A model with deep analysis on a large drug network for drug classification

Drugs are an important means to treat various diseases. They are classified into several classes to indicate their properties and effects. Those in the same class always share some important features. The Kyoto Encyclopedia of Genes and Genomes (KEGG) DRUG recently reported a new drug classification system that classifies drugs into 14 classes. Correct identification of the class for any possible drug-like compound is helpful to roughly determine its effects for a particular type of disease. Experiments could be conducted to confirm such latent effects, thus accelerating the procedures for discovering novel drugs. In this study, this classification system was investigated. A classification model was proposed to assign one of the classes in the system to any given drug for the first time. Different from traditional fingerprint features, which indicated essential drug properties alone and were very popular in investigating drug-related problems, drugs were represented by novel features derived from a large drug network via a well-known network embedding algorithm called Node2vec. These features abstracted the drug associations generated from their essential properties, and they could overview each drug with all drugs as background. As class sizes were of great differences, synthetic minority over-sampling technique (SMOTE) was employed to tackle the imbalance problem. A balanced dataset was fed into the support vector machine to build the model. The 10-fold cross-validation results suggested the excellent performance of the model. This model was also superior to models using other drug features, including those generated by another network embedding algorithm and fingerprint features. Furthermore, this model provided more balanced performance across all classes than that without SMOTE.