# Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective

arXiv: https://arxiv.org/abs/2412.07188 · HTML: https://mlsanity.com/paper/2412.07188/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 55 references that are in the map.
- First posted on arXiv 10 Dec 2024.

## Builds on (most cited first, 30 of 43)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Graph Convolutional Neural Networks for Web-Scale Recommender Systems](https://mlsanity.com/paper/1806.01973/) (2018)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [Graph Neural Networks for Social Recommendation](https://mlsanity.com/paper/1902.07243/) (2019)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [Graph Structure Learning for Robust Graph Neural Networks](https://mlsanity.com/paper/2005.10203/) (2020)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Deep Gaussian Embedding of Graphs: Unsupervised Inductive Learning via Ranking](https://mlsanity.com/paper/1707.03815/) (2017)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Revisiting Graph Neural Networks: All We Have is Low-Pass Filters](https://mlsanity.com/paper/1905.09550/) (2019)
- [Graph Neural Networks with Heterophily](https://mlsanity.com/paper/2009.13566/) (2020)
- [GNNGuard: Defending Graph Neural Networks against Adversarial Attacks](https://mlsanity.com/paper/2006.08149/) (2020)
- [Rethinking Graph Neural Networks for Anomaly Detection](https://mlsanity.com/paper/2205.15508/) (2022)
- [Graph Neural Networks with convolutional ARMA filters](https://mlsanity.com/paper/1901.01343/) (2019)
- [Graph Neural Networks for Graphs with Heterophily: A Survey](https://mlsanity.com/paper/2202.07082/) (2022)
- [How Powerful are Spectral Graph Neural Networks](https://mlsanity.com/paper/2205.11172/) (2022)
- [Revisiting Heterophily For Graph Neural Networks](https://mlsanity.com/paper/2210.07606/) (2022)

## Built on by (most cited first, 3 of 3)

- [CEGA: A Cost-Effective Approach for Graph-Based Model Extraction and Acquisition](https://mlsanity.com/paper/2506.17709/) (2025)
- [A Spectral Decomposition Framework for Multiscale Nonlinear Dimensionality Reduction](https://mlsanity.com/paper/2604.02535/) (2026)
- [SPR: Toward a Graph Foundation Model for Transferable Graph Cognition via Spectral Patterns and Relational Geometry](https://mlsanity.com/paper/2606.03315/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have achieved remarkable success in various graph-based learning tasks. While their performance is often attributed to the powerful neighborhood aggregation mechanism, recent studies suggest that other components such as non-linear layers may also significantly affecting how GNNs process the input graph data in the spectral domain. Such evidence challenges the prevalent opinion that neighborhood aggregation mechanisms dominate the behavioral characteristics of GNNs in the spectral domain. To demystify such a conflict, this paper introduces a comprehensive benchmark to measure and evaluate GNNs' capability in capturing and leveraging the information encoded in different frequency components of the input graph data. Specifically, we first conduct an exploratory study demonstrating that GNNs can flexibly yield outputs with diverse frequency components even when certain frequencies are absent or filtered out from the input graph data. We then formulate a novel research problem of measuring and benchmarking the performance of GNNs from a spectral perspective. To take an initial step towards a comprehensive benchmark, we design an evaluation protocol supported by comprehensive theoretical analysis. Finally, we introduce a comprehensive benchmark on real-world datasets, revealing insights that challenge prevalent opinions from a spectral perspective. We believe that our findings will open new avenues for future advancements in this area. Our implementations can be found at: https://github.com/yushundong/Spectral-benchmark.