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Life sciences · Preprint
arXiv · October 20, 2026
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Graph generative models commonly use graph-specific Transformer architectures to jointly update node and edge features. However, these architectures do not directly benefit from recent hardware-aware attention implementations, limiting their scalability. The adaptation is, however, non-trivial: edge and graph-level features must be injected into pairwise attention scores, graph masks must be respected, and dynamic edge updates remain a major source of quadratic memory usage. We propose an edge-aware attention layer for graph generation that incorporates structural information through head-wise score modulation, while updating edge representations with a lightweight residual mechanism that retains attention-score dependent edge updates. This layer can be effectively implemented using PyTorch's FlexAttention. We achieve similar generation quality to our baseline while reducing peak GPU memory by around 65% and substantially improving training and sampling throughput. These results suggest that the proposed architecture is a practical step toward scalable graph foundation models.