Disclosed are various embodiments for inferring brand similarities using graph neural networks and selection prediction. In one embodiment, a brand-to-brand graph is generated indicating similarities between a set of brands according to at least one of: click-through data or conversion data. Using a first graph neural network (GNN) tower, the brand-to-brand graph is analyzed to determine brand similarities among a first brand identified from a search query and a first set of other brands. Using a second GNN tower, the brand-to-brand graph is analyzed to determine brand similarities among a second brand and a second set of other brands. A level of similarity between the first brand and the second brand is determined based at least in part on an output of the first GNN tower and an output of the second GNN tower.