ICML 2025

Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks

Maya Bechler-Speicher, Ben Finkelshtein, Fabrizio Frasca, Luis Müller, Jan Tönshoff, Antoine Siraudin, V. Zaverkin, Michael M. Bronstein, Mathias Niepert, Bryan Perozzi, Mikhail Galkin, Christopher Morris

Main figure for Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks

Abstract

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Benchmark Results

Tested on 3 datasets

Tables show presented results in global context (best 3 papers + GCN + MLP).

OGB

#ModelROC-AUC ↑Paper
1
Multi-RF Fusion with Multi-GNN Blending
0.8476 ±0.0002
2
HyperFusion
0.8475 ±0.0003
3
PAS+FPs
0.8420 ±0.0015
9
GatedGCN
0.8090 ±0.0160
109
GIN
0.7780 ±0.0182
291
GIN Orig.
0.6965 ±0.0258
This paper
295
GraphConv Orig.
0.6824 ±0.0177
This paper
300
GAT Orig.
0.6721 ±0.0130
This paper

Heterophily Benchmark

#ModelAccuracy ↑Paper
1
UniGAP
0.6375 ±0.0110
2
H2GCN + HalfHop
0.5961 ±0.0100
3
GraphSAGE + HalfHop
0.5897 ±0.0150
12
SAGE
0.5569 ±0.0023
84
MLP
0.5058
153
GAT Re-evaluated
0.4452 ±0.0048
This paper
155
GCN Re-evaluated
0.4430 ±0.0052
This paper
163
SAGE Re-evaluated
0.4335 ±0.0080
This paper
#ModelROC-AUC ↑Paper
1
BuNN
0.9899 ±0.0016
2
DC-GNN
0.9850 ±0.0021
3
Tango -GPS
0.9839 ±0.0054
42
GraphSAGE
0.9358 ±0.0005
114
SAGE Re-evaluated
0.8376 ±0.0071
This paper
129
GAT Re-evaluated
0.7437 ±0.0094
This paper
132
GCN Re-evaluated
0.7290 ±0.0129
This paper
156
MLP
0.5099 ±0.0147
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers)