We study the challenging problem for inference tasks on large-scale graph datasets of Graph Neural Networks: huge time and memory consumption, and try to overcome it by reducing reliance on graph structure. Even though distilling graph knowledge to student MLP is an excellent idea, it faces two major problems of positional information loss and low generalization. To solve the problems, we propose a new three-stage multitask distillation framework. In detail, we use Positional Encoding to capture positional information. Also, we introduce Neural Heat Kernels responsible for graph data processing in GNN and utilize hidden layer outputs matching for better performance of student MLP's hidden layers. To the best of our knowledge, it is the first work to include hidden layer distillation for student MLP on graphs and to combine graph Positional Encoding with MLP. We test its performance and robustness with several settings and draw the conclusion that our work can outperform well with good stability. Code implementation is in https://github.com/lijunxian111/KMP.
Figures & tables
Figure 1: Overall structure of our framework. It consists of three stages: GNN pretraining, distillation and inference. We transfer knowledge to student MLP during stage II. Best viewed in color.
Dataset
Models
SAGE
GCN
GAT
MLP
GLNN(SAGE)
KMP(SAGE)
GLNN(GCN)
KMP(GCN)
GLNN(GAT)
KMP(GAT)
Cora
79.70 ± 1.90
79.58 ± 1.01
81.41 ± 1.15
58.66 ± 2.34
78.99 ± 1.90
79.48 ± 1.48
79.43 ± 0.82
80.03 ± 1.19
79.89 ± 1.44
80.44 ± 1.13
Citeseer
70.53 ± 2.16
70.09 ± 2.23
71.76 ± 1.54
58.01 ± 0.96
71.23 ± 2.13
71.96 ± 2.25
71.24 ± 2.98
72.18 ± 2.23
72.44 ± 1.63
72.72 ± 1.18
Pubmed
75.53 ± 2.39
77.96 ± 2.96
78.30 ± 2.44
67.72 ± 3.34
76.32 ± 2.67
76.80 ± 2.01
77.94 ± 2.95
78.48 ± 1.90
76.44 ± 2.28
76.86 ± 2.40
Amazon Photo
90.26 ± 1.14
87.18 ± 4.05
91.61 ± 0.94
78.39 ± 1.71
92.04 ± 0.91
92.23 ± 0.85
89.97 ± 3.08
90.48 ± 2.55
93.01 ± 0.94
93.19 ± 0.78
Amazon Computer
83.23 ± 1.49
80.19 ± 5.18
83.03 ± 2.30
69.01 ± 3.27
84.41 ± 1.51
84.75 ± 1.10
78.42 ± 4.26
78.96 ± 4.27
83.52 ± 2.17
82.94 ± 2.00
Table 1: Results of teachers, baseline models and KMP for trans setting. The best performance of student model is highlighted.
Dataset
Models
SAGE
GCN
GAT
MLP
GLNN(SAGE)
KMP(SAGE)
GLNN(GCN)
KMP(GCN)
GLNN(GAT)
KMP(GAT)
Cora
78.64 ± 2.06
78.90 ± 1.69
81.10 ± 2.46
58.02 ± 2.72
71.94 ± 2.85
71.85 ± 2.40
72.39 ± 2.30
72.86 ± 2.37
72.41 ± 1.48
72.53 ± 1.38
Citeseer
70.83 ± 2.83
68.26 ± 3.65
70.75 ± 3.29
59.46 ± 4.55
70.80 ± 2.63
71.22 ± 2.04
67.15 ± 2.33
68.04 ± 2.52
68.92 ± 2.94
69.17 ± 3.01
Pubmed
74.86 ± 2.97
74.40 ± 2.94
76.64 ± 2.97
66.14 ± 5.03
74.76 ± 2.69
74.92 ± 3.03
74.89 ± 2.81
75.44 ± 2.75
74.63 ± 2.81
74.53 ± 3.06
Amazon Photo
91.33 ± 1.56
89.28 ± 2.12
92.27 ± 1.50
79.01 ± 1.80
89.75 ± 1.58
90.26 ± 2.43
88.54 ± 1.94
89.10 ± 1.69
90.02 ± 2.48
90.54 ± 1.37
Amazon Computer
82.73 ± 1.54
75.21 ± 3.56
83.38 ± 2.50
67.95 ± 3.88
81.18 ± 2.53
80.94 ± 2.33
74.01 ± 3.26
74.05 ± 4.01
81.08 ± 2.54
81.56 ± 2.57
Table 2: Results of teachers, baseline models and KMP for induc setting. The best performance of student model is highlighted.
