Graph homophily booster: Reimagining the role of discrete features in heterophilic graph learning

Graph neural networks (GNNs) have emerged as a powerful tool for modeling graph-structured data, demonstrating remarkable success in many real-world applications such as complex biological network analysis, neuroscientific analysis, and social network analysis. However, existing GNNs often struggle with heterophilic graphs, where connected nodes tend to have dissimilar features or labels. While numerous methods have been proposed to address this challenge, they primarily focus on architectural designs without directly targeting the root cause of the heterophily problem. These approaches still perform even worse than the simplest MLPs on challenging heterophilic datasets. For instance, our experiments show that 23 latest GNNs still fall behind the MLP on the Actor dataset. This critical challenge calls for an innovative approach to addressing graph heterophily beyond architectural designs. To bridge this gap, we propose and study a new and unexplored paradigm: directly increasing the graph homophily via a carefully designed graph transformation. In this work, we present a simple yet effective framework called Graph Homophily Booster (GRAPHITE) to address graph heterophily. To the best of our knowledge, this work is the first method that explicitly transforms the graph to directly improve the graph homophily. Stemmed from the exact definition of homophily, our proposed GRAPHITE creates feature nodes to facilitate homophilic message passing between nodes that share similar features. Furthermore, we both theoretically and empirically show that our proposed GRAPHITE significantly increases the homophily of originally heterophilic graphs, with only a slight increase in the graph size. Extensive experiments on challenging datasets demonstrate that our proposed GRAPHITE significantly outperforms state-of-the-art methods on heterophilic graphs while achieving comparable accuracy with state-of-the-art methods on homophilic graphs. Furthermore, our proposed graph transformation alone can already enhance the performance of homophilic GNNs on heterophilic graphs, even though they were not originally designed for heterophilic graphs. Our code is publicly available at https://github.com/q-rz/ICLR26-GRAPHITE .