On the Safety of Graph Representation Learning

Graph representation learning (GRL) has evolved from topology-only graph embeddings to task-specific supervised GNNs, and more recently to reusable representations and graph foundation models (GFMs). However, existing evaluations mainly measure clean transfer, adaptation, and task coverage. It remains unclear whether GRL methods stay reliable when deployment stresses affect graph signals, graph contexts, label support, structural groups, or predictive evidence. We introduce GRL-Safety, a multi-axis safety evaluation benchmark for GRL. GRL-Safety evaluates twelve representative methods, spanning topology-only embedding methods, supervised GNNs, self-supervised graph models, and GFMs, on twenty-five graph datasets under standardized evaluation conditions while preserving method-native adaptation. The evaluation covers five safety axes: corruption robustness, OOD generalization, class imbalance, fairness, and interpretation, with per-axis and sub-condition reporting rather than a single aggregate score. Our analysis yields three cross-axis insights that can inspire future research. First, safety behavior is shaped by the interaction between representation design and the stressed graph factor, rather than by method family alone. Second, foundation-era methods show axis-specific strengths rather than broad safety dominance. Third, several deployment regimes remain difficult even for the best evaluated method, revealing capability gaps that require new robustness, adaptation, or training objectives beyond model selection. The benchmark, evaluation protocols, and code are available at: https://github.com/GXG-CS/GRL-Safety.

Generalizing GNNs with Tokenized Mixture of Experts

Deployed graph neural networks (GNNs) are frozen at deployment yet must fit clean data, generalize under distribution shifts, and remain stable to perturbations. We show that static inference induces a fundamental tradeoff: improving stability requires reducing reliance on shift-sensitive features, leaving an irreducible worst-case generalization floor. Instance-conditional routing can break this ceiling, but is fragile because shifts can mislead routing and perturbations can make routing fluctuate. We capture these effects via two decompositions separating coverage vs selection, and base sensitivity vs fluctuation amplification. Based on these insights, we propose STEM-GNN, a pretrain-then-finetune framework with a mixture-of-experts encoder for diverse computation paths, a vector-quantized token interface to stabilize encoder-to-head signals, and a Lipschitz-regularized head to bound output amplification. Across nine node, link, and graph benchmarks, STEM-GNN achieves a stronger three-way balance, improving robustness to degree/homophily shifts and to feature/edge corruptions while remaining competitive on clean graphs.

Molecular Representations in Implicit Functional Space via Hyper-Networks

Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipeline: molecules are encoded as sequences, graphs, or point clouds, mapped to fixed-dimensional embeddings, and then used for task-specific prediction. This paradigm treats molecules as discrete objects, despite their intrinsically continuous and field-like physical nature. We argue that molecular learning can instead be formulated as learning in function space. Specifically, we model each molecule as a continuous function over three-dimensional (3D) space and treat this molecular field as the primary object of representation. From this perspective, conventional molecular representations arise as particular sampling schemes of an underlying continuous object. We instantiate this formulation with MolField, a hyper-network-based framework that learns distributions over molecular fields. To ensure physical consistency, these functions are defined over canonicalized coordinates, yielding invariance to global SE(3) transformations. To enable learning directly over functions, we introduce a structured weight tokenization and train a sequence-based hyper-network to model a shared prior over molecular fields. We evaluate MolField on molecular dynamics and property prediction. Our results show that treating molecules as continuous functions fundamentally changes how molecular representations generalize across tasks and yields downstream behavior that is stable to how molecules are discretized or queried.