Graph Negative Feedback Bias Correction Framework for Adaptive Heterophily Modeling

Graph Neural Networks (GNNs) have demonstrated impressive performance in learning representations from graph-structured data. However, their message-passing mechanism inherently relies on the assumption of label consistency among connected nodes, limiting their applicability to low-homophily settings. Moreover, since message passing operates as a hierarchical diffusion process, GNNs face challenges in capturing long-range dependencies. As network depth increases, the structural noise along heterophilic edges tends to be amplified, resulting in over-smoothing. This issue becomes especially prominent in highly heterophilic graphs, where the propagation of inconsistent semantics across the topology continually exacerbates misaggregation. To address this issue, we propose a novel framework named Layer Embedding Deep Fusion Graph Neural Network (LEDF-GNN). Specifically, we design a Layer Embedding Deep Fusion (LEDF) operator that nonlinearly fuses multi-layer embeddings to capture inter-layer dependencies and effectively alleviate deep propagation degradation. Meanwhile, to mitigate structural heterophily, LEDF-GNN employs a Dual-Topology Parallel Strategy (DTPS) that simultaneously leverages the original and reconstructed topologies, allowing for adaptive structure-semantics co-optimization under diverse homophily conditions. Extensive semi-supervised classification experiments on the citation and image benchmarks demonstrate that, under both homophilic and heterophilic settings, LEDF-GNN consistently outperforms state-of-the-art baselines, validating its effectiveness and generalization capability across diverse graph types.

Heterophily is a prevalent property of real-world graphs and is well known to impair the performance of homophilic Graph Neural Networks (GNNs). Prior work has attempted to adapt GNNs to heterophilic graphs through non-local neighbor extension or architecture refinement. However, the fundamental reasons behind misclassifications remain poorly understood. In this work, we take a novel perspective by examining recurring inductive subgraphs, empirically and theoretically showing that they act as spurious shortcuts that mislead GNNs and reinforce non-causal correlations in heterophilic graphs. To address this, we adopt a causal inference perspective to analyze and correct the biased learning behavior induced by shortcut inductive subgraphs. We propose a debiased causal graph that explicitly blocks confounding and spillover paths responsible for these shortcuts. Guided by this causal graph, we introduce Causal Disentangled GNN (CD-GNN), a principled framework that disentangles spurious inductive subgraphs from true causal subgraphs by explicitly blocking non-causal paths. By focusing on genuine causal signals, CD-GNN substantially improves the robustness and accuracy of node classification in heterophilic graphs. Extensive experiments on real-world datasets not only validate our theoretical findings but also demonstrate that our proposed CD-GNN outperforms state-of-the-art heterophily-aware baselines.

Over the past decade, Graph Neural Networks (GNNs) have achieved great success on machine learning tasks with relational data. However, recent studies have found that heterophily can cause significant performance degradation of GNNs, especially on node-level tasks. Numerous heterophilic benchmark datasets have been put forward to validate the efficacy of heterophily-specific GNNs, and various homophily metrics have been designed to help recognize these challenging datasets. Nevertheless, there still exist multiple pitfalls that severely hinder the proper evaluation of new models and metrics: 1) lack of hyperparameter tuning; 2) insufficient evaluation on the truly challenging heterophilic datasets; 3) missing quantitative evaluation for homophily metrics on synthetic graphs. To overcome these challenges, we first train and fine-tune baseline models on $27$ most widely used benchmark datasets, and categorize them into three distinct groups: malignant, benign and ambiguous heterophilic datasets. We identify malignant and ambiguous heterophily as the truly challenging subsets of tasks, and to our best knowledge, we are the first to propose such taxonomy. Then, we re-evaluate $11$ state-of-the-arts (SOTA) GNNs, covering six popular methods, with fine-tuned hyperparameters on different groups of heterophilic datasets. Based on the model performance, we comprehensively reassess the effectiveness of different methods on heterophily. At last, we evaluate $11$ popular homophily metrics on synthetic graphs with three different graph generation approaches. To overcome the unreliability of observation-based comparison and evaluation, we conduct the first quantitative evaluation and provide detailed analysis.