Organizations: School of Mathematics and Statistics, Shandong University · Academy of Mathematics and Systems Science, Chinese Academy of Sciences · School of Mathematical Sciences, University of Chinese Academy of Sciences · Institute of Information Engineering, Chinese Academy of Sciences · School of Cyber Security, University of Chinese Academy of Sciences
Hypergraph neural networks (HGNNs) have shown remarkable potential in modeling high-order relationships that naturally arise in many real-world data domains. However, existing HGNNs often suffer from shallow propagation, oversmoothing, and limited adaptability to complex hypergraph structures. In this paper, we propose Hypergraph Neural Diffusion (HND), a novel framework that unifies nonlinear diffusion equations with neural message passing on hypergraphs. HND is grounded in a continuous-time hypergraph diffusion equation, formulated via hypergraph gradient and divergence operators, and modulated by a learnable, structure-aware coefficient matrix over hyperedge-node pairs. This partial differential equation (PDE) based formulation provides a physically interpretable view of hypergraph learning, where feature propagation is understood as an anisotropic diffusion process governed by local inconsistency and adaptive diffusion coefficient. From this perspective, neural message passing becomes a discretized gradient flow that progressively minimizes a diffusion energy functional. We derive rigorous theoretical guarantees, including energy dissipation, solution boundedness via a discrete maximum principle, and stability under explicit and implicit numerical schemes. The HND framework supports a variety of integration strategies such as non-adaptive-step (like Runge-Kutta) and adaptive-step solvers, enabling the construction of deep, stable, and interpretable architectures. Extensive experiments on benchmark datasets demonstrate that HND achieves competitive performance. Our results highlight the power of PDE-inspired design in enhancing the stability, expressivity, and interpretability of hypergraph learning.
Figures & tables
Metric
Cora
Citeseer
Pubmed
Cora-CA
DBLP-CA
Zoo
20News
NTU2012
ModelNet40
House
Senate
∣V∣
2708
3312
19177
2708
41302
101
16242
2012
12311
1290
282
∣E∣
1579
1079
7963
1072
22363
43
100
2012
12311
340
315
feat
1433
3703
500
1433
1425
16
100
100
100
100
100
class
7
6
3
7
6
7
4
67
40
2
2
Table 1: Dataset Statistics Summary
Models
Cora
Citeseer
Pubmed
Cora-CA
DBLP-CA
Rank ↓
HNHN
76.36 ± 1.92
72.64 ± 1.57
86.90 ± 0.30
77.19 ± 1.49
86.78 ± 0.29
15
HGNN
79.39 ± 1.36
72.45 ± 1.16
86.44 ± 0.44
82.64 ± 1.65
91.03 ± 0.20
12
HCHA
79.14 ± 1.02
72.42 ± 1.42
86.41 ± 0.36
82.55 ± 0.97
90.92 ± 0.22
14
HyperGCN
78.45 ± 1.26
71.28 ± 0.82
82.84 ± 8.67
79.48 ± 2.08
89.38 ± 0.25
16
UniGCNII
78.81 ± 1.05
73.05 ± 2.21
88.25 ± 0.40
83.60 ± 1.14
91.69 ± 0.19
9
AllSetTransformer
78.59 ± 1.47
73.08 ± 1.20
88.72 ± 0.37
83.63 ± 1.47
91.53 ± 0.23
8
Table 2: Performance comparison on academic hypergraph datasets (Mean accuracy (%) ± standard deviation), with the best results in red , second-best in orange , and third-best in green .
