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In this paper, we proposed a machine learning techniques-based classification approach to identify disease-related lncRNAs by graph auto-encoder (GAE) and random forest (RF) (GAERF). First, we combined the relationship of lncRNA, miRNA and disease into a heterogeneous network. Then, low-dimensional representation vectors of nodes were learned from the network by GAE, which reduce the dimension and heterogeneity of biological data. Taking these feature vectors as input, we trained a RF classifier to predict new lncRNA-disease associations (LDAs). Related experiment results show that the proposed method for the representation of lncRNA-disease characterizes them accurately. GAERF achieves superior performance owing to the ensemble learning method, outperforming other methods significantly. Moreover, case studies further demonstrated that GAERF is an effective method to predict LDAs.<\/jats:p>","DOI":"10.1093\/bib\/bbaa391","type":"journal-article","created":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T20:42:09Z","timestamp":1606855329000},"source":"Crossref","is-referenced-by-count":78,"title":["GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0521-7674","authenticated-orcid":false,"given":"Qing-Wen","family":"Wu","sequence":"first","affiliation":[{"name":"Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, College of Computer Science and Technology, Anhui University, Hefei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3024-1705","authenticated-orcid":false,"given":"Jun-Feng","family":"Xia","sequence":"additional","affiliation":[{"name":"Institute of Physical 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