MUG: Meta-path-aware Universal Heterogeneous Graph Pre-Training

In recent years, the rapid development of foundation models and graph pre-training technologies has spurred increasing interest in constructing a universal pre-trained graph model or Graph Foundation Model (GFM). However, a significant challenge is that existing models are unable to address feature heterogeneity in graph data without textual information, which hinders the transferability of graph models across different datasets. To bridge this gap, we propose the concept of learnable graph patches, which we regard as the smallest semantic units of any graph data. We decompose the graph into learnable graph patches by unfolding the node features and constructing corresponding patch structures separately. We then design a framework that mines transferable information from graph data across domains. Specifically, after extracting graph patches, we propose a patch encoder to extract knowledge from each unit and a patch aggregator to learn how the units are combined into a whole. Due to its domain-agnostic nature, the model can be applied to downstream data across different domains. Furthermore, we analyze the connection between our method and existing graph models, as well as the transferability of the node embeddings it generates. Empirically, our method not only achieves the capability to use multi-domain graphs for pre-training, but also shows enhanced performance across various downstream datasets and tasks. Moreover, we observe consistent improvement in downstream performance as the volume of pre-training data increases.

Recent advances in generic large models, such as GPT and DeepSeek, have motivated the introduction of universality to graph pre-training, aiming to learn rich and generalizable knowledge across diverse domains using graph representations to improve performance in various downstream applications. However, most existing methods face challenges in learning effective knowledge from generic graphs, primarily due to simplistic data alignment and limited training guidance. The issue of simplistic data alignment arises from the use of a straightforward unification for highly diverse graph data, which fails to align semantics and misleads pre-training models. The problem with limited training guidance lies in the arbitrary application of in-domain pre-training paradigms to cross-domain scenarios. While it is effective in enhancing discriminative representation in one data space, it struggles to capture effective knowledge from many graphs. To address these challenges, we propose a novel Latent sEmantic Distribution Alignment (LEDA) model for universal graph pre-training. Specifically, we first introduce a dimension projection unit to adaptively align diverse domain features into a shared semantic space with minimal information loss. Furthermore, we design a variational semantic inference module to obtain the shared latent distribution. The distribution is then adopted to guide the domain projection, aligning it with shared semantics across domains and ensuring cross-domain semantic learning. LEDA exhibits strong performance across a broad range of graphs and downstream tasks. Remarkably, in few-shot cross-domain settings, it significantly outperforms in-domain baselines and advanced universal pre-training models.

While foundation models have revolutionized natural language processing and computer vision by leveraging universal vocabularies, Graph Machine Learning (GML) remains fractured due to the absence of a unified feature and structural representation across diverse domains. Existing works claiming to be Graph Foundation Models (GFMs) are typically restricted to node-level predictions or require fixed feature dimensions, failing to provide a truly task-agnostic backbone for the full spectrum of graph learning applications. In this paper, we introduce the Universal Classifier (UC), which supports arbitrary feature and class cardinalities, unifying node-, edge-, and graph-level objectives under a single similarity-based classification objective. The UC reformulates all node-, edge-, and graph-level prediction tasks as maximizing similarity in the latent space: by lifting heterogeneous features and labels into 3D latent tensors, the model learns transferable features independent of specific input schemas. This architecture allows a single pre-trained model to generalize to node classification, node regression, and link prediction across unseen graphs with varying feature semantics. Experiments show strong zero-shot transfer performance across node-, link-, and graph-level tasks.