Models
Zoo
20Newsgroup
NTU2012
ModelNet40
Senate
House
Rank ↓
HNHN
93.59 ± 5.88
81.35 ± 0.61
89.11 ± 1.44
97.84 ± 1.25
50.93 ± 6.33
67.80 ± 2.59
7
HGNN
92.50 ± 4.58
80.33 ± 0.42
87.72 ± 1.35
95.44 ± 0.33
48.59 ± 4.52
61.39 ± 2.96
12
HCHA
93.65 ± 6.15
80.33 ± 0.80
87.48 ± 1.87
94.48 ± 0.28
48.62 ± 4.41
61.36 ± 2.53
11
HyperGCN
N/A
81.05 ± 0.59
56.36 ± 4.86
75.89 ± 5.26
42.45 ± 3.67
48.32 ± 2.93
14
UniGCNII
93.65 ± 4.37
81.12 ± 0.67
89.30 ± 1.33
98.07 ± 0.23
49.30 ± 4.25
61.70 ± 3.37
8
AllSetTransformer
97.50 ± 3.59
81.38 ± 0.58
88.69 ± 1.24
98.20 ± 0.20
51.83 ± 5.22
69.33 ± 2.20
6
Table 3: Performance comparison on real-world hypergraph datasets (Mean accuracy (%) ± standard deviation), with the best results in red , second-best in orange , and third-best in green .
Model
Homophily
Heterophily
α=1
α=2
α=3
α=4
α=6
α=7
HGNN
92.58 ± 0.57
87.40 ± 0.89
82.32 ± 0.84
77.18 ± 1.08
69.98 ± 0.85
68.41 ± 1.39
HyperGCN
83.40 ± 1.67
78.13 ± 1.57
77.70 ± 1.01
74.90 ± 1.31
52.11 ± 0.75
49.40 ± 1.63
UniGCN
90.42 ± 1.04
82.12 ± 0.67
80.04 ± 0.98
76.86 ± 1.10
52.30 ± 1.18
49.20 ± 0.74
EDGNN
93.88 ± 0.67
89.89 ± 0.59
83.52 ± 0.85
76.65 ± 1.21
52.98 ± 0.78
49.65 ± 1.16
HND-NL
95.02 ± 0.55
90.34 ± 0.85
85.20 ± 1.17
79.41 ± 0.90
73.47 ± 0.95
73.02 ± 0.93
Table 4: Model Performance On Synthetic Hypergraphs with Controlled Heterophily α .
Figure 1: Accuracy(%) with various depths on Cora.
Figure 2: (a) shows the performance on Citeseer under feature gaussian noise. (b) shows the performance on Citeseer under feature uniform noise. (c) shows the performance on Citeseer under feature mask noise. (d) shows the performance on Cora-CA under structure noise.
Figure 3: (a) shows HND-L accuracy on Cora-CA and News20 with various hidden dimensions. (b) shows HND-NL accuracy on Cora-CA and News20 with various hidden dimensions. (c) shows HND-L accuracy on Cora and Zoo with various τ . (d) shows HND-NL accuracy on Cora and Zoo with various τ .
Figure 4: (a)(b)(c) show the visualization of Citeseer node features at t=0 , t=2 and t=4 . (d)(e)(f) show the visualization of Pubmed node features at t=0 , t=2 and t=4 .
Higher-order couplings enhance the expressive power of hypergraph neural networks (HGNNs), but they also intensify representation collapse in deep propagation due to strong multi-way feature mixing. This work investigates hypergraph oversmoothing from a dynamical-systems perspective and develops a reaction--diffusion framework for depth-resistant hypergraph learning. By defining hypergraph gradient and divergence operators, we interpret message passing as an incidence-level diffusion process. The analysis of pure diffusion shows that its continuous semiflow exponentially contracts the null-mode-free component of node representations and drives the Dirichlet energy to zero, revealing hypergraph oversmoothing as an intrinsic transverse-energy dissipation phenomenon. Motivated by this analysis, we propose Hypergraph Neural Reaction--Diffusion (HNRD), which introduces a reaction mechanism acting on the transverse component to compensate diffusion-induced dissipation and stabilize discriminative variations. We establish global well-posedness of the proposed dynamics and prove that the null-mode-free Dirichlet energy remains bounded away from zero. A forward-Euler discretization provides a practical HNRD layer with a stability condition for deep propagation. Experiments on benchmark and synthetic heterophilic hypergraphs demonstrate that HNRD consistently improves over representative hypergraph baselines. Depth, robustness, and efficiency analyses further show that HNRD preserves stable performance and nonzero Dirichlet energy under deep propagation and perturbations. These results provide a principled dynamical framework for designing deep hypergraph architectures that maintain higher-order expressiveness without representation collapse.
