arXiv Machine Learning
4d ago

Diagnosing GNN Failure Modes with Layer-Wise Probe Entropy

The paper introduces a post-hoc diagnostic for graph neural networks that freezes a trained model, fits a linear probe to each layer, and tracks probe accuracy with normalized predictive entropy. By examining layer-wise probe entropy, the authors can distinguish beneficial, neutral, and harmful smoothing effects—something existing geometric measures cannot do. The study also shows that entropy degradation patterns separate two main GNN failure modes: structural mismatch under heterophily, which appears early even in shallow models, and excessive-depth oversmoothing that emerges only as propagation depth increases.

By Shanzi Bao, Mar Gonz\`alez I Catal\`a, Pietro Li\`o
arXiv Machine Learning
Oct 9

How Much Does Message Passing Matter? A Drop-In Study of GNN Layers for Neural Network Graph Regression

The study investigates how different message‑passing (MP) layers affect graph‑level regression performance in Graph Neural Networks (GNNs). By replacing the MP component in four existing GNN regressors with ten varied configurations—including convolutional, isomorphism‑based, and attention‑based designs—the authors evaluate performance across eleven neural‑network graph datasets, measuring metrics such as rank correlation, prediction error, top‑k retrieval, latency, and memory usage. Results show that the choice of MP layer significantly influences outcomes, with the optimal layer depending on graph size, training‑set size, and regression objective; classical layers like GEN, k‑GNN, and PNA outperform attention‑based layers on small graphs, while GATv2 excels on datasets with few large graphs.

By Keith G. Mills, Aedan J. DeFrates, Joong Ho Kim