Powerful Graph Convolutional Networks with Adaptive Propagation Mechanism for Homophily and Heterophily

Tao WangDi JinRui WangDongxiao HeYuxiao Huang

article2022AAAI137 citations

Proposes an adaptive graph convolutional network that dynamically adjusts feature propagation weights based on topological and attribute-driven homophily estimates between node pairs, effectively overcoming standard performance drops on heterophilic graphs.

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Graph Convolutional Networks are essential machine learning tools used to analyze interconnected data across diverse domains, including social network analysis, biology, and recommendation systems. However, conventional network models rely on the foundational assumption of homophily, which presumes that connected entities naturally share identical labels or characteristics. In many critical real-world systems, networks exhibit heterophily—where linked entities belong to entirely different categories, such as opposite-gender interactions in dating networks or distinct amino acids in protein structures. Standard models struggle in these heterophilic environments because their fixed information-passing mechanisms indiscriminately mix conflicting data from dissimilar neighbors.

The article develops and evaluates a new architecture, termed Homophily-Guided Graph Convolutional Network (HOG-GCN), designed to adaptively adjust its internal information propagation mechanism across both homophilic and heterophilic environments.

To address the limitations of prior techniques, the article introduces a dual-source estimation approach that measures the similarity between node pairs using both node characteristics and structural network positions. This estimated relationship matrix dynamically scales information flow: it strengthens signals between same-class nodes while dampening interference from different-class connections across two-step neighborhoods. The system trains the relationship estimation and information propagation jointly in a unified process. The article evaluates this design through semi-supervised classification experiments across seven real-world benchmark datasets—four exhibiting strong heterophily and three exhibiting traditional homophily—using standardized data splits.

The findings show that the proposed method consistently delivers superior predictive accuracy across diverse network types. In heterophilic networks, the architecture outperformed traditional graph models by an average of 24.5% to 26.5% in classification accuracy and surpassed specialized heterophily baselines by 3.9% to 19.0%. On homophilic networks, it achieved competitive or superior accuracy compared to standard models, maintaining top performance across datasets. Experimental parameter analyses established that examining two-step neighborhoods strikes the optimal balance for gathering relevant same-class signals, while broader neighborhood expansion introduces disruptive noise. Visual analysis confirmed that the approach produces sharply separated, well-defined classification boundaries.

These results demonstrate that graph learning systems can overcome structural assumptions without requiring separate model architectures for different types of relational data. For organizations relying on graph-based decision support, anomaly detection, or predictive modeling, this adaptability reduces deployment risk and lowers analytical error rates in complex environments where network relationships deviate from standard assumptions.

Technical leaders and data science teams implementing relational machine learning models should transition from rigid neighborhood aggregation pipelines to adaptive propagation frameworks when processing heterogeneous or mixed-relation graphs. Before full-scale deployment in production environments, teams should benchmark the architecture on domain-specific data and verify neighborhood search depths, as expanding beyond two-step connections risks incorporating unwanted data noise.

The study's empirical validations rely on seven standard benchmark datasets and specific semi-supervised data splits. While the empirical results and theoretical proofs provide strong confidence in the method's core effectiveness, operational performance may vary in extremely large-scale, dynamically changing networks that require specialized scaling optimizations.

arXiv: 2112.13562
Cover for Powerful Graph Convolutional Networks with Adaptive Propagation Mechanism for Homophily and Heterophily

