What Makes Graph Unified? Principles and Generative Sliding-Window Transformer for Graph Foundation Models

2026-07-30

AI Summary

This work addresses the challenge in graph foundation models where heterogeneous node features across domains are difficult to unify, and naive dimension alignment often discards critical semantic information, limiting transferability. To overcome this, the authors propose SliGFM, a novel framework that establishes four guiding principles for graph feature unification: formal consistency, cross-domain transferability, information preservation, and backbone compatibility. Guided by these principles, SliGFM introduces a topology-aware sliding-window Transformer architecture that transforms heterogeneous features into ordered, fixed-dimensional semantic tokens through topological smoothness ranking, a shared sliding-window encoder, smoothness-aware attention mechanisms, and a generative reconstruction objective. Experiments demonstrate that SliGFM effectively captures transferable relational patterns while preserving original feature semantics, significantly enhancing the generalization performance of graph foundation models across diverse downstream tasks.

Abstract

Graph Foundation Models (GFMs) have recently emerged as a promising paradigm for general-purpose graph learning, aiming to learn reusable knowledge that generalizes across diverse graph domains and downstream tasks, reducing the need for specific model development. Achieving this goal requires reconciling the substantial heterogeneity in node features, graph structures, and semantic information across domains. Among them, heterogeneous node features constitute a fundamental input-level barrier, as their dimensionality and semantics vary substantially across datasets. Existing studies typically project or map heterogeneous node features into a fixed-dimensional space, often implicitly equating dimensional uniformity with effective feature unification. Yet dimensional consistency alone does not ensure that the unified features preserve informative semantics and capture transferable patterns that can support cross-domain knowledge transfer. To bridge this conceptual gap, we distill four desiderata for cross-domain graph feature unification: formal uniformity, cross-domain transferability, information preservation, and backbone compatibility. Guided by these principles, we propose SliGFM, a graph foundation model built upon topology-aware sliding-window feature encoding and generative reconstruction. SliGFM orders feature dimensions by topological smoothness and scans the reordered features with a shared sliding-window feature encoder, transforming heterogeneous features into a common space of ordered fixed-dimensional feature tokens. This formulation enables a smoothness-aware transformer to capture transferable relational patterns among feature tokens within each node, while the generative reconstruction objective encourages preservation of the original feature information.

Problem

• Graph Foundation Models
• feature unification
• heterogeneous node features
• cross-domain transferability
• information preservation

Innovation

• Graph Foundation Models
• Feature Unification
• Sliding-Window Transformer
• Topological Smoothness
• Generative Reconstruction