although great efforts have been made to develop miRNA-disease association prediction methods, few attention has been paid to in-depth classification of miRNA-disease associations, e.g. up/down-regulation of miRNAs in diseases. In this paper, we regard known miRNA-disease associations as a signed bipartite network, which has miRNA nodes, disease nodes and two types of edges representing up/down-regulation of miRNAs in diseases, and propose a signed graph neural network method (SGNNMD) for predicting deregulation types of miRNA-disease associations. SGNNMD extracts subgraphs around miRNA-disease pairs from the signed bipartite network and learns structural features of subgraphs via a labeling algorithm and a neural network, and then combines them with biological features (i.e. miRNA-miRNA functional similarity and disease-disease semantic similarity) to build the prediction model. In the computational experiments, SGNNMD achieves highly competitive performance when compared with several baselines, including the signed graph link prediction methods, multi-relation prediction methods and one existing deregulation type prediction method. Moreover, SGNNMD has good inductive capability and can generalize to miRNAs/diseases unseen during the training.
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