LRLSLDA: Laplacian Regularized Least Squares for LncRNA-Disease Association

More and more evidences have indicated that long-non-coding RNAs (lncRNAs) play critical roles in many important biological processes. Therefore, mutations and dysregulations of these lncRNAs would contribute to the development of various complex diseases. Developing powerful computational models for potential disease related lncRNAs identification would benefit biomarker identification and drug discovery for human disease diagnosis, treatment, prognosis and prevention.


In this paper, researchers from the Chinese Academy of Sciences, P.R. China have proposed the assumption that similar diseases tend to be associated with functionally similar lncRNAs. Then, they further developed the method of Laplacian Regularized Least Squares for LncRNA-Disease Association (LRLSLDA) in the semi-supervised learning framework. Although known disease-lncRNA associations in the database are rare, LRLSLDA still obtained an AUC of 0.7760 in the leave-one-out cross validation, significantly improving the performance of previous methods. They also illustrated the performance of LRLSLDA is not sensitive (even robust) to the parameters selection and it can obtain a reliable performance in all the test classes. Plenty of potential disease-lncRNA associations were publicly released and some of them have been confirmed by recent results in biological experiments. It is anticipated that LRLSLDA could be an effective and important biological tool for biomedical research.

AVAILABILITY: The code of LRLSLDA is freely available at


Chen X, Yan GY. (2013) Novel human lncRNA-disease association inference based on lncRNA expression profiles. Bioinformatics  [Epub ahead of print]. [abstract]

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