CDA-SKAG: Predicting circRNA-disease associations using similarity kernel fusion and an attention-enhancing graph autoencoder

Huiqing Wang; Jiale Han; Haolin Li; Liguo Duan; Zhihao Liu; Hao Cheng; Huiqing Wang; Jiale Han; Haolin Li; Liguo Duan; Zhihao Liu; Hao Cheng

doi:10.3934/mbe.2023345

Mathematical Biosciences and Engineering

2023, Volume 20, Issue 5: 7957-7980. doi: 10.3934/mbe.2023345

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CDA-SKAG: Predicting circRNA-disease associations using similarity kernel fusion and an attention-enhancing graph autoencoder

College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China

Academic Editor: Joel Rodrigues

Received: 07 November 2022 Revised: 28 December 2022 Accepted: 02 February 2023 Published: 23 February 2023

Circular RNAs (circRNAs) constitute a category of circular non-coding RNA molecules whose abnormal expression is closely associated with the development of diseases. As biological data become abundant, a lot of computational prediction models have been used for circRNA–disease association prediction. However, existing prediction models ignore the non-linear information of circRNAs and diseases when fusing multi-source similarities. In addition, these models fail to take full advantage of the vital feature information of high-similarity neighbor nodes when extracting features of circRNAs or diseases. In this paper, we propose a deep learning model, CDA-SKAG, which introduces a similarity kernel fusion algorithm to integrate multi-source similarity matrices to capture the non-linear information of circRNAs or diseases, and construct a circRNA information space and a disease information space. The model embeds an attention-enhancing layer in the graph autoencoder to enhance the associations between nodes with higher similarity. A cost-sensitive neural network is introduced to address the problem of positive and negative sample imbalance, consequently improving our model's generalization capability. The experimental results show that the prediction performance of our model CDA-SKAG outperformed existing circRNA–disease association prediction models. The results of the case studies on lung and cervical cancer suggest that CDA-SKAG can be utilized as an effective tool to assist in predicting circRNA–disease associations.
- circRNA–disease association prediction,
- similarity kernel fusion,
- graph autoencoder,
- attention mechanism,
- cost-sensitive neural network
Citation: Huiqing Wang, Jiale Han, Haolin Li, Liguo Duan, Zhihao Liu, Hao Cheng. CDA-SKAG: Predicting circRNA-disease associations using similarity kernel fusion and an attention-enhancing graph autoencoder[J]. Mathematical Biosciences and Engineering, 2023, 20(5): 7957-7980. doi: 10.3934/mbe.2023345

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Abstract

Circular RNAs (circRNAs) constitute a category of circular non-coding RNA molecules whose abnormal expression is closely associated with the development of diseases. As biological data become abundant, a lot of computational prediction models have been used for circRNA–disease association prediction. However, existing prediction models ignore the non-linear information of circRNAs and diseases when fusing multi-source similarities. In addition, these models fail to take full advantage of the vital feature information of high-similarity neighbor nodes when extracting features of circRNAs or diseases. In this paper, we propose a deep learning model, CDA-SKAG, which introduces a similarity kernel fusion algorithm to integrate multi-source similarity matrices to capture the non-linear information of circRNAs or diseases, and construct a circRNA information space and a disease information space. The model embeds an attention-enhancing layer in the graph autoencoder to enhance the associations between nodes with higher similarity. A cost-sensitive neural network is introduced to address the problem of positive and negative sample imbalance, consequently improving our model's generalization capability. The experimental results show that the prediction performance of our model CDA-SKAG outperformed existing circRNA–disease association prediction models. The results of the case studies on lung and cervical cancer suggest that CDA-SKAG can be utilized as an effective tool to assist in predicting circRNA–disease associations.

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