On The Expressive Power of GNN Derivatives
Abstract
Despite significant advances in Graph Neural Networks (GNNs), their limited expressivity remains a fundamental challenge. Research on GNN expressivity has produced many expressive architectures, leading to architecture hierarchies with models of increasing expressive power. Separately, derivatives of GNNs with respect to node features have been widely studied in the context of the oversquashing and over-smoothing phenomena, GNN explainability, and more. To date, these derivatives remain unexplored as a means to enhance GNN expressivity. In this paper, we show that these derivatives provide a natural way to enhance the expressivity of GNNs. We introduce High-Order Derivative GNN (HOD-GNN), a novel method that enhances the expressivity of Message Passing Neural Networks (MPNNs) by leveraging high-order node derivatives of the base model. These derivatives generate expressive structure-aware node embeddings processed by a second GNN in an end-to-end trainable architecture. Theoretically, we show that the resulting architecture family's expressive power aligns with the WL hierarchy. We also draw deep connections between HOD-GNN, Subgraph GNNs, and popular structural encoding schemes. For computational efficiency, we develop a message-passing algorithm for computing high-order derivatives of MPNNs that exploits graph sparsity and parallelism. Evaluations on popular graph learning benchmarks demonstrate HOD-GNN's strong performance on popular graph learning tasks.
Benchmark Results
Tested on 3 datasets 9 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
MoleculeNet
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | HIMP | 0.8740
±0.0050 | |
| 2 | GINE w/ VN | 0.8720
±0.0030 | |
| 3 | NaiveGINe+ K=3 w/ VN | 0.8700
±0.0040 | |
| 14 | GCN | 0.8400
±0.0040 best reported | best at pub: Graph convolutions that can finally model local structure (2020) |
| 24 | GIN | 0.8290
±0.0069 best reported | |
| 83 | PNA | 0.7930
±0.0150 best reported | best at pub: Deep Prompt Tuning for Graph Transformers (2023) |
| 104 | Graph ViT | 0.7851
±0.0077 | This paper |
| 122 | HOD-GNN | 0.7799
±0.0071 | This paper |
| 124 | HyMN | 0.7782
±0.0059 | This paper |
| 135 | GraphSAGE | 0.7744
±0.0038 | |
| 140 | GPSE | 0.7740
±0.0080 | This paper |
| 142 | Policy-Learn | 0.7736
±0.0060 | This paper |
| 168 | Random | 0.7662
±0.0063 | This paper |
| 170 | GIN + Laplacian PE | 0.7660
±0.0030 | This paper |
| 177 | GIN + RWSE | 0.7630
±0.0050 | This paper |
| 178 | Full | 0.7625
±0.0112 | This paper |
| 181 | GSN | 0.7608
±0.0079 | This paper |
| 194 | GPS | 0.7570
±0.0040 | This paper |
| 226 | Reconstr. GNN | 0.7515
±0.0140 | This paper |
LRGB
| # | Model | MAE ↓ | Paper |
|---|---|---|---|
| 1 | GCN | 0.2421
±0.0016 best reported | best at pub: Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence (ICML 2025) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 2 | IPR-MPNN | 0.2422
±0.0007 | |
| 3 | TANGO-GPS | 0.2422
±0.0014 | |
| 5 | GIN | 0.2429
±0.0019 | |
| 7 | GatedGCN | 0.2431
±0.0020 best reported | best at pub: Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence (ICML 2025) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 19 | Graph ViT | 0.2449
±0.0016 best reported | best at pub: Probabilistic Graph Rewiring via Virtual Nodes (NeurIPS 2024) best today: Molecular fingerprints are strong models for peptide function prediction (2025) Difference within reported uncertainty; not counted as underperformance. |
| 23 | HOD-GNN | 0.2450
±0.0011 | This paper |
| 39 | HyMN | 0.2464
±0.0013 | This paper |
| 40 | GPSE + GPS | 0.2464
±0.0025 | This paper |
| 49 | GINE | 0.2473
±0.0017 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 57 | Policy-Learn | 0.2475
±0.0011 | This paper |
| 66 | Exphormer | 0.2481
±0.0007 | This paper |
| 74 | GPSE + GCN | 0.2487
±0.0011 | This paper |
| 79 | GCN + Laplacian PE | 0.2492
±0.0019 | This paper |
| 81 | Subgraphormer 30% | 0.2494
±0.0020 | This paper |
| 88 | GraphGPS+LapPE | 0.2500
±0.0005 | prev best: Benchmarking Positional Encodings for GNNs and Graph Transformers (KDD 2024) |
| 104 | DRew-GCN+LapPE | 0.2517
±0.0011 best reported | best at pub: TANGO: Graph Neural Dynamics via Learned Energy and Tangential Flows (2025) best today: From Message-Passing to Linearized Graph Sequence Models (2026) Difference within reported uncertainty; not counted as underperformance. |
| 133 | GCN + RWSE | 0.2574
±0.0020 | This paper |
| 149 | MixHop-GCN+LapPE | 0.2614
±0.0023 | This paper |
| 150 | DIGL+MPNN+LapPE | 0.2616
±0.0018 | This paper |
| 155 | SAN+LapPE | 0.2680
±0.0040 best reported | best at pub: Learning Efficient Positional Encodings with Graph Neural Networks (ICLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 175 | MOSE | 0.3180
±0.0100 | This paper |
| 183 | GCNII | 0.3471
±0.0010 | This paper |
| 201 | MLP | 0.4351
±0.0008 |
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | S^2GCN | 0.7311
±0.0066 | |
| 2 | S4G | 0.7293
±0.0004 | |
| 3 | BuNN | 0.7276
±0.0065 | |
| 4 | GCN | 0.7261
±0.0011 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 12 | DRew-GCN+LapPE | 0.7150
±0.0044 | This paper |
| 26 | GIN | 0.7059
±0.0089 | |
| 34 | GatedGCN | 0.7006
±0.0033 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 35 | GCNII | 0.6990
±0.0030 best reported | best at pub: LRGB (NeurIPS 2022) |
| 42 | HOD-GNN | 0.6968
±0.0056 | This paper |
| 44 | Graph ViT | 0.6942
±0.0075 best reported | best at pub: A Generalization of ViT/MLP-Mixer to Graphs (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 50 | HyMN | 0.6857
±0.0055 | This paper |
| 51 | MixHop-GCN+LapPE | 0.6843
±0.0049 | This paper |
| 52 | DIGL+MPNN+LapPE | 0.6830
±0.0026 | This paper |
| 71 | GPSE + GPS | 0.6688
±0.0151 | This paper |
| 78 | GINE | 0.6621
±0.0067 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 92 | GraphGPS+LapPE | 0.6535
±0.0041 | prev best: Benchmarking Positional Encodings for GNNs and Graph Transformers (KDD 2024) Improvement within reported uncertainty; not highlighted. |
| 95 | Exphormer | 0.6527
±0.0043 | This paper |
| 110 | Policy-Learn | 0.6459
±0.0018 | This paper |
| 115 | Subgraphormer 30% | 0.6415
±0.0052 | This paper |
| 116 | SAN+LapPE | 0.6384
±0.0121 | This paper |
| 117 | MOSE | 0.6350
±0.0110 | This paper |
| 122 | GPSE + GCN | 0.6316
±0.0085 | This paper |
| 123 | SignNet | 0.6314
±0.0059 | This paper |
| 128 | GCN + Laplacian PE | 0.6218
±0.0055 | This paper |
| 135 | GCN + RWSE | 0.6067
±0.0069 | This paper |
| 181 | MLP | 0.4060
±0.0021 |
