Graph-less Neural Networks: Teaching Old MLPs New Tricks via Distillation
Abstract
Graph Neural Networks (GNNs) are popular for graph machine learning and have shown great results on wide node classification tasks. Yet, they are less popular for practical deployments in the industry owing to their scalability challenges incurred by data dependency. Namely, GNN inference depends on neighbor nodes multiple hops away from the target, and fetching them burdens latency-constrained applications. Existing inference acceleration methods like pruning and quantization can speed up GNNs by reducing Multiplication-and-ACcumulation (MAC) operations, but the improvements are limited given the data dependency is not resolved. Conversely, multi-layer perceptrons (MLPs) have no graph dependency and infer much faster than GNNs, even though they are less accurate than GNNs for node classification in general. Motivated by these complementary strengths and weaknesses, we bring GNNs and MLPs together via knowledge distillation (KD). Our work shows that the performance of MLPs can be improved by large margins with GNN KD. We call the distilled MLPs Graph-less Neural Networks (GLNN s) as they have no inference graph dependency. We show that GLNN s with competitive accuracy infer faster than GNNs by 146-273 and faster than other acceleration methods by 14-27. Under a production setting involving both transductive and inductive predictions across 7 datasets, GLNN accuracies improve over stand-alone MLPs by 12.36\
Benchmark Results
Tested on 4 datasets 2 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 348 | GLNN | 0.8360
±0.0022 best reported | best today: Frameless Graph Knowledge Distillation (2023) |
| 724 | MLP | 0.7768 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 229 | GLNN | 0.7400
±0.0002 best reported | best today: Frameless Graph Knowledge Distillation (2023) Difference within reported uncertainty; not counted as underperformance. |
| 259 | SAGE | 0.7361
±0.0190 best reported | best at pub: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) best today: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 | |
| 116 | SAGE | 0.8881
±0.0015 best reported | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 428 | GLNN | 0.8027
±0.0036 best reported |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 | |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.8297
±0.0216 | |
| 46 | GraphSAGE | 0.9120
±0.0029 | |
| 236 | GLNN | 0.8750
±0.0060 best reported | best today: Training MLPs on Graphs without Supervision (2024) |
| 320 | MLP | 0.8463 best reported |