Abstract

Graph Convolutional Networks (GCNs) have been widely applied in various fields due to their significant power on processing graph-structured data. Typical GCN and its variants work under a homophily assumption (i.e., nodes with same class are prone to connect to each other), while ignoring the heterophily which exists in many real-world networks (i.e., nodes with different classes tend to form edges). Existing methods deal with heterophily by mainly aggregating higher-order neighborhoods or combing the immediate representations, which leads to noise and irrelevant information in the result. But these methods did not change the propagation mechanism which works under homophily assumption (that is a fundamental part of GCNs). This makes it difficult to distinguish the representation of nodes from different classes. To address this problem, in this paper we design a novel propagation mechanism, which can automatically change the propagation and aggregation process according to homophily or heterophily between node pairs. To adaptively learn the propagation process, we introduce two measurements of homophily degree between node pairs, which is learned based on topological and attribute information, respectively. Then we incorporate the learnable homophily degree into the graph convolution framework, which is trained in an end-to-end schema, enabling it to go beyond the assumption of homophily. More importantly, we theoretically prove that our model can constrain the similarity of representations between nodes according to their homophily degree. Experiments on seven real-world datasets demonstrate that this new approach outperforms the state-of-the-art methods under heterophily or low homophily, and gains competitive performance under homophily.

Table of Contents

  • Introduction
  • Preliminaries
  • Notations and Problem Descriptions
  • The Framework
  • Overview
  • Homophily Degree Matrix Estimation
  • Homophily-guided Propagation
  • Optimization Objective
  • Theoretical Analysis
  • Experiments
  • Experimental Setup
  • Visualization
  • Node Classification
  • Parameter Analysis
  • Homophily Degree Matrix Analysis
  • Conclusion
  • Acknowledgments
  • References

Knowls

  1. Knowl 1 — HOG-GCN adaptive homophily-guided propagation

    model/method

    HOG-GCN is a graph convolutional network for semi-supervised node classification that changes feature propagation according to a learned homophily degree matrix. For an undirected graph with adjacency matrix A∈Rn×nA\in\mathbb{R}^{n\times n}, node-feature matrix X∈Rn×fX\in\mathbb{R}^{n\times f}, and CC node classes, define the kk-order adjacency matrix as Ak=∑r=1kArA_k=\sum_{r=1}^{k}A^r. Let H∈Rn×nH\in\mathbb{R}^{n\times n} encode the estimated homophily degree between node pairs, and let D^\widehat D be diagonal with D^ii=∑j(Ak⊙H)ij\widehat D_{ii}=\sum_j(A_k\odot H)_{ij}, where ⊙\odot denotes elementwise multiplication. The propagation layer is

    Z(l)=σ ⁣(μZ(l−1)We(l)+ξD^−1(Ak⊙H)Z(l−1)Wn(l)),Z(0)=X.Z^{(l)}=\sigma\!\left(\mu Z^{(l-1)}W_e^{(l)}+\xi\widehat D^{-1}(A_k\odot H)Z^{(l-1)}W_n^{(l)}\right),\qquad Z^{(0)}=X.

    Here Z(l)∈Rn×dlZ^{(l)}\in\mathbb{R}^{n\times d_l} is the layer-ll representation, We(l)W_e^{(l)} and Wn(l)W_n^{(l)} are learnable ego- and neighborhood-transformation matrices, σ\sigma is an activation function, and μ,ξ\mu,\xi weight the ego and neighborhood representations. Thus, high-homophily pairs receive stronger feature influence, while low-homophily pairs receive weaker influence; ego features are handled separately to preserve node-specific information. The paper uses k=2k=2 in its main experiments.

  2. Knowl 2 — Attribute-based homophily estimation

    model/method

    HOG-GCN estimates homophily from node attributes with a graph-independent multilayer perceptron. For node features X∈Rn×fX\in\mathbb{R}^{n\times f} and CC classes, the MLP computes

    Zm(l)=σ ⁣(Zm(l−1)Wm(l)),Zm(0)=X,Z_m^{(l)}=\sigma\!\left(Z_m^{(l-1)}W_m^{(l)}\right),\qquad Z_m^{(0)}=X,

    where Wm(l)W_m^{(l)} is learnable and ZmZ_m denotes the final-layer output. A row-wise softmax produces the class-probability matrix B∈Rn×CB\in\mathbb{R}^{n\times C}:

