Drug Effect Classification Using Frequency-Based Graph Traversal Approach

Classifying drugs into symptomatic (SYM) and disease-modifying (DM) categories is essential for understanding their therapeutic effect and plays a key role in drug repurposing. While many computational approaches focus on drug-target prediction, they often ignore the nature of the drug's action on disease progression. This study proposes a graph-based strategy to classify drugs as SYM or DM based on their effect on disease treatment. We construct a heterogeneous network comprising genes, diseases, and drugs, and apply a guided shortest path traversal framework for drug effect classification. During this traversal, certain genes appear frequently in the shortest metapaths linking diseases and drugs. These recurrent genes are identified based on their frequency of occurrence in known drug-disease paths. For a new drug-disease pair, if the traversal path contains recurrent genes marked for a specific treatment type, we classify the drug accordingly. Over and above classifying the drugs, the proposed method incorporates the metapath-based framework to improve interpretability. Experimental results show that our model achieves significantly better classification accuracy compared to advanced machine learning and deep learning methods. A case study on multiple sclerosis further supports the biological relevance of our approach.