Background Numerous studies on discovering the roles of long non-coding RNAs (lncRNAs) in the occurrence, development and prognosis progresses of various human diseases have drawn substantial attentions. Since only a tiny portion of lncRNA-disease associations have been properly annotated, an increasing number of computational methods have been proposed for predicting potential lncRNA-disease associations. However, traditional predicting models lack the ability to precisely extract features of biomolecules, it is urgent to find a model which can identify potential lncRNA-disease associations with both efficiency and accuracy. Results In this study, we proposed a novel model, SVDNVLDA, which gained the linear and non-linear features of lncRNAs and diseases with Singular Value Decomposition (SVD) and node2vec methods respectively. The integrated features were constructed from connecting the linear and non-linear features of each entity, which could effectively enhance the semantics contained in ultimate representations. And an XGBoost classifier was employed for identifying potential lncRNA-disease associations eventually. Conclusions We propose a novel model to predict lncRNA-disease associations. This model is expected to identify potential relationships between lncRNAs and diseases and further explore the disease mechanisms at the lncRNA molecular level.

Long non-coding RNAs (lncRNAs) do not encode proteins, yet they have been well established to be involved in complex regulatory functions, and lncRNA regulatory dysfunction can lead to a variety of human complex diseases. LncRNAs mostly exert their functions by regulating the expressions of target genes, and accurate prediction of potential lncRNA target genes would be helpful to further understanding the functional annotations of lncRNAs. Considering the limitations in traditional computational methods for predicting lncRNA target genes, a novel model which was named Weighted Average Fusion Network Representation learning for predicting LncRNA Target Genes (WAFNRLTG) was proposed. First, a novel heterogeneous network was constructed by integrating lncRNA sequence similarity network, mRNA sequence similarity network, lncRNA-mRNA interaction network, lncRNA-miRNA interaction network and mRNA-miRNA interaction network. Next, four popular network representation learning methods were utilized to gain the representation vectors of lncRNA and mRNA nodes. Then, the representations of lncRNAs and target genes in the heterogeneous network were obtained with the weighted average fusion network representation learning method. Finally, we merged the representations of lncRNAs and related target genes to form lncRNA-gene pairs, trained the XGBoost classifier and predicted potential lncRNA target genes. In five-cross validations on the training and independent datasets, the experimental results demonstrated that WAFNRLTG obtained better AUC scores (0.9410, 0.9350) and AUPR scores (0.9391, 0.9350). Moreover, case studies of three common lncRNAs were performed for predicting their potential lncRNA target genes and the results confirmed the effectiveness of WAFNRLTG. The source codes and all data of WAFNRLTG can be freely downloaded at https://github.com/HGDYZW/WAFNRLTG.

Accumulated evidence of biological clinical trials has shown that long non-coding RNAs (lncRNAs) are closely related to the occurrence and development of various complex human diseases. Research works on lncRNA–disease relations will benefit to further understand the pathogenesis of human complex diseases at the molecular level, but only a small proportion of lncRNA–disease associations has been confirmed. Considering the high cost of biological experiments, exploring potential lncRNA–disease associations with computational approaches has become very urgent. In this study, a model based on closest node weight graph of the spatial neighborhood (CNWGSN) and edge attention graph convolutional network (EAGCN), LDA-EAGCN, was developed to uncover potential lncRNA–disease associations by integrating disease semantic similarity, lncRNA functional similarity, and known lncRNA–disease associations. Inspired by the great success of the EAGCN method on the chemical molecule property recognition problem, the prediction of lncRNA–disease associations could be regarded as a component recognition problem of lncRNA–disease characteristic graphs. The CNWGSN features of lncRNA–disease associations combined with known lncRNA–disease associations were introduced to train EAGCN, and correlation scores of input data were predicted with EAGCN for judging whether the input lncRNAs would be associated with the input diseases. LDA-EAGCN achieved a reliable AUC value of 0.9853 in the ten-fold cross-over experiments, which was the highest among five state-of-the-art models. Furthermore, case studies of renal cancer, laryngeal carcinoma, and liver cancer were implemented, and most of the top-ranking lncRNA–disease associations have been proven by recently published experimental literature works. It can be seen that LDA-EAGCN is an effective model for predicting potential lncRNA–disease associations. Its source code and experimental data are available at https://github.com/HGDKMF/LDA-EAGCN.