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Inferring Disease-Associated Piwi-Interacting RNAs via Graph Attention Networks

By Kai Zheng, Zhu-Hong You, Lei Wang, Leon Wong, Zhan-Heng Chen, Han-Jing Jiang

Posted 09 Jan 2020
bioRxiv DOI: 10.1101/2020.01.08.898155

Motivation: PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and so-matic tissues, and correlates with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes out gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. This study aims to make preliminary attempts on bio-network based graph mining. Results: In this study, we present a method based on graph attention network to identify potential and biologically significant piRNA-disease associations (PDAs), called GAPDA. The attention mechanism can calculate a hidden representation of an association in the network based on neighbor nodes and assign weights to the input to make decisions. In particular, we introduced the attention-based Graph Neural Networks to the field of bio-association prediction for the first time, and proposed an abstract network topology suitable for small samples. Specifically, we combined piRNA sequence information and disease semantic similarity with piRNA-disease association network to construct a new attribute network. In the experiment, GAPDA performed excellently in five-fold cross-validation with the AUC of 0.9038. Not only that, but it still has superior performance compared to methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such prob-lems and can be an excellent supplement for future biomedical research.

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