Graph Foundation Models

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9 papers in the last four weeks, up 200% on the four weeks before. 0.1% of all new papers.

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Latest papers 68

Oct 8, 2026cs.LG

Is Real-World Training Data Necessary for Generalist Graph Anomaly Detection?

Generalist graph anomaly detection (GAD) aims to build a foundation model that detects anomalies on arbitrary unseen graphs without retraining or fine-tuning. Sufficient data are essential for foundation model training, yet generalist GAD still faces a data shortage, as real-world anomalous graphs are scarce and costly to collect and annotate. To fill this gap, we propose AG-FORGE, an Anomalous Graph generation Forge for automatic synthesis of anomalous graphs, exploring the feasibility of synthetic data-driven training for generalist GAD. Empirically, we find that synthetic data can achieve performance comparable to real-world training, but fail to push the performance boundary further due to the limited capacity of existing methods. To further unlock model capacity as training data scale up, we develop TS-GGAD, a Topology-Semantic coordinated Generalist GAD that captures complementary topological and semantic anomaly evidence, together with a curriculum learning strategy tailored to large-scale synthetic training. Extensive experiments on 14 real-world datasets demonstrate that TS-GGAD, trained on data generated by AG-FORGE, significantly outperforms state-of-the-art methods.

Yujing Liu, Yixin Liu, Yue Tan +4

School of Information and Communication Technology, Griffith University, Australia · School of Computer Science and Technology, Tongji University, China

Anomaly Detection Graph Foundation Models Synthetic Data Pretraining Synthetic Anomaly Generation

Oct 6, 2026cs.LG

Towards One-for-All Foundation Model for Attributed Graph Clustering

Attributed graph clustering aims to discover node groups by jointly exploiting node attributes and graph topology, yet its unsupervised nature makes model selection and adaptation inherently difficult. Existing methods typically train and tune a separate model for each input graph, leading to costly and fragile pipelines that often fail to transfer across graphs with different feature spaces, structural patterns, and attribute-structure correlations. In this paper, we study a one-for-all alternative: can a single model be trained once and directly applied to diverse attributed graphs without graph-specific training, fine-tuning, or hyperparameter search? We propose OFAG, a foundation model for attributed graph clustering. Building upon Prior-data Fitted Networks, OFAG learns a reusable clustering inference strategy from synthetic attributed graphs generated under broad priors over latent clusters, node attributes, and graph structures. To handle incompatible feature spaces across graphs, OFAG adopts a dimension-agnostic signal-wise graph encoder that treats each feature channel as a graph signal and models its response to shared graph filters. The model is trained with a hyperspherical clustering objective, producing clustering-friendly node representations in a single forward pass at inference time. On ten datasets, one frozen OFAG model achieves the best mean performance and average rank across NMI, ACC, ARI, and F1, while completing all ten datasets in 12.43 minutes total---over 6* faster than the second-fastest baseline and nearly 28* faster than the second-best on clustering quality. Our code and pretrained checkpoint are available at https://github.com/Cloudy1225/OFAG, allowing practitioners to directly apply OFAG to their own attributed graph datasets without additional training or tuning.

Yunhui Liu, Xudong Jin, Kang Zhang +5

State Key Laboratory for Novel Software Technology Nanjing University Nanjing, China

Graph Representation Learning Graph Foundation Models Graph Clustering

Oct 5, 2026cs.LG

To Learn is to Wander: Learning Across Graphs and Tasks with Random Walks

Graph foundation models aim to transfer across graphs, feature spaces, relational schemas, and prediction tasks, yet existing approaches typically generalize only within particular graph modalities or tasks. We propose Wander, a graph foundation model designed to operate across these settings within a single pretrained checkpoint. Following the prior-predictive perspective, we formulate graph learning as completion of a partially observed graph. We realize this task-general view through a common interface based on random walks, allowing the same model to operate across homogeneous and multi-relational graphs with varying features, labels, and relational schemas. Wander can increase its structural context at inference time without changing its learned parameters and, under suitable assumptions, universally approximates the corresponding Bayes-optimal predictor on bounded connected graphs. Empirically, a single pretrained checkpoint achieves state-of-the-art or highly competitive results across node classification, homogeneous link prediction, and knowledge-graph link prediction. Moreover, joint pretraining across graph modalities and tasks preserves performance in specialized settings while enabling positive transfer and the composition of separately learned capabilities at inference time.