Dataset
Models
SAGE
GCN
GAT
MLP
GLNN(SAGE)
KMP(SAGE)
GLNN(GCN)
KMP(GCN)
GLNN(GAT)
KMP(GAT)
OGBN-Arxiv
71.54 ± 0.47
69.84 ± 0.41
73.45 ± 0.29
54.12 ± 2.97
64.48 ± 1.29
64.31 ± 0.50
60.07 ± 0.18
60.96 ± 1.11
63.45 ± 4.06
65.02 ± 2.23
OGBN-Products
78.07 ± 0.06
75.02 ± 0.23
78.35 ± 0.14
60.88 ± 0.17
67.44 ± 0.60
68.01 ± 0.52
66.92 ± 0.41
66.07 ± 0.64
67.53 ± 0.33
68.20 ± 0.69
Table 3: Results of teachers, baseline models and KMP for trans setting on large-scale graph datasets. The best performance of student model is highlighted.
Dataset
Models
SAGE
GCN
GAT
MLP
GLNN(SAGE)
KMP(SAGE)
GLNN(GCN)
KMP(GCN)
GLNN(GAT)
KMP(GAT)
OGBN-Arxiv
70.53 ± 0.58
69.79 ± 0.41
—
54.46 ± 2.75
58.83 ± 0.33
59.31 ± 0.22
58.94 ± 0.71
60.01 ± 1.02
—
—
OGBN-Products
77.25 ± 0.22
74.93 ± 0.15
—
61.05 ± 0.36
65.24 ± 0.39
65.93 ± 0.53
64.37 ± 0.13
63.95 ± 0.17
—
—
Table 4: Results of teachers, baseline models and KMP for induc setting on large-scale graph datasets. The best performance of student model is highlighted. (’—’ means that the GNN shows poor performance and we do not use it as teacher.)
Dataset
Models(SAGE teacher, trans)
Models(SAGE teacher, induc)
KMP(ours)
KMP+PE(ours)
SA−MLP
KMP(ours)
KMP+PE(ours)
SA−MLP
Cora
79.48 ± 1.48
80.97 ± 1.03
79.33 ± 1.55
71.85 ± 2.40
71.90 ± 1.81
71.54 ± 2.26
Citeseer
71.96 ± 2.25
72.07 ± 2.51
71.25 ± 1.57
71.22 ± 2.04
71.46 ± 2.65
70.95 ± 2.49
Pubmed
76.80 ± 2.01
76.58 ± 2.84
76.45 ± 2.50
74.92 ± 3.03
74.71 ± 2.09
74.99 ± 3.74
Amazon Photo
92.27 ± 1.50
92.38 ± 0.82
90.67 ± 0.93
90.26 ± 2.43
90.77 ± 0.84
90.27 ± 1.44
Amazon Computer
84.75 ± 1.10
85.10 ± 1.66
83.38 ± 2.50
80.94 ± 2.33
81.50 ± 2.58
81.01 ± 2.89
Table 5: Results of KMP+PE, KMP and SA-MLP for both trans and inductive setting. The best performance of the student model is highlighted.
Figure 2: Results of Robustness study with different teachers on three datasets. The x-axis shows percentage of feature noise and y-axis means test accuracy(%).
Figure 3: Results of sensitiveness study with different teachers on three datasets. Mean and variance of test accuracy reported. We study if changes of γ can influence student MLP’s performance greatly. The x-axis shows different γ s and y-axis means test accuracy(%) with them.
Dataset
Models
Teacher
MLP
GLNN
KMP
MiniGC
91.90 ± 3.47
66.35 ± 5.36
75.44 ± 4.69
78.95 ± 5.01
Table 6: Results for graph classification on MiniGC dataset. The best performance of student model is highlighted.
Appendix figures & tables5 assets
Supplementary material from the paper’s appendix.
