KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations

Wu, J.; Ning, Z.; Ding, Y.; Wang, Y.; Peng, Q.; Fu, L.

doi:10.1101/2023.03.28.534642

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bioRxiv · 10.1101/2023.03.28.534642

KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations

Wu, J.·Ning, Z.·Ding, Y.·Wang, Y.·Peng, Q.·Fu, L.

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Abstract

Recent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease.

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Wu, J., Ning, Z., Ding, Y., Wang, Y., Peng, Q., Fu, L.. 2023-03-29. KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations. https://doi.org/10.1101/2023.03.28.534642

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