    B=softmax⁡(Zm),B=\operatorname{softmax}(Z_m),

    so BicB_{ic} is the MLP-estimated probability that node viv_i belongs to class cc. The MLP is trained on the labeled node set VLV_L using cross-entropy between its predictions and the known one-hot labels. The attribute-derived homophily matrix is

    S=BBT,Sij=bibjT,S=BB^{\mathsf T},\qquad S_{ij}=b_i b_j^{\mathsf T},

    where bib_i and bjb_j are the class-probability vectors for nodes viv_i and vjv_j. Thus, SijS_{ij} measures the similarity of the two nodes' predicted class distributions and can provide class-aware propagation guidance even when graph edges are heterophilic.

  3. Knowl 3 — Topology-based generalized label propagation

    model/method

    To estimate homophily from graph topology without assuming that adjacent nodes share a class, HOG-GCN learns edge weights through generalized label propagation. For an adjacency matrix AA and neighborhood order kk, it uses Ak=∑r=1kArA_k=\sum_{r=1}^{k}A^r. A learnable matrix T∈Rn×nT\in\mathbb{R}^{n\times n} assigns weights to existing kk-order neighborhoods; it does not add or remove graph connections. With initial soft labels Y(0)∈Rn×CY^{(0)}\in\mathbb{R}^{n\times C} equal to one-hot labels on labeled nodes and zero vectors on unlabeled nodes, the propagation is

    Y(l)=Dk−1(Ak⊙T)Y(l−1),Y^{(l)}=D_k^{-1}(A_k\odot T)Y^{(l-1)},

    where DkD_k is diagonal with (Dk)ii=∑j(Ak⊙T)ij(D_k)_{ii}=\sum_j(A_k\odot T)_{ij}. The matrix TT is learned by minimizing the labeled-node cross-entropy

    T∗=arg⁡min⁡T  1∣VL∣∑va∈VLJ(y^alp,ya),T^*=\arg\min_T\;\frac{1}{|V_L|}\sum_{v_a\in V_L}J(\widehat y_a^{\mathrm{lp}},y_a),

    where y^alp\widehat y_a^{\mathrm{lp}} is the propagated class distribution, yay_a is the known one-hot label, and JJ is cross-entropy. Because weights that improve classification of labeled nodes increase the influence of compatible class information, the learned TT serves as a topology-derived homophily estimate.

  4. Knowl 4 — Combined homophily degree matrix

    equation

    HOG-GCN combines attribute-derived homophily S=BBTS=BB^{\mathsf T} with topology-derived homophily TT using two nonnegative weighting hyperparameters α\alpha and β\beta:

    H=αS+βT.H=\alpha S+\beta T.

    Here H,S,T∈Rn×nH,S,T\in\mathbb{R}^{n\times n}, and HijH_{ij} controls the feature-propagation weight between nodes viv_i and vjv_j. The matrix SS can provide homophily estimates for arbitrary node pairs, whereas TT is learned only on the kk-order neighborhoods used for propagation. Entries of HH outside the propagation neighborhoods do not affect the graph convolution because they are removed by the elementwise product with AkA_k.

  5. Knowl 5 — End-to-end optimization of propagation and homophily estimation

    model/method

    HOG-GCN jointly trains the graph convolution parameters, the attribute MLP, and the topology-weight matrix so that homophily estimation and feature propagation improve one another. Let ZZ be the final graph-convolution representation, R=softmax⁡(Z)R=\operatorname{softmax}(Z) the node-class predictions, Θg\Theta_g the graph-convolution parameters, Θm\Theta_m the MLP parameters, and TT the learnable topology-weight matrix. The three supervised losses are the graph-convolution loss LgcnL_{\mathrm{gcn}}, the attribute-MLP loss LmlpL_{\mathrm{mlp}}, and the generalized-label-propagation loss LlpL_{\mathrm{lp}}. The complete training objective is

    (Θg∗,Θm∗,T∗)=arg⁡min⁡Θg,Θm,T(Lgcn+λLmlp+γLlp),(\Theta_g^*,\Theta_m^*,T^*) =\arg\min_{\Theta_g,\Theta_m,T} \left(L_{\mathrm{gcn}}+\lambda L_{\mathrm{mlp}}+\gamma L_{\mathrm{lp}}\right),

    where λ\lambda and γ\gamma balance the auxiliary MLP and label-propagation losses against the final node-classification loss. The learned matrix H=αBBT+βTH=\alpha BB^{\mathsf T}+\beta T guides feature propagation, while the resulting predictions provide supervision that updates both sources of homophily information.