Louis Tichelman, Xingyue Huang, Jinwoo Kim +1

TU Wien · AITHYRA · University of Oxford +1

Multi-Task Learning Transfer Learning Graph Foundation Models KG Completion

Sep 30, 2026cs.LG

NodeGround: A Node Classification Benchmark in the Graph Foundation Model Era

Can a pretrained graph model replace training and tuning a separate predictor for each dataset? Answering this requires evaluating prediction quality alongside computational cost. We present NodeGround, a node classification benchmark that puts graph foundation models (GFMs) and dataset-specific supervised learning under a common evaluation framework. The benchmark spans 51 datasets and evaluates six GFMs alongside 15 supervised methods under two label-availability regimes. Shared data partitions, validation-only model selection, controlled hyperparameter searches, and multiple predictive metrics make comparisons systematic, while workflow measurements account for adaptation, training, tuning, and inference. The results favor carefully tuned graph neural networks overall. GraphPFN reaches third place by Elo when more labels are available, yet its relative strengths vary substantially with dataset properties. Efficiency comparisons further qualify the benefits of pretrained reuse: GVT and GraphPFN appear on the Pareto frontiers when supervised methods are represented by their default and fully tuned configurations. Adding intermediate tuning budgets removes this advantage for GVT and leaves GraphPFN extending the estimated frontier in the label-rich setting alone. Thus, reusing pretrained parameters does not yet provide a broadly reliable route to either stronger predictions or cheaper workflows. We release the evaluation pipeline, run-level records, and an open leaderboard at https://github.com/nums-ai/nodeground.

Jinmo Lee, Dooho Lee, Minho Jeong +1

Nums AI

Graph Foundation Models Node Classification

Sep 29, 2026cs.AI

Support-Set Target Leakage in Relational Foundation Models during In-Context Learning: Model Dependence and Evaluation Reliability

Relational in-context learning (ICL) uses labeled support examples and their linked relational context to predict labels for new queries. This creates a failure mode when target-derived features are present in the support context but unavailable for the query. We study this setting as support-set target leakage. We construct 20 controlled target-derived features that vary in signal fidelity, representation, semantic transparency, coverage, and zero-, one-, and two-hop relational placement, and evaluate them across 13 RelBench tasks and five relational ICL configurations that vary the ICL head, message-passing depth, pretraining cohort, or relational encoder architecture. We evaluate matched 0-hop, 1-hop, and 2-hop leakage settings, together with a Full leakage condition containing all 20 leaker columns. Within the tested configurations, target-table (0-hop) and Full leakage produce the largest aggregate deviations from clean evaluation, while higher-hop effects are often weaker, consistent with differences in effective exposure associated with temporal reachability, sampling, and aggregation fidelity. Leakage effects are strongly task- and model-dependent and can reverse relative conclusions between model variants even when aggregate changes are small. For leaker detection, we compare an Integrated Gradients (IG)-based screening method with mutual information (MI) and leave-one-column-out (LOCO) on a common Baseline subset. Ranking quality is strongest in the high-impact 0-hop and Full leakage conditions, but detector-based removal does not consistently restore the clean evaluation. A four-task rel-salt case study further shows the same evaluation concern with native-schema leakage candidates from the original relational schema. These results identify the support/query information boundary as an important component of reliable relational ICL evaluation.

