Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks
Not on the map. Why?
Abstract (arXiv)
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.
Key facts. Cited by 53 papers in the map (data through 14 Oct 2026). Builds on 88 of its 126 references that are in the map. First posted on arXiv 20 Feb 2025.
Builds on
88 of 126 references.
References · 88
- 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,361
- 2017Graph Attention Networkscited by 8,923
- 2017Inductive Representation Learning on Large Graphscited by 6,320
- 2018How Powerful are Graph Neural Networks?cited by 4,393
- 2017Neural Message Passing for Quantum Chemistrycited by 3,487
- 2024Gemini 1.5: Unlocking multimodal understanding across millions of tokens of contextcited by 3,224
- 2022Training Compute-Optimal Large Language Modelscited by 3,019
- 2022Emergent Abilities of Large Language Modelscited by 2,512
- 2020Open Graph Benchmark: Datasets for Machine Learning on Graphscited by 2,163
- 2017Deep Setscited by 1,421
- 2018Relational inductive biases, deep learning, and graph networkscited by 1,360
- 2021Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gaugescited by 1,167
38 more
- 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,051
- 2016Geometric deep learning: going beyond Euclidean datacited by 1,048
- 2019Strategies for Pre-training Graph Neural Networkscited by 971
- 2018Representation Learning on Graphs with Jumping Knowledge Networkscited by 877
- 2018Hierarchical Graph Representation Learning with Differentiable Poolingcited by 787
- 2016Automatic chemical design using a data-driven continuous representation of moleculescited by 765
- 2018Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point cloudscited by 746
- 2020TUDataset: A collection of benchmark datasets for learning with graphscited by 728
- 2022Recipe for a General, Powerful, Scalable Graph Transformercited by 713
- 2021E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentialscited by 708
- 2020Benchmarking Graph Neural Networkscited by 680
- 2019GraphSAINT: Graph Sampling Based Inductive Learning Methodcited by 618
- 2017SchNet: A continuous-filter convolutional neural network for modeling quantum interactionscited by 571
- 2020Directional Message Passing for Molecular Graphscited by 561
- 2023Are Emergent Abilities of Large Language Models a Mirage?cited by 523
- 2022DiGress: Discrete Denoising diffusion for graph generationcited by 520
- 2020Graph Neural Networks in Recommender Systems: A Surveycited by 494
- 2022MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fieldscited by 474
- 2021Equivariant message passing for the prediction of tensorial properties and molecular spectracited by 441
- 2021Attention is Not All You Need: Pure Attention Loses Rank Doubly Exponentially with Depthcited by 419
- 2019Provably Powerful Graph Networkscited by 389
- 2023A critical look at the evaluation of GNNs under heterophily: Are we really making progress?cited by 343
- 2021Graph Neural Networks with Learnable Structural and Positional Representationscited by 333
- 2021OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphscited by 329
- 2018GuacaMol: Benchmarking Models for De Novo Molecular Designcited by 297
- 2021Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Predictioncited by 275
- 2021Combinatorial optimization and reasoning with graph neural networkscited by 268
- 2022Long Range Graph Benchmarkcited by 263
- 2022Learning Local Equivariant Representations for Large-Scale Atomistic Dynamicscited by 256
- 2019A Fair Comparison of Graph Neural Networks for Graph Classificationcited by 244
- 2023DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimizationcited by 221
- 2023What Algorithms can Transformers Learn? A Study in Length Generalizationcited by 199
- 2022Pure Transformers are Powerful Graph Learnerscited by 188
- 2020Design Space for Graph Neural Networkscited by 182
- 2022Graph neural networks for materials science and chemistrycited by 182
- 2020Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learningcited by 149
- 2023Temporal Graph Benchmark for Machine Learning on Temporal Graphscited by 138
- 2022Equivariant 3D-Conditional Diffusion Models for Molecular Linker Designcited by 122
50 most cited of 88 All 88 (JSON)
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Citing papers per year: 2025: 25; 2026: 28.
53 papers.
