Scoring multiple features to predict drug disease associations using information fusion and aggregation

Abstract

Prediction of drug–disease associations is one of the current fields in drug repositioning that has turned into a challenging topic in pharmaceutical science. Several available computational methods use network-based and machine learning approaches to reposition old drugs for new indications. However, they often ignore features of drugs and diseases as well as the priority and importance of each feature, relation, or interactions between features and the degree of uncertainty. When predicting unknown drug–disease interactions there are diverse data sources and multiple features available that can provide more accurate and reliable results. This information can be collectively mined using data fusion methods and aggregation operators. Therefore, we can use the feature fusion method to make high-level features. We have proposed a computational method named scored mean kernel fusion (SMKF), which uses a new method to score the average aggregation operator called scored mean. To predict novel drug indications, this method systematically combines multiple features related to drugs or diseases at two levels: the drug–drug level and the drug–disease level. The purpose of this study was to investigate the effect of drug and disease features as well as data fusion to predict drug–disease interactions. The method was validated against a well-established drug–disease gold-standard dataset. When compared with the available methods, our proposed method outperformed them and competed well in performance with area under cover (AUC) of 0.91, F-measure of 84.9% and Matthews correlation coefficient of 70.31%.

Keywords:

• Data fusion
• multiple features
• drug–disease interaction
• kernel fusion
• support vector machine

Acknowledgements

The authors gratefully acknowledge the collaboration of Dr Alireza Vazifedoost.