Zhiheng Zhou, Mengyao Zhou, Yancheng Chen +3
School of Mathematics and Statistics, Shandong University, Weihai, Shandong 264209, China · Academy of Mathematics and Systems Science, Chinese Academy of Sciences and also with the University of Chinese Academy of Sciences, Beijing 100190, China
Hypergraph neural networks (HGNNs) have demonstrated strong capabilities in modeling complex higher-order relationships. However, existing HGNNs often suffer from over-smoothing as the number of layers increases and lack effective control over message passing among nodes. Inspired by the theory of Ricci flow in differential geometry, we theoretically establish that introducing discrete Ricci flow into hypergraph structures can effectively regulate node feature evolution and thereby alleviate over-smoothing. Building on this insight, we propose Ricci Flow-guided Hypergraph Neural Diffusion(RFHND), a novel message passing paradigm for hypergraphs guided by discrete Ricci flow. Specifically, RFHND is based on a PDE system that describes the continuous evolution of node features on hypergraphs and adaptively regulates the rate of information diffusion at the geometric level, preventing feature homogenization and producing high-quality node representations. Experimental results show that RFHND significantly outperforms existing methods across multiple benchmark datasets and demonstrates strong robustness, while also effectively mitigating over-smoothing.
Mengyao Zhou, Zhiheng Zhou, Xiao Han +3
the Academy of Mathematics and Systems Science, Chinese Academy of Sciences and also with the University of Chinese Academy of Sciences, Beijing 100190, China · the School of Mathematics and Statistics, Shandong University, Weihai, Shandong 264209, China · School of Artificial Intelligence, Beihang University, Beijing 100191, China +1
Hypergraph neural networks have shown powerful capability in modeling higher-order relations, yet their predictive uncertainty remains underexplored. Unlike pairwise graphs, uncertainty in hypergraphs arises not only from noisy attributes and ambiguous labels, but also from variations in node-hyperedge incidence structures and complex higher-order dependencies. Existing approaches mainly estimate uncertainty from final predictions or rely on computationally expensive ensembles and Bayesian inference, limiting their ability to capture uncertainty evolution during representation learning. In this paper, we propose Hypergraph Neural Stochastic Diffusion(HyperNSD), a stochastic differential equation framework for uncertainty estimation on hypergraphs. HyperNSD models hypergraph representations as stochastic processes evolving over node-hyperedge incidence structures. A learnable drift function captures deterministic higher-order diffusion dynamics, while a learnable stochastic forcing function characterizes structural ambiguity and representation noise. Predictive uncertainty is directly quantified through the variability of stochastic representation trajectories, providing an intrinsic uncertainty measure beyond post-hoc confidence scores. We formulate HyperNSD with neural drift and diffusion networks, enabling joint learning of prediction and uncertainty propagation. Theoretical analyses establish well posedness, perturbation stability,permutation equivariance, and numerical convergence of the proposed stochastic dynamics. Experiments on multiple hypergraph benchmarks demonstrate that HyperNSD achieves reliable uncertainty estimation for out-of-distribution and misclassification detection while preserving competitive prediction accuracy. These results provide a principled stochastic-dynamical framework for trustworthy higher-order representation learning.
Zhiheng Zhou, Mengyao Zhou, Dengyi Zhao +2
School of Mathematics and Statistics, Shandong University, Weihai, Shandong 264209, China · Academy of Mathematics and Systems Science, Chinese Academy of Sciences and also with the University of Chinese Academy of Sciences, Beijing 100190, China