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- 2025Turning Tabular Foundation Models into Graph Foundation Modelscited by 35
- 2025Equivariance Everywhere All At Once: A Recipe for Graph Foundation Modelscited by 17
- 2025Bringing Graphs to the Table: Zero-shot Node Classification via Tabular Foundation Modelscited by 16
- 2026No Need to Train Your RDB Foundation Modelcited by 10
- 2025GraphRAFT: Retrieval Augmented Fine-Tuning for Knowledge Graphs on Graph Databasescited by 7
- 2025HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representationscited by 5
- 2026GNN Explanations that do not Explain and How to find Themcited by 5
- 2026Billion-Scale Graph Foundation Modelscited by 5
- 2025Bridging Theory and Practice in Link Representation with Graph Neural Networkscited by 4
- 2025What Do Temporal Graph Learning Models Learn?cited by 4
- 2026Fixed Aggregation Features Can Rival GNNscited by 4
- 2026Bridging Academia and Industry: A Comprehensive Benchmark for Attributed Graph Clusteringcited by 4
38 more
- 2026A Fair Evaluation of Graph Foundation Models for Node Property Predictioncited by 4
- 2025Generating Directed Graphs with Dual Attention and Asymmetric Encodingcited by 3
- 2025CosmoBench: A Multiscale, Multiview, Multitask Cosmology Benchmark for Geometric Deep Learningcited by 3
- 2025AI for Scientific Discovery is a Social Problemcited by 3
- 2025When Structure Doesn't Help: LLMs Do Not Read Text-Attributed Graphs as Effectively as We Expectedcited by 3
- 2025Graph Alignment for Benchmarking Graph Neural Networks and Learning Positional Encodingscited by 2
- 2025Are We Really Measuring Progress? Transferring Insights from Evaluating Recommender Systems to Temporal Link Predictioncited by 2
- 2025GraphUniverse: Synthetic Graph Generation for Evaluating Inductive Generalizationcited by 2
- 2025Generalizable Insights for Graph Transformers in Theory and Practicecited by 2
- 2026Rethinking GNNs and Missing Features: Challenges, Evaluation and a Robust Solutioncited by 2
- 2026Position: Don't be Afraid of Over-Smoothing And Over-Squashingcited by 2
- 2026Relatron: Automating Relational Machine Learning over Relational Databasescited by 2
- 2026GrapHist: Graph Self-Supervised Learning for Histopathologycited by 2
- 2026Have Graph -- Will Lift? The Case for Higher-Order Benchmarkscited by 2
- 2025ATOM: A Pretrained Neural Operator for Multitask Molecular Dynamicscited by 1
- 2025Graph Homomorphism Distortion: A structural (pseudo)-metric for attributed graphscited by 1
- 2026Beyond the Academic Monoculture: A Unified Framework and Industrial Perspective for Attributed Graph Clusteringcited by 1
- 2026Cluster Attention for Graph Machine Learningcited by 1
- 2026Measuring Structure in Graph Benchmark Datasets Using Graph Invariantscited by 1
- 2025Directed Semi-Simplicial Learning with Applications to Brain Activity Decodingcited by 0
- 2025Why Isn't Relational Learning Taking Over the World?cited by 0
- 2025Exact Generalisation Error Exposes Benchmarks Skew Graph Neural Networks Success (or Failure)cited by 0
- 2025CrediBench: Building Web-Scale Network Datasets for Information Integritycited by 0
- 2025Permutation-Invariant Spectral Learning via Dyson Diffusioncited by 0
- 2025Bridging the Divide: End-to-End Sequence-Graph Learningcited by 0
- 2025The Human Brain as a Combinatorial Complexcited by 0
- 2025How Smoothing is N-simplicial Attention?cited by 0
- 2026Position: Evaluation of ECG Representations Must Be Fixedcited by 0
- 2026MolGraphBench: A Benchmark of GNN Architectures for Molecular Regression Taskscited by 0
