Towards Multi-Label Graph Foundation Models: from Single-Vector Representation Learning to Multi-Semantic Basis Learning
Authors: Dongxiao He, Jiayu Zhang, Jitao Zhao, Yi Wang, Di Jin
Organizations: Tianjin University Tianjin, China
Abstract
Multi-label node classification is an important yet challenging task in graph learning, where nodes exhibit multiple semantics simultaneously. Existing methods for multi-label node classification can effectively model multiple labels, while only considering in-domain scenarios where the model needs to be trained and tested within the same graph domain, resulting in limited cross-domain generalization. Recently, Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable graph representations across diverse graph domains and downstream tasks. However, existing GFMs are built upon single-label assumption, where all nodes are arbitrarily regarded as containing only one class of semantic and embedded into a single representation. For multi-label nodes, such a representation essentially approximates multiple semantics with a single point in the representation space, inevitably leading to semantic entanglement and making simultaneous discrimination of multiple labels difficult. To address these limitations, we propose a Multi-Semantic Basis Graph Foundation Model (MSB-GFM), a framework for cross-domain multi-label node classification. Specifically, we introduce a multi-semantic basis representation learning paradigm that models each multi-label node as an adaptive composition of semantic bases, thereby enabling flexible representational capacity for modeling multiple semantics. Furthermore, we develop a semantic-structure dual-channel architecture with domain adversarial training for effective cross-domain knowledge transfer. Extensive experiments demonstrate the effectiveness of our model.
Graph foundation models (GFMs) seek transferable representations across graph domains but are limited by structural heterogeneity and incompatible node feature spaces. We propose Structure-Centric Graph Foundation Models (SCGFM), which treat graph topology as the primary source of transferable knowledge. Modeling graphs as metric measure spaces, SCGFM introduces learnable geometric bases that define a shared structural coordinate system. Graphs are aligned to these bases via Gromov-Wasserstein distances, yielding structure-aligned latent representations that accommodate heterogeneous graph topologies. To address feature incompatibility, SCGFM employs a structure-aware feature re-encoding mechanism that unifies node representations without assuming a fixed feature dimensionality or requiring dataset-specific preprocessing. Experiments on graph- and node-level tasks demonstrate strong in-domain and cross-domain generalization, outperforming existing GFM approaches.
Graph foundation models (GFMs) have emerged as a promising paradigm for transferring knowledge across graph domains and tasks. Real-world graphs associate nodes with text, images, and other modalities, making multimodal graphs essential for representing complex entities and relations. Moreover, collecting labels and adapting models for every new graph domain is costly and often infeasible, motivating zero-shot transfer. Unfortunately, zero-shot transfer on multimodal graphs remains underexplored. Existing GNN-based graph foundation models typically require downstream adaptation, whereas LLM-based graph methods mainly address unimodal graphs or tasks within a single domain. This setting presents two key challenges. First, models must generalize knowledge from individual modalities while capturing transferable cross-modal relations. Second, without target-domain fine-tuning, node representations remain entangled with domain-specific structures and modality-specific characteristics, obscuring shared concepts in unseen domains. To address these challenges, we propose CHARM, a multimodal graph foundation model with hierarchical context modeling for zero-shot transfer. CHARM replaces isolated raw nodes with hierarchical graph contexts that capture multimodal semantics and cross-modal relations. These contexts map domain-specific node patterns to shared high-level concepts, reducing reliance on target-domain supervision or adaptation. A modality-aware graph context encoder integrates multimodal information with graph structure and converts the resulting representations into graph tokens for a large language model . Experiments show consistent improvements on zero-shot multimodal graph tasks.
Dynamic graphs are ubiquitous in real-world systems, and building generalizable dynamic Graph Foundation Models has become a frontier in graph learning. However, dynamic graphs from different domains pose fundamental challenges to unified modeling, as their semantic and temporal patterns are inherently inconsistent, making the multi-domain pre-training difficult. Consequently, the widely used "pretrain-then-finetune" paradigm often suffers from severe negative knowledge transfer. To the best of our knowledge, there exists no multi-domain dynamic GFM. In this work, we propose DyGFM, a Dynamic Graph Foundation Model over multiple domains based on decoupled and divergence-conditioned prompting. To disentangle transferable semantics from the domain-specific dynamics, we introduce a dual-branch pre-training strategy with semantic-temporal decoupling. To alleviate negative transfer during domain adaptation, we further develop a cross-domain routing mechanism with divergence-aware expert selection. To enable efficient downstream fine-tuning, we design a divergence-conditioned prompt generator that injects lightweight, learnable graph prompts tailored to semantic and temporal traits. Extensive experiments on continuous dynamic graph benchmarks demonstrate that DyGFM consistently outperforms 12 state-of-the-art baselines on both node classification and link prediction tasks, achieving superior effectiveness and efficiency.