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MVGNCDA:基于多视图图卷积网络和网络嵌入识别潜在的环状RNA-疾病关联

MVGNCDA: Identifying Potential circRNA-Disease Associations Based on Multi-view Graph Convolutional Networks and Network Embeddings.

作者信息

Sun Guicong, Zheng Mengxin, Fan Yongxian, Pan Xiaoyong

机构信息

School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China.

Department of Automation, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, 200240, China.

出版信息

Interdiscip Sci. 2025 Feb 17. doi: 10.1007/s12539-025-00690-x.

Abstract

Increasing evidences have indicated that circular RNAs play a crucial role in the onset and progression of various diseases. However, exploring potential disease-associated circRNAs using conventional experimental techniques remains both time-intensive and costly. Recently, various computational approaches have been developed to detect the circRNA-disease associations. Nevertheless, due to the sparsity of the data and the inefficient utilization of similarity representation, it is still a challenge to effectively detect unknown circRNA-disease associations using multisource data. In this work, we propose an innovative computational framework, MVGNCDA, which merges a multi-view graph convolutional network (GCN) and biased random walk-based network embeddings to evaluate potential circRNA-disease associations from multisource data. First, we calculate disease semantic similarity, circRNA functional similarity, and their Gaussian interaction profile (GIP) kernel and cosine similarity. MVGNCDA utilizes multi-view GCNs to extract local node embeddings of diseases and circRNAs in the context of multisource information. Then, we construct a heterogeneous network utilizing integrated similarity and verified circRNA-disease associations, which is subsequently used to learn global node embeddings. Furthermore, the final fused local and global node embeddings are decoded to evaluate the circRNA-disease associations using a bilinear decoder. The fivefold cross-validation results demonstrate that MVGNCDA outperforms existing methods across five public datasets. Moreover, case study also confirms that MVGNCDA is capable of efficiently identifying unknown circRNA-disease associations.

摘要

越来越多的证据表明,环状RNA在各种疾病的发生和发展中起着至关重要的作用。然而,使用传统实验技术探索潜在的疾病相关环状RNA既耗时又昂贵。最近,已经开发了各种计算方法来检测环状RNA与疾病的关联。然而,由于数据的稀疏性和相似性表示的低效利用,利用多源数据有效检测未知的环状RNA与疾病的关联仍然是一个挑战。在这项工作中,我们提出了一种创新的计算框架MVGNCDA,它融合了多视图图卷积网络(GCN)和基于有偏随机游走的网络嵌入,以从多源数据中评估潜在的环状RNA与疾病的关联。首先,我们计算疾病语义相似性、环状RNA功能相似性及其高斯相互作用轮廓(GIP)核和余弦相似性。MVGNCDA利用多视图GCN在多源信息的背景下提取疾病和环状RNA的局部节点嵌入。然后,我们利用综合相似性和已验证的环状RNA与疾病的关联构建一个异构网络,随后用它来学习全局节点嵌入。此外,最终融合的局部和全局节点嵌入通过双线性解码器进行解码,以评估环状RNA与疾病的关联。五折交叉验证结果表明,MVGNCDA在五个公共数据集上优于现有方法。此外,案例研究也证实MVGNCDA能够有效地识别未知的环状RNA与疾病的关联。

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