# A Comprehensive Benchmark on Spectral GNNs: The Impact on Efficiency, Memory, and Effectiveness

arXiv: https://arxiv.org/abs/2406.09675 · HTML: https://mlsanity.com/paper/2406.09675/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 89 of its 151 references that are in the map.
- First posted on arXiv 14 Jun 2024.

## Builds on (most cited first, 30 of 89)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [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)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [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)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [Graph Signal Processing: Overview, Challenges and Applications](https://mlsanity.com/paper/1712.00468/) (2017)
- [Deep Learning on Graphs: A Survey](https://mlsanity.com/paper/1812.04202/) (2018)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods](https://mlsanity.com/paper/2110.14446/) (2021)
- [Spectral Temporal Graph Neural Network for Multivariate Time-series Forecasting](https://mlsanity.com/paper/2103.07719/) (2021)
- [Towards Deeper Graph Neural Networks](https://mlsanity.com/paper/2007.09296/) (2020)
- [SIGN: Scalable Inception Graph Neural Networks](https://mlsanity.com/paper/2004.11198/) (2020)
- [Diffusion-Convolutional Neural Networks](https://mlsanity.com/paper/1511.02136/) (2015)

## Built on by (most cited first, 6 of 6)

- [The Heterophilic Graph Learning Handbook: Benchmarks, Models, Theoretical Analysis, Applications and Challenges](https://mlsanity.com/paper/2407.09618/) (2024)
- [Towards Graph Foundation Models: Training on Knowledge Graphs Enables Transferability to General Graphs](https://mlsanity.com/paper/2410.12609/) (2024)
- [Spectro-Riemannian Graph Neural Networks](https://mlsanity.com/paper/2502.00401/) (2025)
- [When Deepfake Detection Meets Graph Neural Network:a Unified and Lightweight Learning Framework](https://mlsanity.com/paper/2508.05526/) (2025)
- [OpenGLT: A Comprehensive Benchmark of Graph Neural Networks for Graph-Level Tasks](https://mlsanity.com/paper/2501.00773/) (2025)
- [Spectral Graph Neural Networks with Hermite Polynomials: A Comprehensive Study](https://mlsanity.com/paper/2609.28979/) (2026)

## Abstract (arXiv)

With recent advancements in graph neural networks (GNNs), spectral GNNs have received increasing popularity by virtue of their ability to retrieve graph signals in the spectral domain. These models feature uniqueness in efficient computation as well as rich expressiveness, which stems from advanced management and profound understanding of graph data. However, few systematic studies have been conducted to assess spectral GNNs, particularly in benchmarking their efficiency, memory consumption, and effectiveness in a unified and fair manner. There is also a pressing need to select spectral models suitable for learning specific graph data and deploying them to massive web-scale graphs, which is currently constrained by the varied model designs and training settings. In this work, we extensively benchmark spectral GNNs with a focus on the spectral perspective, demystifying them as spectral graph filters. We analyze and categorize 35 GNNs with 27 corresponding filters, spanning diverse formulations and utilizations of the graph data. Then, we implement the filters within a unified spectral-oriented framework with dedicated graph computations and efficient training schemes. In particular, our implementation enables the deployment of spectral GNNs over million-scale graphs and various tasks with comparable performance and less overhead. Thorough experiments are conducted on the graph filters with comprehensive metrics on effectiveness and efficiency, offering novel observations and practical guidelines that are only available from our evaluations across graph scales. Different from the prevailing belief, our benchmark reveals an intricate landscape regarding the effectiveness and efficiency of spectral graph filters, demonstrating the potential to achieve desirable performance through tailored spectral manipulation of graph data.