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LGCDA:基于局部和全局特征融合的 circRNA-疾病关联预测。

LGCDA: Predicting CircRNA-Disease Association Based on Fusion of Local and Global Features.

出版信息

IEEE/ACM Trans Comput Biol Bioinform. 2024 Sep-Oct;21(5):1413-1422. doi: 10.1109/TCBB.2024.3387913. Epub 2024 Oct 9.

Abstract

CircRNA has been shown to be involved in the occurrence of many diseases. Several computational frameworks have been proposed to identify circRNA-disease associations. Despite the existing computational methods have obtained considerable successes, these methods still require to be improved as their performance may degrade due to the sparsity of the data and the problem of memory overflow. We develop a novel computational framework called LGCDA to predict circRNA-disease associations by fusing local and global features to solve the above mentioned problems. First, we construct closed local subgraphs by using k-hop closed subgraph and label the subgraphs to obtain rich graph pattern information. Then, the local features are extracted by using graph neural network (GNN). In addition, we fuse Gaussian interaction profile (GIP) kernel and cosine similarity to obtain global features. Finally, the score of circRNA-disease associations is predicted by using the multilayer perceptron (MLP) based on local and global features. We perform five-fold cross validation on five datasets for model evaluation and our model surpasses other advanced methods.

摘要

circRNA 被证明与许多疾病的发生有关。已经提出了几种计算框架来识别 circRNA-疾病关联。尽管现有的计算方法已经取得了相当大的成功,但这些方法仍然需要改进,因为它们的性能可能会由于数据的稀疏性和内存溢出问题而降低。我们开发了一种名为 LGCDA 的新计算框架,通过融合局部和全局特征来预测 circRNA-疾病关联,以解决上述问题。首先,我们使用 k-跳封闭子图构建封闭的局部子图,并对子图进行标记,以获得丰富的图模式信息。然后,使用图神经网络 (GNN) 提取局部特征。此外,我们融合高斯相互作用分布 (GIP) 核和余弦相似度来获得全局特征。最后,基于局部和全局特征,使用多层感知机 (MLP) 预测 circRNA-疾病关联的分数。我们在五个数据集上进行了五折交叉验证,以评估模型,我们的模型优于其他先进的方法。

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