- 2026SketchGraphNet: A Memory-Efficient Hybrid Graph Transformer for Large-Scale Sketch Corpora Recognitioncited by 0
- 2026Graph Rewiring in GNNs to Mitigate Over-Squashing and Over-Smoothing: A Surveycited by 0
- 2026No Triangulation Without Representation: Generalization in Topological Deep Learningcited by 0
- 2026RAwR: Role-Aware Rewiring via Approximate Equitable Partitioncited by 0
- 2026OgBench: A Framework for Evaluating Graph Neural Networks on Omics Datacited by 0
- 2026Deep Neural Sheaf Diffusioncited by 0
- 2026Graph Machine Learning: An Opportunity for Power Systemscited by 0
- 2026An Investigation of the NeurIPS and ICML 2025 Position Trackscited by 0
- 2026Not All Nodes Are Created Equal: Homophily-Aware Stratification for Stable GNN Evaluationcited by 0
50 most cited of 53 All 53 (JSON)
- 2026PATTERN Can Be Solved from Memory: Generator-Aware Baselines for Synthetic Node Classification10 Oct 2026
- 2026The Universal Classifier for Graph Learning28 Sep 2026
- 2026Do Temporal Link Predictors Need Learned Memory? A Smoothed-Count Baseline with a Handful of Parameters28 Sep 2026
- 2026Not All Nodes Are Created Equal: Homophily-Aware Stratification for Stable GNN Evaluation16 Sep 2026
- 2026Graph Machine Learning: An Opportunity for Power Systems17 Aug 2026
- 2026An Investigation of the NeurIPS and ICML 2025 Position Tracks6 Jul 2026
- 2026A Fair Evaluation of Graph Foundation Models for Node Property Prediction23 Jun 2026
- 2026Deep Neural Sheaf Diffusion18 May 2026
- 2026OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data15 May 2026
- 2026RAwR: Role-Aware Rewiring via Approximate Equitable Partition10 May 2026
- 2026Have Graph -- Will Lift? The Case for Higher-Order Benchmarks8 May 2026
- 2026No Triangulation Without Representation: Generalization in Topological Deep Learning7 May 2026
38 more
- 2026Measuring Structure in Graph Benchmark Datasets Using Graph Invariants7 May 2026
- 2026Graph Rewiring in GNNs to Mitigate Over-Squashing and Over-Smoothing: A Survey1 May 2026
- 2026Cluster Attention for Graph Machine Learning8 Apr 2026
- 2026Beyond the Academic Monoculture: A Unified Framework and Industrial Perspective for Attributed Graph Clustering21 Mar 2026
- 2026SketchGraphNet: A Memory-Efficient Hybrid Graph Transformer for Large-Scale Sketch Corpora Recognition8 Mar 2026
- 2026Relatron: Automating Relational Machine Learning over Relational Databases26 Feb 2026
- 2026GrapHist: Graph Self-Supervised Learning for Histopathology24 Feb 2026
- 2026MolGraphBench: A Benchmark of GNN Architectures for Molecular Regression Tasks24 Feb 2026
- 2026Position: Evaluation of ECG Representations Must Be Fixed19 Feb 2026
- 2026No Need to Train Your RDB Foundation Model14 Feb 2026
- 2026Bridging Academia and Industry: A Comprehensive Benchmark for Attributed Graph Clustering9 Feb 2026
- 2026Billion-Scale Graph Foundation Models4 Feb 2026
- 2026GNN Explanations that do not Explain and How to find Them28 Jan 2026
- 2026Fixed Aggregation Features Can Rival GNNs27 Jan 2026
- 2026Position: Don't be Afraid of Over-Smoothing And Over-Squashing12 Jan 2026
- 2026Rethinking GNNs and Missing Features: Challenges, Evaluation and a Robust Solution8 Jan 2026
- 2025How Smoothing is N-simplicial Attention?17 Dec 2025
- 2025The Human Brain as a Combinatorial Complex22 Nov 2025
- 2025When Structure Doesn't Help: LLMs Do Not Read Text-Attributed Graphs as Effectively as We Expected20 Nov 2025
- 2025Generalizable Insights for Graph Transformers in Theory and Practice11 Nov 2025
- 2025Graph Homomorphism Distortion: A structural (pseudo)-metric for attributed graphs4 Nov 2025
