When Missingness Follows the Graph: Beyond Feature Propagation for Missing Features

Missing data is ubiquitous in real-world datasets. Traditional methods either discard incomplete samples or apply imputation techniques that ignore potentially informative missingness patterns, implicitly assuming that missingness occurs randomly. However, missingness patterns might provide additional information. We propose pattern-aware graph neural networks that explicitly encode which features are missing alongside observed values. We used four encoding strategies -- learned embeddings, frozen random embeddings, statistical features, and hierarchical representations -- across seven UCI datasets with naturally occurring missingness. Our Pattern-aware methods achieve substantial improvements over baselines, with an average improvement of 17% in balanced accuracy and 22% in F1-macro across all datasets. The benefits vary significantly by dataset: annealing shows dramatic improvement (+80% balanced accuracy), while hepatitis and soybean show minimal gains (+4--5%). Notably, even simple random pattern embeddings perform comparably to learned embeddings (0.650 vs 0.663 balanced accuracy), suggesting that distinguishing between patterns may be more important than task-specific optimization. Our ablation study reveals that attention mechanisms, while helpful, are not critical when pattern information is available -- simple mean aggregation with pattern awareness achieves 0.640 balanced accuracy compared to 0.645 for attention-based variants.

Clustering on graphs where both node attributes and structural links are partially missing remains a challenging task. Existing methods typically rely on imputation-then-clustering on single-view missingness incomplete graphs, which are vulnerable to cross-view error propagation and cluster-boundary blurring under simultaneous attribute and structure missingness. To address these limitations, we propose a Robust Graph Clustering Network for Multiple Missing Data (RGCN), which is designed to handle simultaneous node attribute and graph structure incompleteness. RGCN introduces three key innovations: First, we design a view-decoupled dual-branch imputation to mitigate interference and enable mutual enhancement in recovering missing data. Second, we employ a multi-hyperspherical mixture prior to enhance intra-cluster compactness and inter-cluster separability on a directional latent manifold. Third, a boundary-aware contrastive enhancement objective mitigates the blurring of clusters caused by imputation bias. Extensive experiments on real-world datasets demonstrate that RGCN consistently outperforms state-of-the-art baselines under various missing patterns.

Graph neural networks have achieved strong performance on graph-structured data, but their effectiveness depends heavily on the quality of the observed graph. In real applications, graph topology is often imperfect: noisy edges may connect unrelated nodes, while missing edges may prevent useful information from being propagated. Existing robust graph learning methods mainly address this problem by removing suspicious edges or by learning a new graph structure during training. However, edge removal alone cannot recover missing connections, and graph structure learning may introduce additional optimization complexity. In this paper, we propose Topology-Aware Gaussian Repair (TAGR), a simple graph repair framework for robust message passing in graph neural networks. Instead of learning a dense adjacency matrix, TAGR constructs a sparse feature-neighborhood graph using an adaptive Gaussian kernel and combines it with a topology-aware residual correction of the observed graph. The Gaussian repair component introduces auxiliary edges between feature-similar nodes, while the residual correction preserves and reweights the original topology according to local feature and structural consistency. The repaired graph can be used directly with standard graph neural networks without changing their architectures. Extensive experiments on benchmark citation networks show that TAGR improves the robustness of GNNs under both noisy-edge and missing-edge settings. The analysis further show that Gaussian feature-neighborhood repair provides the main robustness gain, while topology-aware residual correction improves stability when the observed graph is incomplete. These results suggest that effective graph robustness can be achieved through lightweight sparse graph repair rather than dense graph structure learning.