Appendix
Dataset
Nodes
Edges
Feature dim
Classes
Cora
2708
5429
1433
7
Citeseer
3327
4732
3703
6
Pubmed
19717
44324
500
3
Amazon Photo
7487
119043
745
8
Amazon Computer
13381
245778
767
10
OGBN-Arxiv
169343
1166243
128
40
Appendix
Table 7: Details of the seven used datasets
GCN
SAGE
GAT
number of layers
2
2
2
hidden layer dim
64
128
128
weight decay
0.001
5e-4
0.01
dropout ratio
0.8
0
0.6
attention dropout ratio
—
—
0.6
fan_out
—
5,5
—
Appendix
Table 8: Experiment settings for the 5 datasets.
γ
0.1,0.3,0.5,0.7,0.9,1,3,10,30
temperature( t )
0.25,0.5,1,2,4,10
θ (percentage of hard labels)
0,0.2,0.4,0.6,0.8,1
learning rate
0.01,5e-3,1e-3,5e-4,1e-4
Appendix
Table 9: Grid Search of hyperparameters.
Figure 4: Results of trainable kernel on three benchmark datasets, compared to kernels without self training
GNN-to-MLP distillation aims to retain the predictive accuracy of a message-passing teacher while deploying a graph-free MLP at inference. Existing methods mainly transfer node-wise predictions or use confidence-based reweighting, but they do not specify where the student should preserve the teacher's graph-induced geometry. We show that this omission leads to two spectral failure modes in the student's representation space. On sparse graphs, the student suffers from spectral underfit, missing high-energy teacher directions concentrated near boundary regions. On dense graphs, it suffers from spectral overfit, retaining spurious directions that the teacher has collapsed through aggregation. Motivated by an energy-weighted teacher-student alignment objective, we propose Graph Geometry-aware MLP (G^2MLP), a training-time distillation framework guided by Ollivier-Ricci curvature. Curvature identifies where the two spectral errors concentrate and is used to allocate supervision between prediction-level and representation-level alignment. The deployed model remains a standard MLP and requires no graph access at inference. Across node-classification benchmarks, G^2MLP consistently improves over graph-free distillation baselines, reduces the teacher-student rank gap in both regimes, and transfers without architectural changes to Graph Transformer teachers and link prediction.
Zhewei Chen, Hao Zhu, Jiaojiao Jiang +1
Australian National University · Data61, CSIRO · University of New South Wales
Temporal knowledge graphs (TKGs) support reasoning over time-evolving facts, yet state-of-the-art models are often computationally heavy and costly to deploy. Existing compression and distillation techniques are largely designed for static graphs; directly applying them to temporal settings may overlook time-dependent interactions and lead to performance degradation. We propose an LLM-assisted distillation framework specifically designed for temporal knowledge graph reasoning. Beyond a conventional high-capacity temporal teacher, we incorporate a large language model as an auxiliary instructor to provide enriched supervision. The LLM supplies broad background knowledge and temporally informed signals, enabling a lightweight student to better model event dynamics without increasing inference-time complexity. Training is conducted by jointly optimizing supervised and distillation objectives, using a staged alignment strategy to progressively integrate guidance from both teachers. Extensive experiments on multiple public TKG benchmarks with diverse backbone architectures demonstrate that the proposed approach consistently improves link prediction performance over strong distillation baselines, while maintaining a compact and efficient student model. The results highlight the potential of large language models as effective teachers for transferring temporal reasoning capability to resource-efficient TKG systems.
Wang Xing, Wei Song, Siyu Lin +2
School of Computer Science and Technology, Xidian University · School of Computing and Artificial Intelligence, Southwest Jiaotong University · School of Information Science and Engineering, Chongqing Jiaotong University
Hypergraph knowledge distillation aims to retain the predictive performance of a hypergraph neural network (HNN) teacher while reducing inference costs through a lightweight student model. In this work, we observe that HNNs exhibit substantially lower prediction performance on heterophilic nodes connected through semantically diverse hyperedges, indicating that the reliability of teacher knowledge varies across nodes. Motivated by this observation, we propose HADES, a heterophily-aware adaptive distillation method for hypergraph neural networks. HADES quantifies node heterophily and leverages it as an estimate of teacher reliability to modulate the transfer of teacher knowledge during distillation. Experimental results on real-world hypergraphs demonstrate that HADES consistently improves student performance across different HNN teachers and distillation objectives. In many cases, the resulting student models surpass the predictive performance of their teachers while achieving up to 12.3 times faster inference.
Joohee Cho, David Yoon Suk Kang, Yunyong Ko
Chung-Ang University · Seoul, South Korea · Chungbuk National University +1