Advancing Graph Foundation Models: A Data-Centric Perspective

Recently, Graph Foundation Models (GFMs) have emerged as a significant research topic in graph machine learning. Compared with traditional graph neural networks, GFMs demonstrate impressive zero-shot generalization across different domains and tasks through large-scale pre-training on extensive and diverse graph data. Despite the initial success of pre-training, existing GFMs face challenges such as extreme time consumption and the presence of redundancy and noise in pre-training data. To alleviate these issues, we present the first exploration of data-centric GFM, which aims to optimize pre-training data (i.e., a set of subgraphs) to establish a more efficient GFM while maintaining robust performance across various downstream tasks. We propose DCGFM, a plug-and-play approach for Data-Centric GFM that incorporates the idea of data pruning to remove redundant and less informative subgraphs from the pre-training data, thereby improving both efficiency and effectiveness. Specifically, DCGFM consists of two components: (1) a model-agnostic hard pruning module that filters out subgraphs with lower informativity scores by considering both the semantics and structures of subgraphs; and (2) a model-aware soft pruning module that dynamically prunes subgraphs with lower loss values in each pre-training epoch with a gradient rescaling strategy. Extensive experiments on representative GFM backbones demonstrate DCGFM's efficiency and effectiveness. Remarkably, DCGFM achieves even better performance using only 30% of the pre-training data. Codes and data are available at https://github.com/Yuhan1i/DCGFM.