A novel graph mining approach to predict and evaluate food-drug interactions

Abstract

Abstract Food-drug interactions (FDIs) arise when nutritional dietary consumption regulates biochemical mechanisms involved in drug metabolism. This study proposes FDMine, a novel systematic framework that models the FDI problem as a homogenous graph. Our dataset consists of 788 unique approved small molecule drugs with metabolism-related drug-drug interactions and 320 unique food items, composed of 563 unique compounds. The potential number of interactions is 87,192 and 92,143 for disjoint and joint versions of the graph. We defined several similarity subnetworks comprising food-drug similarity, drug-drug similarity, and food-food similarity networks. A unique part of the graph involves encoding the food composition as a set of nodes and calculating a content contribution score. To predict new FDIs, we considered several link prediction algorithms and various performance metrics, including the precision@top (top 1%, 2%, and 5%) of the newly predicted links. The shortest path-based method has achieved a precision of 84%, 60% and 40% for the top 1%, 2% and 5% of FDIs identified, respectively. We validated the top FDIs predicted using FDMine to demonstrate its applicability, and we relate therapeutic anti-inflammatory effects of food items informed by FDIs. FDMine is publicly available to support clinicians and researchers.