- 2025Bridging the Divide: End-to-End Sequence-Graph Learning29 Oct 2025
- 2025What Do Temporal Graph Learning Models Learn?10 Oct 2025
- 2025Permutation-Invariant Spectral Learning via Dyson Diffusion9 Oct 2025
- 2025ATOM: A Pretrained Neural Operator for Multitask Molecular Dynamics7 Oct 2025
- 2025CrediBench: Building Web-Scale Network Datasets for Information Integrity27 Sep 2025
- 2025GraphUniverse: Synthetic Graph Generation for Evaluating Inductive Generalization25 Sep 2025
- 2025Exact Generalisation Error Exposes Benchmarks Skew Graph Neural Networks Success (or Failure)12 Sep 2025
- 2025Bringing Graphs to the Table: Zero-shot Node Classification via Tabular Foundation Models8 Sep 2025
- 2025AI for Scientific Discovery is a Social Problem8 Sep 2025
- 2025Turning Tabular Foundation Models into Graph Foundation Models28 Aug 2025
- 2025Why Isn't Relational Learning Taking Over the World?17 Jul 2025
- 2025CosmoBench: A Multiscale, Multiview, Multitask Cosmology Benchmark for Geometric Deep Learning4 Jul 2025
- 2025Bridging Theory and Practice in Link Representation with Graph Neural Networks30 Jun 2025
- 2025Generating Directed Graphs with Dual Attention and Asymmetric Encoding19 Jun 2025
- 2025Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models17 Jun 2025
- 2025Are We Really Measuring Progress? Transferring Insights from Evaluating Recommender Systems to Temporal Link Prediction14 Jun 2025
- 2025Directed Semi-Simplicial Learning with Applications to Brain Activity Decoding23 May 2025
50 newest of 53 All 53 (JSON)
- 2025Turning Tabular Foundation Models into Graph Foundation Modelscited by 35
- 2025Equivariance Everywhere All At Once: A Recipe for Graph Foundation Modelscited by 17
- 2025Bringing Graphs to the Table: Zero-shot Node Classification via Tabular Foundation Modelscited by 16
- 2026No Need to Train Your RDB Foundation Modelcited by 10
- 2025HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representationscited by 5
- 2026GNN Explanations that do not Explain and How to find Themcited by 5
- 2026Billion-Scale Graph Foundation Modelscited by 5
- 2025Bridging Theory and Practice in Link Representation with Graph Neural Networkscited by 4
- 2025What Do Temporal Graph Learning Models Learn?cited by 4
- 2026Fixed Aggregation Features Can Rival GNNscited by 4
- 2026Bridging Academia and Industry: A Comprehensive Benchmark for Attributed Graph Clusteringcited by 4
- 2026A Fair Evaluation of Graph Foundation Models for Node Property Predictioncited by 4
12 most cited of 51 All 51 (JSON)
- 2026PATTERN Can Be Solved from Memory: Generator-Aware Baselines for Synthetic Node Classification10 Oct 2026
- 2026The Universal Classifier for Graph Learning28 Sep 2026
- 2026Do Temporal Link Predictors Need Learned Memory? A Smoothed-Count Baseline with a Handful of Parameters28 Sep 2026
- 2026Not All Nodes Are Created Equal: Homophily-Aware Stratification for Stable GNN Evaluation16 Sep 2026
- 2026Graph Machine Learning: An Opportunity for Power Systems17 Aug 2026
- 2026An Investigation of the NeurIPS and ICML 2025 Position Tracks6 Jul 2026
- 2026A Fair Evaluation of Graph Foundation Models for Node Property Prediction23 Jun 2026
- 2026Deep Neural Sheaf Diffusion18 May 2026
- 2026OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data15 May 2026
- 2026RAwR: Role-Aware Rewiring via Approximate Equitable Partition10 May 2026
- 2026Have Graph -- Will Lift? The Case for Higher-Order Benchmarks8 May 2026
- 2026No Triangulation Without Representation: Generalization in Topological Deep Learning7 May 2026
12 newest of 51 All 51 (JSON)