Graph Convolutional Attention: A Spectral Perspective on Graph Denoising and Diffusion
Authors: Shervin Khalafi, Igor Krawczuk, Sergio Rozada, Charilaos Kanatsoulis, Antonio G Marques, Alejandro Ribeiro
Organizations: University of Pennsylvania · King Juan Carlos University · Stanford University
Abstract
Denoising graphs is a fundamental problem in graph learning and the core operation of graph diffusion models. Attention-based architectures like graph transformers have recently shown promise in denoising graphs. However, our principled understanding of attention-based graph denoising remains limited, making it unclear whether standard attention is the right mechanism for this task. Here we show that, under a denoising objective, linear attention is suboptimal and can only learn an average spectral denoising filter over the training distribution. This creates a fundamental limitation as graphs often vary spectrally across the distribution. To overcome this limitation, we introduce Spectral Attention, which directly utilizes the input graph spectrum and provably outperforms linear attention by a margin governed by the spectral diversity of the distribution. We then derive Graph Convolutional Attention (GCA), a practical and permutation-equivariant realization of this idea that implements spectral denoising through graph-filtered queries and keys. For stochastic block models, GCA provably matches the idealized Spectral Attention mechanism. We further show that the softmax operation, that follows the attention, provides additional denoising by approximately projecting noisy eigenvectors onto the clean eigenspace. Empirically, replacing linear attention with GCA consistently improves graph denoising and diffusion on synthetic and real datasets, with gains strongly correlated with spectral diversity. In DiGress, GCA matches standard graph-transformer performance without computing expensive structural features, and when combined with the recently proposed PEARL positional encodings, avoids explicit eigendecomposition computations resulting in faster inference without degrading quality. The code can be found here: github.com/shervinkhalafi/graph_conv_att
Transformer-based architectures have become the dominant paradigm for Continuous-Time Dynamic Graph (CTDG) learning, yet their performance remains limited on temporally shifted datasets. In this work, we identify attention dispersion as a shared failure mode of dynamic graph Transformers under temporal distribution shift. Through controlled ablation contrasting structurally and temporally distinguished historical neighbors against random ones, we show that prediction depends on a class of critical nodes that carry consistently more predictive signal than arbitrary neighbors. However, existing Transformers fail to focus on these nodes even when they are present in the input, as temporal shift weakens attention contrast and produces overly dispersed attention distributions. This diagnosis suggests a simple and transferable fix: replace standard attention with differential attention, which suppresses common-mode attention and amplifies distinctive token-level signals. When added to three representative CTDG Transformer baselines, differential attention consistently improves performance, with gains concentrated on high-shift datasets. Attention-level measurements further confirm the mechanism, showing reduced attention entropy and increased attention mass on critical nodes. Building on these findings, we introduce DiffDyG, a reference implementation combining differential attention with standard input encodings. Across 9 benchmarks and three negative sampling protocols, DiffDyG achieves SOTA performance, with especially large gains on the most shifted datasets.
Spectral graph neural networks (GNNs) interpret message passing as frequency-selective filtering. While low-order spectral filters are efficient, their limited selectivity often leads to weak attenuation outside the passband, whereas high-order alternatives introduce optimization challenges. We propose DCQ-GNN, a spectral GNN based on a compact bank of adaptive convex--concave quadratic filters. By restricting the filter order to two while explicitly exploiting complementary curvature, DCQ-GNN improves spectral selectivity as quantified by Dirichlet energy and entropy measures without resorting to high-order polynomial expansions. The model fuses filter outputs through a node-adaptive gating mechanism to enable node-wise structure-aware spectral selection. We provide a formal spectral analysis grounded in Dirichlet energy attenuation, von Neumann entropy, and curvature polarity, and derive explicit characterizations of filter behavior across varying levels of homophily and structural perturbations. Extensive benchmarks on 10 datasets show that DCQ-GNN ties for the top average rank (3.0) on heterophilic graphs and obtains the second-best rank (4.2) on homophilic graphs, remaining competitive with representative high-order polynomial spectral filters. Furthermore, under strong structural perturbations, DCQ-GNN exhibits substantially smaller performance degradation compared to both first-order and high-order baselines. These results demonstrate that curvature-aware quadratic banks provide a robust and efficient alternative to high-order spectral models while preserving optimization stability and computational efficiency.
Deep Graph Neural Networks (GNNs) are essential for capturing complex dependencies in graph-structured data. However, scaling GNNs to depth remains challenging, as stacking layers leads to representation collapse and diminishing sensitivity due to repeated aggregation. While Neural Sheaf Diffusion (NSD) provides strong theoretical guarantees against such collapse, these guarantees do not translate to practice: as depth increases, the disagreement signal of the sheaf Laplacian vanishes, limiting the contribution of deeper layers. We identify mechanisms that hinder NSD effectiveness at depth and propose \emph{Deep Neural Sheaf Diffusion} (DNSD), which replaces the sheaf Laplacian with a sheaf adjacency operator to maintain informative signals across layers. This is complemented by normalization, odd nonlinearities, and gating. To provide a principled explanation of the expected performance improvement, we contrast sheaf diffusion to graph attention mechanisms, highlighting that DNSD replaces scalar attention scores with matrix-valued edge functions and normalizes node representations rather than attention scores. We demonstrate empirically that DNSD effectively utilizes deep aggregation in graph tasks, outperforming GNN and NSD baselines with up to 30pp accuracy on synthetic long-range datasets, and consistently outperforming them on real-world benchmarks. These results position sheaf-based architectures as a promising building block for graph foundation models by supporting effective deep architectures.