Long noncoding RNAs (lncRNAs) are a class of noncoding RNA molecules longer than 200 nucleotides. Recent studies have uncovered their functional roles in diverse cellular processes and tumorigenesis. Therefore, identifying novel disease-related lncRNAs might deepen our understanding of disease etiology. However, due to the relatively small number of verified associations between lncRNAs and diseases, it remains a challenging task to reliably and effectively predict the associated lncRNAs for given diseases. In this paper, we propose a novel multiview consensus graph learning method to infer potential disease-related lncRNAs. Specifically, we first construct a set of similarity matrices for lncRNAs and diseases by taking advantage of the known associations. We then iteratively learn a consensus graph from the multiple input matrices and simultaneously optimize the predicted association probability based on a multi-label learning framework. To convey the utility of our method, three state-of-the-art methods are compared with our method on three widely used datasets. The experiment results illustrate that our method could obtain the best prediction performance under different cross validation schemes. The case study analysis implemented for uterine cervical neoplasms further confirmed the utility of our method in identifying lncRNAs as potential prognostic biomarkers in practice.
Background: Long non-coding RNAs (lncRNAs) are nonprotein-coding transcripts of more than 200 nucleotides in length. In recent years, studies have shown that long non-coding RNAs (lncRNA) play a vital role in various biological processes, complex disease diagnosis, prognosis, and treatment. Objective: Analysis of known lncRNA-disease associations and the prediction of potential lncRNA-disease associations are necessary to provide the most probable candidates for subsequent experimental validation. Methods: In this paper, we present a novel robust computational framework for lncRNA-disease association prediction by combining the ℓ1-norm graph with multi-label learning. Specifically, we first construct a set of similarity matrices for lncRNAs and diseases using known associations. Then, both lncRNA and disease similarity matrices are adaptively re-weighted to enhance the robustness via the ℓ1-norm graph. Lastly, the association matrix is updated with a graph-based multi-label learning framework to uncover the underlying consistency between the lncRNA space and the disease space. Results : We compared the proposed method with the four latest methods on five widely used data sets. The experimental results show that our method can achieve comparable performance in both five-fold cross-validation and leave-one-disease-out cross-validation prediction tasks. The case study of prostate cancer further confirms the practicability of our approach in identifying lncRNAs as potential prognostic biomarkers. Conclusion: Our method can serve as a useful tool for the prediction of novel lncRNA-disease associations.
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