Constructing discriminative feature space for LncRNA-protein interaction based on deep autoencoder and marginal fisher analysis.

Long non-coding RNAs (lncRNAs) play important roles by regulating proteins in many biological processes and life activities. To uncover molecular mechanisms of lncRNA, it is very necessary to identify interactions of lncRNA with proteins. Recently, some machine learning methods were proposed to detect lncRNA-protein interactions according to the distribution of known interactions. The performances of these methods were largely dependent upon: (1) how exactly the distribution of known interactions was characterized by feature space; (2) how discriminative the feature space was for distinguishing lncRNA-protein interactions. Because the known interactions may be multiple and complex model, it remains a challenge to construct discriminative feature space for lncRNA-protein interactions. To resolve this problem, a novel method named DFRPI was developed based on deep autoencoder and marginal fisher analysis in this paper. Firstly, some initial features of lncRNA-protein interactions were extracted from the primary sequences and secondary structures of lncRNA and protein. Secondly, a deep autoencoder was exploited to learn encode parameters of the initial features to describe the known interactions precisely. Next, the marginal fisher analysis was employed to optimize the encode parameters of features to characterize a discriminative feature space of the lncRNA-protein interactions. Finally, a random forest-based predictor was trained on the discriminative feature space to detect lncRNA-protein interactions. Verified by a series of experiments, the results showed that our predictor achieved the precision of 0.920, recall of 0.916, accuracy of 0.918, MCC of 0.836, specificity of 0.920, sensitivity of 0.916 and AUC of 0.906 respectively, which outperforms the concerned methods for predicting lncRNA-protein interaction. It may be suggested that the proposed method can generate a reasonable and effective feature space for distinguishing lncRNA-protein interactions accurately. The code and data are available on https://github.com/D0ub1e-D/DFRPI.