Roshan Reddy Upendra, Alexandre Dorais, Joe Meyer +6

SAP Palo Alto, CA, USA · SAP Montreal, Canada · SAP Seattle, WA, USA

Relational Foundation Models Data Leakage In-Context Learning Graph Foundation Models Relational Deep Learning

Sep 27, 2026cs.LG

ZeroGAR: Benchmarking the Adversarial Robustness of Zero-Shot Graph Models

Zero-shot graph models (ZGMs), which learn transferable knowledge from source graphs and directly apply to unseen target graphs without any adaptation, have achieved promising performance and attracted considerable attention. Despite their proliferation, existing ZGMs are predominantly evaluated on clean graphs, while existing graph robustness benchmarks mainly focus on supervised settings, leaving a fundamental question largely unexplored: How robust are ZGMs when their unseen target graphs are exposed to adversarial manipulation? In this paper, we answer this question by proposing ZeroGAR, the first systematic benchmark for evaluating the adversarial robustness of ZGMs. ZeroGAR evaluates 13 representative ZGMs from 3 different paradigms on 8 graph datasets across 4 domains, covering both in-domain and cross-domain transfer under structural, textual, and node injection attacks with multiple perturbation budgets. It further investigates whether existing graph defenses remain effective in the zero-shot setting. Extensive experiments reveal that strong clean zero-shot performance does not guarantee adversarial robustness, with three key findings: (1) Vulnerability patterns are related to model prediction mechanisms: GNN-based methods are particularly vulnerable to structural and node injection attacks, whereas LLM-based methods are more vulnerable to textual attacks; (2) Stronger LLM backbones introduce a structure-text robustness trade-off; (3) Existing graph defense methods do not consistently improve zero-shot robustness and may compromise clean performance. We hope that ZeroGAR will facilitate rapid, equitable evaluation and inspire further innovative research in ZGM security.

Zhongjian Zhang, Xiao Wang, Busheng Zhang +5

Beijing University of Posts and Telecommunications · Beihang University · Tsinghua University +2

Graph Representation Learning Adversarial Attacks Adversarial Robustness Graph Foundation Models LLMs for Graph Learning

Sep 24, 2026cs.LG

ICE: Task-Aligned Clifford Latent Fields for Multimodal Graph Foundation Models

Multimodal attributed graphs connect entities, visual content, language, and observed relations. Learning one foundation across such graphs requires more than compressing each node into a fused Euclidean vector. The representation must preserve entity semantics, construct interaction state from graph neighborhoods, and expose that state to prediction units with different geometry. Our empirical study shows why these requirements are inseparable. Higher-grade channels recover pair relations across the foundation graphs, specialized queries reveal information hidden by a generic readout, and rigid blade isolation removes cross-grade capacity. We therefore introduce ICE (Interaction-aware Clifford Encoder), a multimodal graph foundation model built on a node-indexed Clifford latent field. Topology, text, and images enter explicit Cl(3) addresses. Edge-aware geometric products transform these directions into scalar, bivector, and trivector relations over observed neighborhoods. A protected Grade-1 route preserves entity semantics, while the full grade and depth bank remains available to fresh node and link heads. We establish exact cross-grade reachability, node-permutation equivariance, and a bound on the task residual around the semantic score. Experiments span one shared foundation over eleven graphs, six node-classification datasets, three link-prediction datasets, and matched few-shot tasks. ICE ranks first in all 30 reported supervised and few-shot comparisons. Core removals reduce every task summary, and mechanism controls connect the gains to higher-order transport, retained multidepth structure, semantic protection, and direct field access.

Xunkai Li, Xu Wang, Yinlin Zhu +4

Department of Computer Science, Beijing Institute of Technology, Beijing, China · School of Airspace Science and Engineering, Shandong University, WeiHai, China · School of Computer Science and Engineering, Sun Yat-sen University, GuangZhou, China

Graph Foundation Models Multimodal Graph Learning Node Classification

Sep 22, 2026cs.LG

Signed Graph Pre-Training and Prompt Learning

Signed graphs arise in trust--distrust networks, financial correlation systems, biological interaction graphs, and many other domains in which edges can be positive or negative and may also be directed. While signed graph neural networks have improved task-specific learning, graph transfer learning on signed graphs remains underdeveloped. In this paper, we introduce TopoSIGN, a pioneer topology-guided graph pre-training and prompt learning framework for signed graphs. TopoSIGN combines a structural encoder built on the magnetic signed Laplacian with a novel persistent-homology branch that summarizes signed topology through Dowker-complex persistence images. The fused embeddings are then transferred to a prompt learning function. Experimental results on synthetic and real-world datasets demonstrate the efficacy of TopoSIGN in extracting useful structural information in signed graphs, as well as the adaptability and flexibility of the proposed general framework.