  6. Knowl 6 — Representation-similarity guarantee from homophily-weighted propagation

    theoretical result

    For HOG-GCN representations ZiZ_i and ZjZ_j of nodes viv_i and vjv_j, the homophily-guided propagation corresponds to minimizing the weighted smoothness objective

    O=12∑vi∈V∑vj∈Nk(vi)Hij∥Zi−Zj∥22,O=\frac{1}{2}\sum_{v_i\in V}\sum_{v_j\in N_k(v_i)}H_{ij}\lVert Z_i-Z_j\rVert_2^2,

    where Nk(vi)N_k(v_i) is the set of kk-order neighbors of viv_i, HijH_{ij} is the learned homophily degree, and ∥⋅∥2\lVert\cdot\rVert_2 is the Euclidean norm. Under the paper's assumption that HH is symmetric, the corresponding normalized propagation operator is D^−1(Ak⊙H)\widehat D^{-1}(A_k\odot H), with D^ii=∑j(Ak⊙H)ij\widehat D_{ii}=\sum_j(A_k\odot H)_{ij}. Ignoring nonlinear activations and taking an initial transformed feature matrix Z(0)=XWZ^{(0)}=XW, the ll-step propagation is

    Z(l)=[D^−1(Ak⊙H)]lXW.Z^{(l)}=\left[\widehat D^{-1}(A_k\odot H)\right]^lXW.

    Consequently, pairs with larger learned homophily degrees incur a stronger penalty for dissimilar representations and are driven toward greater representation similarity, whereas low-homophily pairs exert weaker smoothing pressure. This gives HOG-GCN a mechanism for avoiding indiscriminate smoothing across heterophilic edges.

  7. Knowl 7 — Evaluation design across homophilic and heterophilic graphs

    experimental setup

    HOG-GCN was evaluated on transductive node classification using seven real-world graphs: four heterophilic networks—Texas, Wisconsin, Cornell, and Film—and three homophilic citation networks—Cora, Citeseer, and Pubmed. Accuracy was averaged over 10 random train/validation/test splits; each split used 48% of nodes per class for training, 32% for validation, and the remaining nodes for testing. All compared methods used the same splits.

    The comparison included attribute-only MLP, topology-only DeepWalk, homophily-oriented GCN and GAT, and heterophily-oriented H2GCN, CPGNN-MLP, CPGNN-Cheby, GPR-GNN, AM-GCN, and Geom-GCN. HOG-GCN used a two-layer 512-hidden-unit MLP, a two-layer graph convolution with 256 hidden units, α=1\alpha=1, β=0.1\beta=0.1, γ=1\gamma=1, and μ=1\mu=1, optimized with Adam and PyTorch's default initialization. The dataset statistics were:

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  8. Knowl 8 — Node-classification performance

    data/table

    The following values are mean test accuracy (%) ±\pm standard deviation over the 10 splits. The table compares HOG-GCN with attribute-only, topology-only, conventional GNN, and heterophily-oriented baselines across four heterophilic and three homophilic datasets. HOG-GCN obtains the best overall mean accuracy and mean rank, and its strongest advantage is on the heterophilic graphs.

