Affiliations: School of Computer Science, Wuhan University, Wuhan 430072, China
Correspondence:
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Corresponding author. Juan Liu, School of Computer Science, Wuhan University, Wuhan 430072, China. E-mail: [email protected].
Abstract: Uncovering the potential treatment associations of the drug-disease pairs is a research focus of drug repositioning. However, it is time-consuming and costly to verify the potential treatment relation between a drug and a disease by “wet” experiment methods. Fortunately, along with the accumulation of large amount of data and the development of machine learning methods, lots of computational methods to predict the drug-disease treatment associations have been proposed. In order to build the prediction model based on machine learning techniques, both plenty of positive and negative training samples are required. In the case of biological experiments, however, we can only verify whether a drug cures a disease, yet we are unable to answer whether a drug definitely cannot treat a disease. Correspondently, there are only positive and unlabeled samples in the data. Being lack of validated negative samples, most computational methods assume the unlabeled samples to be negative ones and randomly select some unlabeled samples and positive samples to train the prediction models. Obviously, the unlabeled samples are not necessarily negative, and some of them may be positive just remaining uncovered via experiments. In this paper, we propose a method called PUDrDi which directly make use of the positive and unlabeled samples to train a Biased-SVM classifier. Moreover, we combine the drug and disease features together to represent a drug-disease pair, in which we use chemical substructures and symptoms as the features to represent drugs and diseases respectively. The experiment results demonstrate that PUDrDi outperforms some other methods. The case study further shows the practicality of PUDrDi.
