Predicting Parkinson's disease genes based on node2vec and autoencoder

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Abstract

Identifying genes associated with Parkinson's disease plays an extremely important role in the diagnosis and treatment of Parkinson's disease. In recent years, based on the guilt-by-association hypothesis, many methods have been proposed to predict disease-related genes, but few of these methods are designed or used for Parkinson's disease gene prediction. In this paper, we propose a novel prediction method for Parkinson's disease gene prediction, named N2A-SVM. N2A-SVM includes three parts: extracting features of genes based on network, reducing the dimension using deep neural network, and predicting Parkinson's disease genes using a machine learning method. The evaluation test shows that N2A-SVM performs better than existing methods. Furthermore, we evaluate the significance of each step in the N2A-SVM algorithm and the influence of the hyper-parameters on the result. In addition, we train N2A-SVM on the recent dataset and used it to predict Parkinson's disease genes. The predicted top-rank genes can be verified based on literature study.

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APA

Peng, J., Guan, J., & Shang, X. (2019). Predicting Parkinson’s disease genes based on node2vec and autoencoder. Frontiers in Genetics, 10(APR). https://doi.org/10.3389/fgene.2019.00226

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