    Could not parse LaTeX table

    On the four heterophilic graphs, HOG-GCN is the best-performing method on every dataset, with mean accuracy 73.245%73.245\%, compared with 46.75%46.75\% for GCN and 48.7975%48.7975\% for GAT; the corresponding improvements are 26.4926.49 and 24.4724.47 percentage points. On the homophilic graphs, HOG-GCN is best on Citeseer, second-best on Cora and Pubmed, and remains competitive with methods designed for strong homophily.

  9. Knowl 9 — Effect of propagation order and homophily-source weights

    empirical result

    The paper varied the neighborhood order kk from 1 through 6 for both generalized label propagation and homophily-guided feature propagation. On the heterophilic Texas and Cornell graphs, accuracy improved substantially when moving from k=1k=1 to k=2k=2. On homophilic Cora and Citeseer, the improvement at k=2k=2 was slight, and accuracy decreased as kk increased from 2 to 6. These results support using a small receptive field: two-hop neighborhoods can recover useful same-class information in heterophilic graphs, whereas larger neighborhoods increasingly introduce irrelevant or noisy information.

    The paper also varied α\alpha and β\beta, the weights of attribute-derived and topology-derived homophily, respectively, between 0 and 1. On Texas, performance was poor when either source was ignored (α=0\alpha=0 or β=0\beta=0), and the best observed setting was α=0.4\alpha=0.4, β=0.6\beta=0.6. On homophilic Cora, performance was comparatively stable across the weight settings. Thus, combining attributes and topology is particularly important for fine-grained propagation control in heterophilic graphs.

  10. Knowl 10 — Learned homophily separates same-class and different-class edges

    empirical result

    The learned homophily degree matrix was analyzed on two-hop neighborhoods of the heterophilic Texas graph and the homophilic Cora graph. In both graphs, node pairs belonging to the same class received higher homophily degrees than node pairs belonging to different classes. HOG-GCN therefore assigns larger propagation weights to same-class edges and smaller weights to different-class edges, regardless of whether the overall graph is heterophilic or homophilic. This empirical separation indicates that the learned matrix captures local class compatibility rather than merely reproducing the graph's global homophily level.

  11. Knowl 11 — Representation visualization on Citeseer

    empirical result

    Two-dimensional t-SNE projections of learned Citeseer node representations were compared for GCN, H2GCN, CPGNN, GPR-GNN, and HOG-GCN. HOG-GCN produced the clearest class-separated clusters and the highest apparent within-class similarity. GCN and CPGNN showed dispersed same-class points with mixing between different classes, while H2GCN and GPR-GNN produced intermediate separation with less distinct class boundaries. The visualization is consistent with HOG-GCN's homophily-weighted smoothness mechanism: it encourages similarity for compatible node pairs while reducing mixing across incompatible pairs.

Coverage note — No substantial contributed material was omitted; proof derivations, background, related work, acknowledgements, and references were excluded as non-knowls.

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Citation

MLA
Wang, T., et al. “Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily”. arXiv, 2021, http://arxiv.org/abs/2112.13562v1.
APA
Wang, T., Wang, R., Jin, D., He, D., & Huang, Y. (2021). Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily. arXiv. http://arxiv.org/abs/2112.13562v1
Chicago
Wang, T., R. Wang, D. Jin, D. He, and Y. Huang. 2021. “Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily”. arXiv. http://arxiv.org/abs/2112.13562v1.
Harvard
Wang, T. et al. (2021) “Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily”, arXiv [Preprint]. Available at: http://arxiv.org/abs/2112.13562v1.
Vancouver
1. Wang T, Wang R, Jin D, He D, Huang Y (2021) Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily. arXiv

BibTeX

@article{wang2021powerful,
  title = {Powerful Graph Convolutioal Networks with Adaptive Propagation Mechanism for Homophily and Heterophily},
  author = {Wang, Tao and Wang, Rui and Jin, Di and He, Dongxiao and Huang, Yuxiao},
  year = {2021},
  journal = {arXiv},
  url = {http://arxiv.org/abs/2112.13562v1},
  eprint = {2112.13562}
}
Metadata:arXiv

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