# OpenGLT: A Comprehensive Benchmark of Graph Neural Networks for Graph-Level Tasks

arXiv: https://arxiv.org/abs/2501.00773 · HTML: https://mlsanity.com/paper/2501.00773/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 65 of its 130 references that are in the map.
- First posted on arXiv 1 Jan 2025.

## Builds on (most cited first, 30 of 65)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [GraphSAINT: Graph Sampling Based Inductive Learning Method](https://mlsanity.com/paper/1907.04931/) (2019)
- [Deep Graph Contrastive Representation Learning](https://mlsanity.com/paper/2006.04131/) (2020)
- [Graph U-Nets](https://mlsanity.com/paper/1905.05178/) (2019)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (2020)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing](https://mlsanity.com/paper/1905.00067/) (2019)
- [Self-Attention Graph Pooling](https://mlsanity.com/paper/1904.08082/) (2019)
- [Graph Structure Learning for Robust Graph Neural Networks](https://mlsanity.com/paper/2005.10203/) (2020)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [A Fair Comparison of Graph Neural Networks for Graph Classification](https://mlsanity.com/paper/1912.09893/) (2019)
- [Learning Discrete Structures for Graph Neural Networks](https://mlsanity.com/paper/1903.11960/) (2019)
- [Identity-aware Graph Neural Networks](https://mlsanity.com/paper/2101.10320/) (2021)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [Convergence Analysis of Two-layer Neural Networks with ReLU Activation](https://mlsanity.com/paper/1705.09886/) (2017)
- [Nested Graph Neural Networks](https://mlsanity.com/paper/2110.13197/) (2021)
- [NAGphormer: A Tokenized Graph Transformer for Node Classification in Large Graphs](https://mlsanity.com/paper/2206.04910/) (2022)

## Abstract (arXiv)

Graphs are fundamental data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which involve predicting properties or labels for entire graphs, are crucial for applications like molecular property prediction and subgraph counting. While Graph Neural Networks (GNNs) have shown significant promise for these tasks, their evaluations are often limited by narrow datasets, insufficient architecture coverage, restricted task scope and scenarios, and inconsistent experimental setups, making it difficult to draw reliable conclusions across domains. In this paper, we present a comprehensive experimental study of GNNs on graph-level tasks, systematically categorizing them into five types: node-based, hierarchical pooling-based, subgraph-based, graph learning-based, and self-supervised learning-based GNNs. We propose a unified evaluation framework OpenGLT, which standardizes evaluation across four domains (social networks, biology, chemistry, and motif counting), two task types (classification and regression), and three real-world scenarios (clean, noisy, imbalanced, and few-shot graphs). Extensive experiments on 20 models across 26 classification and regression datasets reveal that: (i) no single architecture dominates both effectiveness and efficiency universally, i.e., subgraph-based GNNs excel in expressiveness, graph learning-based and SSL-based methods in robustness, and node-based and pooling-based models in efficiency; and (ii) specific graph topological features such as density and centrality can partially guide the selection of suitable GNN architectures for different graph characteristics.