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 graph alignment framework that simultaneously enhances node distinctiveness and enforces geometric consistency across latent spaces. Our approach introduces a dual-pass encoder that combines low-pass and high-pass spectral filters to generate embeddings that are both structure-aware and highly discriminative. To address latent space misalignment, we incorporate a geometry-aware functional map module that learns bijective and isometric transformations between graph embeddings, ensuring consistent geometric relationships across different representations. 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. Additionally, comprehensive evaluation on vision-language benchmarks using diverse pretrained models shows that our framework effectively generalizes beyond graph domains, enabling unsupervised alignment of vision and language representations.