On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks

Heterophily, or the tendency of connected nodes in networks to have different class labels or dissimilar features, has been identified as challenging for many Graph Neural Network (GNN) models. While the challenges of applying GNNs for node classification when class labels display strong heterophily are well understood, it is unclear how heterophily affects GNN performance in other important graph learning tasks where class labels are not available. In this work, we focus on the link prediction task and systematically analyze the impact of heterophily in node features on GNN performance. Theoretically, we first introduce formal definitions of homophilic and heterophilic link prediction tasks, and present a theoretical framework that highlights the different optimizations needed for the respective tasks. We then analyze how different link prediction encoders and decoders adapt to varying levels of feature homophily and introduce designs for improved performance. Our empirical analysis on a variety of synthetic and real-world datasets confirms our theoretical insights and highlights the importance of adopting learnable decoders and GNN encoders with ego- and neighbor-embedding separation in message passing for link prediction tasks beyond homophily.

Bias Amplification Enhances Minority Group Performance

Neural networks produced by standard training are known to suffer from poor accuracy on rare subgroups despite achieving high accuracy on average, due to the correlations between certain spurious features and labels. Previous approaches based on worst-group loss minimization (e.g. Group-DRO) are effective in improving worse-group accuracy but require expensive group annotations for all the training samples. In this paper, we focus on the more challenging and realistic setting where group annotations are only available on a small validation set or are not available at all. We propose BAM, a novel two-stage training algorithm: in the first stage, the model is trained using a bias amplification scheme via introducing a learnable auxiliary variable for each training sample; in the second stage, we upweight the samples that the bias-amplified model misclassifies, and then continue training the same model on the reweighted dataset. Empirically, BAM achieves competitive performance compared with existing methods evaluated on spurious correlation benchmarks in computer vision and natural language processing. Moreover, we find a simple stopping criterion based on minimum class accuracy difference that can remove the need for group annotations, with little or no loss in worst-group accuracy. We perform extensive analyses and ablations to verify the effectiveness and robustness of our algorithm in varying class and group imbalance ratios.

Interpretable Sparsification of Brain Graphs: Better Practices and Effective Designs for Graph Neural Networks

Brain graphs, which model the structural and functional relationships between brain regions, are crucial in neuroscientific and clinical applications involving graph classification. However, dense brain graphs pose computational challenges including high runtime and memory usage and limited interpretability. In this paper, we investigate effective designs in Graph Neural Networks (GNNs) to sparsify brain graphs by eliminating noisy edges. While prior works remove noisy edges based on explainability or task-irrelevant properties, their effectiveness in enhancing performance with sparsified graphs is not guaranteed. Moreover, existing approaches often overlook collective edge removal across multiple graphs. To address these issues, we introduce an iterative framework to analyze different sparsification models. Our findings are as follows: (i) methods prioritizing interpretability may not be suitable for graph sparsification as they can degrade GNNs' performance in graph classification tasks; (ii) simultaneously learning edge selection with GNN training is more beneficial than post-training; (iii) a shared edge selection across graphs outperforms separate selection for each graph; and (iv) task-relevant gradient information aids in edge selection. Based on these insights, we propose a new model, Interpretable Graph Sparsification (IGS), which enhances graph classification performance by up to 5.1% with 55.0% fewer edges. The retained edges identified by IGS provide neuroscientific interpretations and are supported by well-established literature.

Size Generalizability of Graph Neural Networks on Biological Data: Insights and Practices from the Spectral Perspective

We investigate the question of whether the knowledge learned by graph neural networks (GNNs) from small graphs is generalizable to large graphs in the same domain. Prior works suggest that the distribution shift, particularly in the degree distribution, between graphs of different sizes can lead to performance degradation in the graph classification task. However, this may not be the case for biological datasets where the degrees are bounded and the distribution shift of degrees is small. Even with little degree distribution shift, our observations show that GNNs' performance on larger graphs from the same datasets still degrades, suggesting other causes. In fact, there has been a lack of exploration in real datasets to understand the types and properties of distribution shifts caused by various graph sizes. Furthermore, previous analyses of size generalizability mostly focus on the spatial domain. To fill these gaps, we take the spectral perspective and study the size generalizability of GNNs on biological data. We identify a distribution shift between small and large graphs in the eigenvalues of the normalized Laplacian/adjacency matrix, indicating a difference in the global node connectivity, which is found to be correlated with the node closeness centrality. We further find that despite of the variations in global connectivity, graphs of different sizes share similar local connectivity, which can be utilized to improve the size generalizability of GNNs. Based on our spectral insights and empirical observations, we propose a model-agnostic strategy, SIA, which uses size-irrelevant local structural features, i.e., the local closeness centrality of a node, to guide the learning process. Our empirical results demonstrate that our strategy improves the graph classification performance of various GNNs on small and large graphs when training with only small graphs.