Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning
Abstract
Graph neural networks (GNNs) have become a standard paradigm for graph representation learning, yet their message passing mechanism implicitly assumes that messages can be represented by source node embeddings, an assumption that fails in heterophilic graphs. While existing methods attempt to address heterophily through graph structure refinement or adaptation of neighbor aggregation, they often overlook the semantic potential of node text, relying on suboptimal message representation for propagation and compromise performance on homophilic graphs. To address these limitations, we propose LEMP4HG, a novel language model (LM)-enhanced message passing approach for heterophilic graph learning. Specifically, for text-attributed graphs (TAG), we leverage a LM to explicitly model inter-node semantic relationships from paired node texts, synthesizing semantically informed messages for propagation. To ensure practical efficiency, we further introduce an active learning–inspired strategy guided by a tailored heuristic, MVRD, which selectively enhances messages for node pairs most affected by message passing. Extensive experiments demonstrate that LEMP4HG consistently outperforms state-of-the-art methods on heterophilic graphs while maintaining robust performance on homophilic graphs under a practical computational budget.
Benchmark Results
Tested on 6 datasets 18 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | This paper |
| 4 | RevGAT+T | 0.8824 | This paper |
| 5 | SAGE+T | 0.8823 | This paper |
| 8 | Jacobi | 0.8778 | This paper |
| 9 | SAGE | 0.8771 | prev best: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 11 | GPR | 0.8755 | This paper |
| 12 | APPNP | 0.8754 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 14 | LEMP | 0.8729 | This paper |
| 15 | GBK | 0.8723 | This paper |
| 17 | OGNN | 0.8684 | This paper |
| 18 | GCNII | 0.8674 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 19 | RevGAT | 0.8665 | This paper |
| 20 | H2GCN | 0.8660 | prev best: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 21 | FAGCN | 0.8655 | This paper |
| 22 | Disam | 0.8651 | This paper |
| 23 | JKNet | 0.8629 | |
| 25 | SATA | 0.8602 | This paper |
| 26 | MLP+LLM_features | 0.8597 | |
| 27 | Cheby | 0.8597 | This paper |
| 31 | GAT | 0.8533 | prev best: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 54 | GIN | 0.8303
±0.0021 | |
| 237 | MLP | 0.7469
±0.0085 |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Jacobi | 0.8968 | This paper |
| 2 | GPR | 0.8953 | This paper |
| 3 | LEMP4HG | 0.8939 | This paper |
| 4 | SAGE | 0.8933 | prev best: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 5 | OGNN | 0.8908 | This paper |
| 6 | GCN | 0.8868 | prev best: Towards Graph Foundation Models: Learning Generalities Across Graphs via Task-Trees (ICML 2024) |
| 7 | JKNet | 0.8862 | prev best: IGNN-Solver: A Graph Neural Solver for Implicit Graph Neural Networks (2024) |
| 8 | RevGAT | 0.8859 | |
| 9 | GAT | 0.8829 | prev best: Towards Graph Foundation Models: Learning Generalities Across Graphs via Task-Trees (ICML 2024) |
| 13 | GCNII | 0.8738 | prev best: Rethinking Node-wise Propagation for Large-scale Graph Learning (WWW 2024) |
| 27 | MLP+LLM_features | 0.8634 | |
| 28 | Cheby | 0.8634 | This paper |
| 29 | APPNP | 0.8634 | prev best: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 83 | GraphSAGE | 0.8287 | |
| 351 | MLP | 0.6605
±0.0020 |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 111 | OGNN | 0.8622
±0.0412 best reported | best at pub: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 127 | SEGSL | 0.8590 | This paper |
| 128 | RevGAT+T | 0.8590 | This paper |
| 129 | LEMP+T | 0.8590 | This paper |
| 140 | SAGE+T | 0.8526 | This paper |
| 156 | MLP+LLM_features | 0.8462 | This paper |
| 157 | Cheby | 0.8462 | This paper |
| 169 | GBK | 0.8397 | This paper |
| 174 | LLM4HeG | 0.8362 | This paper |
| 178 | GPR | 0.8333 | This paper |
| 189 | SAGE | 0.8269 | prev best: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 190 | LEMP | 0.8269 | This paper |
