identification of lncRNA-disease associations by learning to rank

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Identifying the associations between lncRNA and disease is helpful for the treatment and diagnosis of complex diseases. The existing computational methods mainly focus on the identification of associations between known lncRNA and known disease. However, with the application of high-throughput sequencing in lncRNA research, more and more lncRNAs have been detected. Predicting diseases related with newly-found lncRNAs has not yet been fully explored in existing methods. Therefore, there is an urgent need for developing a powerful computational method to predict diseases related with newly-found lncRNAs.

In this paper, we propose a Learning to Rank (LTR)-based method called iLncDA-LTR to predict diseases related with newly-found lncRNAs. iLncDA-LTR treats the problem of identifying associations between newly-found lncRNAs and diseases as information retrieval task, in which newly-found lncRNAs and diseases are regarded as queries and documents, respectively. For a given newly-found lncRNA (query), iLncDA-LTR integrates multiple relevant information into LTR for predicting candidate diseases associated with query lncRNA. The flowchart of iLncDA-LTR model is shown in Fig.1, which contains three main steps, including data processing, feature representation and candidate disease ranking.

iPiDA-LTR web server
Fig.1. The flowchart of iLncDA-LTR (i) Data processing: based on multiple relevant data sources, iLncDA-LTR first calculates lncRNA sequence similarity and disease semantic similarity, respectively. Besides, the lncRNA-disease association matrix is also constructed. (ii) Feature representation: pair scores are calculated by three component methods with lncRNA similarities, disease similarities and lncRNA-disease association matrix, and iLncDA-LTR combines pair scores and disease semantic attribute as feature vectors. (iii) Candidate disease ranking: the feature vectors are used to train the LTR model, and the trained model can be utilized to calculate the relevant degree between diseases and newly-found query lncRNAs, based on which candidate diseases are ranked.