Zihan Mei, Rong Pan, Yuzhou Chen +1

Arizona State University · University of California, Riverside

Prompt Learning Graph Representation Learning Transfer Learning Graph Foundation Models Topological Representation Learning

Sep 17, 2026cs.LG

SCGFM-ART: Amortized Relational Transport for Structure-Centric Graph Foundation Models

Graph foundation models (GFMs) aim to learn transferable representations across severely heterogeneous graph domains. However, severe domain shifts in topology, graph scale, and feature semantics impede the construction of a unified, domain-agnostic representation space. To address this, we propose SCGFM-ART, a structure-centric GFM framework that aligns arbitrary graphs onto a shared relational atlas via Amortized Relational Transport (ART). The relational atlas serves as a universal coordinate system defined by a finite set of relational landmarks (bases), while ART directly predicts reusable, end-to-end graph-to-base transport plans, bypassing costly runtime Gromov-Wasserstein optimizations. Under this formulation, SCGFM-ART decomposes a graph into a unified representation: globally via its relational response coordinates relative to the atlas, and locally via its node-to-role structural correspondences. These correspondences project disparate node attributes into a canonical role space, resolving structural and semantic heterogeneity within a singular alignment interface. Rigorously modeling graphs and atlas bases as finite measured relational spaces, we establish coordinate fidelity bounds, prove stability under predicted transport plans, and derive an amortized coverage bound that guarantees our learning objective tightly surrogates ideal relational coverage. Benchmarked across 14 cross-domain graph- and node-level classification tasks, SCGFM-ART achieves state-of-the-art transferability, securing superior average ranks of 2.29 and 1.14, respectively. Topological perturbation analyses demonstrate that node-role transport retains fine-grained structural nuances beyond global coordinates. On real-world benchmarks, the amortized formulation yields 44.2 to 85.1 times faster frozen target-domain inference by avoiding iterative alignment at test time.

Xiaodong He, Xincheng Wang, Zhao Kang

University of Electronic Science and Technology of China, Chengdu, China

Graph Representation Learning Cross-Domain Transfer Learning Graph Foundation Models Optimal Transport

Sep 16, 2026cs.LG

FoundAna: A GNN-assisted Foundation Model for Graph Anomaly Detection

Graph anomaly detection aims to identify graph structures (e.g., nodes, edges, or subgraphs) that deviate significantly from expected patterns, which supports critical applications in fraud detection, spam identification, network intrusion, etc. Despite the growing methods in the field, existing approaches follow a one-model-per-dataset paradigm, limiting their transferability across diverse real-world scenarios due to task heterogeneity, label scarcity, and domain variability. In this work, we introduce FoundAna, a GNN-assisted Foundation Model for Graph Anomaly Detection - the first foundation model framework designated for generalizable, cross-graph anomaly detection by combining GNNs and transformers. FoundAna integrates an anomaly detection-specific GNN component with a standard transformer encoder augmented by four complementary positional encodings, which enable the model to capture both local and global structural information. Specifically, the positional encoding enriched node representations are passed through attribute and adjacency decoders, and the reconstruction errors serve as the anomaly score. Extensive experiments on nine benchmark datasets spanning financial, social, and citation network domains demonstrate that FoundAna consistently outperforms state-of-the-art baselines. The code implementation and Supplementary materials are here: https://github.com/FoundAna331/FoundAna.

