Graph Alignment via Dual-Pass Spectral Encoding and Latent Space Communication

Graph alignment, the problem of identifying corresponding nodes across multiple graphs, is fundamental to numerous applications. Most existing unsupervised methods embed node features into latent representations to enable cross-graph comparison without ground-truth correspondences. However, these methods suffer from two critical limitations: the degradation of node distinctiveness due to oversmoothing in GNN-based embeddings, and the misalignment of latent spaces across graphs caused by structural noise, feature heterogeneity, and training instability, ultimately leading to unreliable node correspondences. We propose a novel framework employing a dual-pass encoder to inject high-frequency discriminability into node features, paired with a geometry-aware functional map module that learns bijective and isometric transformations to align latent spaces while acting as a low-pass filter on correspondences, enforcing smoothness and robustness as a structural prior in map space. Extensive experiments on graph benchmarks demonstrate that our method consistently outperforms existing unsupervised alignment baselines, exhibiting superior robustness to structural inconsistencies and challenging alignment scenarios. The implementation is available at https://github.com/ maysambehmanesh/GADL .