João Mattos

João Mattos, Arlei Silva

We propose Mochi, a Graph Foundation Model that addresses task unification and training efficiency by adopting a meta-learning based training framework. Prior models pre-train with reconstruction-based objectives such as link prediction, and assume that the resulting representations can be aligned with downstream tasks through a separate unification step such as class prototypes. We demonstrate through synthetic and real-world experiments that this procedure, while simple and intuitive, has limitations that directly affect downstream task performance. To address these limitations, Mochi pre-trains on few-shot episodes that mirror the downstream evaluation protocol, aligning the training objective with inference rather than relying on a post-hoc unification step. We show that Mochi, along with its more powerful variant Mochi++, achieves competitive or superior performance compared to existing Graph Foundation Models across 25 real-world graph datasets spanning node classification, link prediction, and graph classification, while requiring 8$\sim$27 times less training time than the strongest baseline.

João Mattos, Debolina Halder Lina, Arlei Silva

Link prediction is a fundamental task in graph machine learning with applications, ranging from social recommendation to knowledge graph completion. Fairness in this setting is critical, as biased predictions can exacerbate societal inequalities. Prior work adopts a dyadic definition of fairness, enforcing fairness through demographic parity between intra-group and inter-group link predictions. However, we show that this dyadic framing can obscure underlying disparities across subgroups, allowing systemic biases to go undetected. Moreover, we argue that demographic parity does not meet desired properties for fairness assessment in ranking-based tasks such as link prediction. We formalize the limitations of existing fairness evaluations and propose a framework that enables a more expressive assessment. Additionally, we propose a lightweight post-processing method combined with decoupled link predictors that effectively mitigates bias and achieves state-of-the-art fairness-utility trade-offs.

João Mattos, Zexi Huang, Mert Kosan et al.

Link prediction is a fundamental problem in graph data. In its most realistic setting, the problem consists of predicting missing or future links between random pairs of nodes from the set of disconnected pairs. Graph Neural Networks (GNNs) have become the predominant framework for link prediction. GNN-based methods treat link prediction as a binary classification problem and handle the extreme class imbalance -- real graphs are very sparse -- by sampling (uniformly at random) a balanced number of disconnected pairs not only for training but also for evaluation. However, we show that the reported performance of GNNs for link prediction in the balanced setting does not translate to the more realistic imbalanced setting and that simpler topology-based approaches are often better at handling sparsity. These findings motivate Gelato, a similarity-based link-prediction method that applies (1) graph learning based on node attributes to enhance a topological heuristic, (2) a ranking loss for addressing class imbalance, and (3) a negative sampling scheme that efficiently selects hard training pairs via graph partitioning. Experiments show that Gelato outperforms existing GNN-based alternatives.