Suprim Nakarmi, Chahana Dahal, Yue Zhao +2

Department of Computer Science, University of Nevada Las Vegas, Las Vegas, USA · Department of Computer Science, University of Southern California, Los Angeles, USA

Graph Neural Networks Reconstruction-Based Anomaly Detection Graph Foundation Models Anomaly Detection

Sep 12, 2026cs.LG

Reification as a Transferable Vocabulary: Zero-Shot Link Prediction with Vanilla GNNs

Knowledge graph foundation models such as ULTRA achieve zero-shot link prediction on unseen graphs through dedicated architectures that hard-code a transfer mechanism. In this work we move that mechanism out of the architecture and into the representation, by \emph{reifying} the input graph: every fact becomes a node, connected to its subject, object, and relation type through a fixed vocabulary of six meta-relations, with relation types as anonymous shared nodes rather than model parameters. On this representation, five textbook GNNs (GAT, GINE with sum and with mean+max aggregation, GraphSAGE, R-GCN), each trained on a single knowledge graph of 4,245 triples for 30 minutes on one NVIDIA A100, transfer zero-shot to 40 inductive link-prediction benchmarks. The best of them, an off-the-shelf GAT, matches ULTRA, a dedicated foundation model pretrained on three graphs, across ULTRA's own evaluation suite. The same fixed vocabulary extends to relational databases, a row becoming an entity and a foreign-key column a relation type; a preliminary probe on two unseen databases, with no cell values, schema text or in-context labels, shows a model of this family pretrained on three knowledge graphs ranking foreign-key targets far above random-initialization and degree controls. We release the code, the checkpoints, and the evaluation pipeline for all 40 benchmarks.

Camille Pradel

Matr

Graph Neural Networks Link Prediction Graph Foundation Models Knowledge Graphs KG Completion

Sep 8, 2026cs.LG

Chimaera: A Mixture-of-Graph-Experts Architecture for Cross-Task and Cross-Dataset Graph Learning

Designing foundation models for graphs is challenging due to the irregular structure of graphs and the different sizes and characteristics of embeddings. Chimaera integrates mixture-of-experts with graph foundation models (GFM). It integrates different GFM architectures, such as graph prompts and linear GNN models. Large language models are used to generate embeddings, and experts can be trained and combined following different strategies, GFMs, embeddings, etc. Furthermore, Chimaera extends existing linear GNNs to support link-level and graph-level tasks in addition to node-level tasks. Empirical analyses are performed on same-task and cross-task experiments with node, link, and graph classification tasks using six benchmark text-attributed graph datasets. The experiments demonstrate the effectiveness of Chimaera and its capabilities for transfer across tasks and datasets. Further insights include the need to use both large and small language models to generate embeddings for the experts, a strong cross-task transferability of simple but effective linear GNNs, and using few samples only to provide strong results.

Jonathan Frank, David Richerby, Ansgar Scherp

University of Ulm · University of Essex

Graph Neural Networks Text-Attributed Graph Learning Transfer Learning Graph Foundation Models Mixture-of-Experts Models LLMs for Graph Learning

Aug 31, 2026cs.LG

Context Window Failures in Relational Foundation Models

Recent Relational Deep Learning architectures have been proposed as foundation models for multi-table relational data, yet they impose constrained neighborhood budgets that force row truncation when an entity has many related records. We introduce Animus, a synthetic financial dataset in which predicting customer income requires aggregating up to tens of thousands of transactions. On the raw representation, three recently proposed models (RT, Griffin, RelGT) achieve

R^2 \le 0.18

; a single, routine, temporal pre-aggregation step recovers

R^2

up to

0.65

. This questions whether current relational foundation models are ready for high-cardinality real-world data.

Denis Oliveira Correa, Francisco Galuppo Azevedo

Kunumi Institute, Brazil · Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.

