This disclosure involves generating graph data structures that model inter-feature dependencies for use with machine-learning models to predict end-user behavior. For example, a processing device receives an input dataset and a request to modify a first input feature of the input dataset. The processing device uses a graph data structure that models the inter-feature dependencies to modify the input dataset by propagating the modification of the first input feature to a second input feature dependent on the first input feature. The modification to the second input feature is a function of at least (a) the value of the first input feature and (b) a weight assigned to an edge linking the first input feature to the second input feature within the directed graph. The processing device then applies a trained machine-learning model to the modified input dataset to generate a prediction of an outcome.