Modality-free Graph In-context Alignment

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.

Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable representations across diverse graph domains. Recent advancements in GFMs have been largely dominated by two paradigms: Graph Neural Network and Large Language Model (LLM) based methods. However, these methods often face a fundamental dilemma between training with limited data and a heavy reliance on textual attributes. Tabular foundation models (TFMs) offer a potential alternative, as node features and representations can be naturally organized in a tabular form. However, how to enable TFMs to effectively capture structural information of graphs remains largely unexplored. The key challenge is to learn a graph-to-table alignment mechanism that enables graph structural understanding for TFMs. To address this, we propose GTAlign, a surprisingly simple yet effective Graph-to-Table Alignment framework for text-free Graph Foundation Model. Specifically, we first pretrain a graph encoder that maps diverse graphs into a unified latent space to capture domain-agnostic graph representations. To further bridge the gap between graph topology and the tabular representation space, we propose community-guided continual pre-training, where pseudo-labels derived from graph community are used to construct few-shot prediction episodes. Lastly, we adapt the graph encoder for an unseen target domain and perform in-context inference. Extensive experiments on five benchmark datasets demonstrate that GTAlign significantly outperforms state-of-the-art baselines on both node and graph classification, offering a simple, effective, and text-free GFM model. Code will be released upon acceptance.

Heterogeneous graph representation learning (HGRL) is essential for modeling complex systems with diverse node and edge types. However, most existing methods are limited to closed-world settings with shared schemas and feature spaces, hindering cross-domain generalization. While recent graph foundation models improve transferability, they often target homogeneous graphs, rely on domain-specific schemas, or require rich textual attributes. Consequently, text-free and few-shot cross-domain HGRL remains underexplored. To address this, we propose CrossHGL, a foundation framework that preserves and transfers multi-relational structural semantics without external textual supervision. Specifically, a semantic-preserving transformation strategy homogenizes heterogeneous graphs while encoding interaction semantics into edge features. Based on this, a prompt-aware multi-domain pre-training framework with a Tri-Prompt mechanism captures transferable knowledge across feature, edge, and structure perspectives via self-supervised contrastive learning. For target-domain adaptation, we develop a parameter-efficient fine-tuning strategy that freezes the pre-trained backbone and performs few-shot classification via prompt composition and prototypical learning. Experiments on node-level and graph-level tasks show that CrossHGL consistently outperforms state-of-the-art baselines, yielding average relative improvements of 25.1% and 7.6% in Micro-F1 for node and graph classification, respectively, while remaining competitive in challenging feature-degenerated settings.