Bilevel Graph Structure Learning, Revisited: Inner-Channel Origins of the Reported Gain

We introduce a constrained two-view framework for node prediction that aligns structure-conditioned GNN embeddings with a structure-free feature prior learned by an anchor model. Conventional Graph Neural Networks (GNNs) couple feature transformation and neighborhood aggregation, which renders them vulnerable to topology noise and heterophilous connections. To decouple this dependency, our framework utilizes an independent anchor network to capture intrinsic attribute features via a self-supervised reconstruction objective. Furthermore, we propose a Channel-Split Adaptive Gated GNN (CSAG-GNN) that dynamically routes representations between global spectral smoothing and local spatial discrimination through a node-wise gating mechanism. We propose a stable cyclic alternating optimization strategy to solve the resulting coupled bi-level objective, preventing mutual representation drift during training. Empirical results on both homophilous and heterophilous benchmarks show balanced performance gains and structural robustness over competitive baselines.

Bilevel mixed-integer linear optimization problems model hierarchical decision processes in which a leader anticipates the optimal response of a follower. Although expressive, these problems are computationally challenging because lower-level optimality is embedded in the leader's feasible region. Value-function reformulations replace the nested follower optimization with a constraint involving the follower's optimal value, but evaluating this value function exactly can itself be expensive. This paper introduces Graph4BiLO, a graph neural network (GNN) approach for learning bilevel value functions from variable--constraint graph representations. In contrast to fixed-length multilayer perceptron (MLP) representations, the GNN uses shared message-passing parameters and can therefore be applied across multiple problem sizes with a single trained model. The learned ReLU network is encoded exactly as mixed-integer linear constraints and embedded in an approximate single-level formulation. A repair step subsequently re-solves the follower problem for the selected leader decision to recover a bilevel-feasible follower response. We evaluate Graph4BiLO on knapsack interdiction instances with 20--100 items against the exact MibS solver and the learning-based Neur2BiLO method. Graph4BiLO obtains objective values comparable to Neur2BiLO across all tested sizes while avoiding size-specific neural networks. An additional out-of-distribution experiment demonstrates zero-shot transfer from 20-item training instances to previously unseen 40- and 60-item instances. However, embedding message passing at every graph node substantially increases the resulting mixed-integer formulation size and solve time. These results identify a central tradeoff between size-generalizable graph representations and the computational cost of embedding GNNs within optimization models.

Graph neural networks for node classification are typically trained by gradient descent over hundreds or thousands of epochs. Recent work has shown that, when properly tuned, classic GCN/SAGE/GAT architectures can match graph transformers on many node-classification benchmarks. We ask a complementary question: how much of this performance can be recovered by deterministic closed-form solvers, and what guarantees does this enable? We introduce a routed closed-form framework selected by adjusted homophily. For assortative graphs, we use SGC-style propagation followed by Ridge regression; for heterophilous graphs, we introduce LCF-Net, a layer-wise closed-form graph feature-refinement network whose per-layer Ridge solves are capped by a Gaussian kernel-Ridge head. Across 14 benchmarks, including ogbn-arxiv and ogbn-proteins, our closed-form predictors match or beat the best vanilla 2-layer GCN/SAGE/GAT on 9 of 9 measured datasets, tie tuned deep recipes within one standard deviation on 9 of 12 small benchmarks, and exceed the OGB-leaderboard plain GCN on both large graphs. The remaining heterophilous gap closely tracks the gain from vanilla 2-layer to deep SAGE, suggesting that the residual difference is primarily architectural. Because our predictors are explicit solutions of deterministic linear systems, modified graph inputs can be re-solved to obtain retrain-equivalent parameters. We formalize exact graph-object unlearning for label, feature, edge, node, and subgraph modifications, prove K-hop locality for Ridge components, and verify exactness across 109 configurations. On ogbn-arxiv, localized updates give $21$--$45\times$ speedups over full re-solving and roughly $10^{6}\times$ speedups over gradient retraining. Structural-inversion experiments further quantify the privacy floor of exact retraining and the additional leakage of approximate graph-unlearning methods.