| 207 | RevGAT | 0.8205 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 216 | Disam | 0.8141 | This paper |
| 234 | SATA | 0.8077 | This paper |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Graph Wave Networks (WWW 2025) |
| 292 | Jacobi | 0.7692 | This paper |
| 392 | JKNet | 0.6410 | prev best: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 24 | MLP | 0.9136
±0.0070 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 38 | FAGCN | 0.8852
±0.0133 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 39 | RevGAT+T | 0.8846 | This paper |
| 50 | SAGE+T | 0.8718 | This paper |
| 51 | OGNN | 0.8703
±0.0473 best reported | best at pub: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 57 | MLP+LLM_features | 0.8654 | This paper |
| 58 | Cheby | 0.8654 | This paper |
| 59 | LEMP+T | 0.8654 | This paper |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Heterophily-informed Message Passing (TMLR 2025) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 86 | LEMP | 0.8526 | This paper |
| 87 | LLM4HeG | 0.8524 | This paper |
| 100 | Disam | 0.8462 | This paper |
| 115 | RevGAT | 0.8397 | This paper |
| 125 | GBK | 0.8333 | This paper |
| 126 | SEGSL | 0.8333 | This paper |
| 138 | SAGE | 0.8269 | prev best: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 139 | GPR | 0.8269 | This paper |
| 157 | GraphSAGE | 0.8196
±0.0739 | |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 162 | SATA | 0.8141 | This paper |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Differentiable Cluster Graph Neural Network (2024) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 210 | Jacobi | 0.7756 | This paper |
| 241 | JKNet | 0.6603 |
Heterophily Benchmark
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Polynormer-r | 0.8591
±0.0074 | |
| 2 | DC-GNN | 0.8588
±0.0081 | |
| 3 | TANGO-GPS | 0.8566
±0.0101 | |
| 28 | GAT | 0.8443
±0.0100 best reported | best at pub: TopoBench: A Framework for Benchmarking Topological Deep Learning (2024) |
| 50 | GCN | 0.8364
±0.0067 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 76 | SAGE | 0.8243
±0.0044 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 77 | GraphSAGE | 0.8243
±0.0044 | |
| 97 | RevGAT+T | 0.7991 | This paper |
| 99 | RevGAT | 0.7968 | This paper |
| 102 | LEMP+T | 0.7897 | This paper |
| 105 | LEMP | 0.7867 | This paper |
| 106 | GCNII | 0.7861 | This paper |
| 107 | SAGE+T | 0.7848 | This paper |
| 108 | JKNet | 0.7838 | This paper |
| 109 | Disam | 0.7835 | This paper |
| 112 | Jacobi | 0.7817 | This paper |
| 113 | H2GCN | 0.7815 | prev best: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 114 | SATA | 0.7815 | This paper |
| 115 | GPR | 0.7813 | This paper |
| 116 | FAGCN | 0.7812 | prev best: Evolving Computation Graphs (ICML 2023) Improvement within reported uncertainty; not highlighted. |
| 118 | APPNP | 0.7809 | This paper |
| 119 | OGNN | 0.7803 | This paper |
| 120 | GBK | 0.7799 | This paper |
| 121 | MLP+LLM_features | 0.7793 | This paper |
| 122 | Cheby | 0.7793 | This paper |
| 139 | MLP | 0.7362
±0.0020 |
Other Graph Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MA-GCL | 0.8883
±0.0030 | |
| 2 | CCA-SSG | 0.8842
±0.0030 | |
| 3 | ARIEL | 0.8827
±0.0020 | |
| 9 | GAT | 0.8693
±0.0030 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) |
| 10 | GCN | 0.8651
±0.0050 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) |
| 33 | GIN | 0.4916
±0.0102 | |
| 36 | RevGAT+T | 0.4722 | This paper |
| 37 | LEMP+T | 0.4675 | This paper |
| 38 | SAGE | 0.4648 | This paper |
| 39 | SAGE+T | 0.4639 | This paper |
| 40 | RevGAT | 0.4590 | This paper |
| 41 | LEMP | 0.4590 | This paper |
| 43 | GPR | 0.4554 | This paper |
| 44 | Jacobi | 0.4554 | This paper |
| 45 | JKNet | 0.4551 | This paper |
| 46 | APPNP | 0.4534 | This paper |
| 50 | GCNII | 0.4429 | This paper |
| 51 | Disam | 0.4410 | This paper |
| 52 | OGNN | 0.4366 | This paper |
| 53 | FAGCN | 0.4319 | This paper |
| 55 | MLP+LLM_features | 0.4275 | This paper |
| 56 | Cheby | 0.4275 | This paper |
| 57 | GBK | 0.4274 | This paper |
| 58 | SATA | 0.4237 | This paper |
| 61 | H2GCN | 0.4071 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
