Bootstrap Learning for Combinatorial Graph Alignment with Sequential GNNs

Abstract: Graph neural networks (GNNs) have struggled to outperform traditional optimization methods on combinatorial problems, limiting their practical impact. We address this gap by introducing a novel chaining procedure for the graph alignment problem, a fundamental NP-hard task of finding optimal node correspondences between unlabeled graphs using only structural information. Our method trains a sequence of GNNs where each network learns to iteratively refine similarity matrices produced by previous networks. During inference, this creates a bootstrap effect: each GNN improves upon partial solutions by incorporating discrete ranking information about node alignment quality from prior iterations. We combine this with a powerful architecture that operates on node pairs rather than individual nodes, capturing global structural patterns essential for alignment that standard message-passing networks cannot represent. Extensive experiments on synthetic benchmarks demonstrate substantial improvements: our chained GNNs achieve over 3x better accuracy than existing methods on challenging instances, and uniquely solve regular graphs where all competing approaches fail. When combined with traditional optimization as post-processing, our method substantially outperforms state-of-the-art solvers on the graph alignment benchmark.