GSLCDA: An Unsupervised Deep Graph Structure Learning Method for Predicting CircRNA-Disease Association

• Published in: IEEE journal of biomedical and health informatics Vol. 28; no. 3; pp. 1742 - 1751
• Main Authors: Wang, Lei, Li, Zheng-Wei, You, Zhu-Hong, Huang, De-Shuang, Wong, Leon
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.03.2024; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Aging; Algorithms; Apoptosis; Biological system modeling; Breast Neoplasms - genetics; Cancer; Cell differentiation; Cell proliferation; CircRNA; CircRNA-disease association (CDA); Circular RNA; Colorectal carcinoma; Computational Biology - methods; Data models; Datasets; Disease; Diseases; Female; graph structure learning; Heterogeneous networks; Humans; K-nearest neighbors algorithm; Learning; Lung cancer; Lung Neoplasms; multi-source information heterogeneous network; Network topologies; Pathogenesis; RNA; RNA, Circular - genetics; Semantics; Teaching methods; Topology
• ISSN: 2168-2194; 2168-2208
• DOI: 10.1109/JBHI.2023.3344714

Growing studies reveal that Circular RNAs (circRNAs) are broadly engaged in physiological processes of cell proliferation, differentiation, aging, apoptosis, and are closely associated with the pathogenesis of numerous diseases. Clarification of the correlation among diseases and circRNAs is of great clinical importance to provide new therapeutic strategies for complex diseases. However, previous circRNA-disease association prediction methods rely excessively on the graph network, and the model performance is dramatically reduced when noisy connections occur in the graph structure. To address this problem, this paper proposes an unsupervised deep graph structure learning method GSLCDA to predict potential CDAs. Concretely, we first integrate circRNA and disease multi-source data to constitute the CDA heterogeneous network. Then the network topology is learned using the graph structure, and the original graph is enhanced in an unsupervised manner by maximize the inter information of the learned and original graphs to uncover their essential features. Finally, graph space sensitive k-nearest neighbor (KNN) algorithm is employed to search for latent CDAs. In the benchmark dataset, GSLCDA obtained 92.67% accuracy with 0.9279 AUC. GSLCDA also exhibits exceptional performance on independent datasets. Furthermore, 14, 12 and 14 of the top 16 circRNAs with the most points GSLCDA prediction scores were confirmed in the relevant literature in the breast cancer, colorectal cancer and lung cancer case studies, respectively. Such results demonstrated that GSLCDA can validly reveal underlying CDA and offer new perspectives for the diagnosis and therapy of complex human diseases.