Relational Foundation Models Graph Foundation Models Relational Deep Learning Tabular Regression

Aug 11, 2026cs.LG

ProTAGAD: A Foundation Model for TAG Anomaly Detection with Decoupled Topological and Textual Prototypes

Text-Attributed Graphs (TAGs), endowed with abundant textual content along with topological structures, have emerged as a versatile backbone for real-world anomaly detection spanning large language model security, social network moderation, and cyber threat identification. Unlike conventional Graph Anomaly Detection (GAD), which relies primarily on structural irregularities, TAG anomaly detection must jointly leverage both topological patterns and fine-grained textual semantics to capture nuanced anomalous behaviors. The current GNN-based anomaly detectors adopt holistic message-passing schemes that indiscriminately fuse structural proximity and textual semantics during propagation, leading to deep cross-modality coupling. This entanglement acts as a noise amplifier, obscuring subtle anomalous signals and directly giving rise to the Blurred-Anomaly-Boundary (BAB) issue by rendering normal-anomalous decision boundaries poorly separable. This challenge is further amplified for graph foundation models that require robust cross-domain generalization. To bridge this gap, we introduce a novel foundation model for TAG anomaly detection featuring decoupled topological and textual prototypes. Our framework constructs dual prototype banks to independently model structural normality and semantic consistency, effectively isolating anomaly cues that are otherwise diluted during coupled aggregation. Extensive experiments across 14 diverse benchmark datasets demonstrate that our method consistently achieves state-of-the-art performance in cross-domain settings. Notably, the ablation studies further corroborate the prevalence of the BAB issue in conventional coupled TAG anomaly detectors, and show that our decoupled prototype design effectively mitigates this challenge.

Ziyan Wang, Liwen Wu, Cheng Xie +3

School of Software and AI, Yunnan University, Kunming, China

Prototype Learning Text-Attributed Graph Learning Graph Foundation Models Anomaly Detection

Aug 10, 2026cs.IR

PreGress: Ranking-Native Pre-training and Prompting for Graph Node Ranking

Node ranking is a fundamental problem in graph information retrieval, measuring the relative importance of nodes and supporting a wide range of applications such as influence analysis, recommendation, and graph-based retrieval augmented generation. However, exact computation of graph-based ranking measures is often computationally prohibitive at scale. Existing GNN-based ranking methods provide scalable approximations, but they are typically tailored to individual ranking criteria and require retraining for each downstream task, which limits their transferability and efficiency. Recent graph pre-training approaches aim to enable knowledge transfer across tasks, yet their learning objectives are largely misaligned with node ranking, resulting in suboptimal adaptability to ranking-oriented applications. To address these limitations, we propose PreGress, the first ranking-native pre-training and prompting framework for supporting a wide range of node ranking tasks. PreGress performs multi-task pre-training using our carefully designed objectives, including degree centrality prediction and attribute reconstruction, to jointly capture structural and attribute information. To support heterogeneous ranking criteria, we design lightweight, task-specific prompt modules that adapt a frozen ranking backbone to downstream tasks without full retraining. Experiments on six public graphs and two real-world query-to-item benchmarks---Yelp2018 and MovieLens-100K---together with a controlled five-criterion graph-access study demonstrate strong ranking quality with low task-specific state overhead.

Lujie Ban, Jiasheng shi, Yingli Zhou +5

School of Data Science, The Chinese University of Hong Kong, Shenzhen, China · GTS, Huawei Technologies Co., Ltd., China

Learning to Rank Prompt Tuning Graph Foundation Models

Aug 9, 2026cs.LG

Neural Message Passing on Structural Interaction Graphs for Fully-Inductive Graph Neural Networks

A central obstacle in building graph foundation models is the input heterogeneity in terms of feature space dimensionality, semantics, and structure. Such heterogeneity limits the capability of graph neural networks to generalize to new graphs with unseen feature spaces. We address the transferability challenge with SIGIL, a framework that maps any attributed graph to a unified representation space of fixed dimension. Given a graph, SIGIL lifts it to a structural interaction graph, where nodes are the input feature dimensions and weighted, typed edges encode feature alignment across multiple orders of the graph's connectivity. A relational message-passing network embeds each feature dimension into a shared space, transforming the original node features, of arbitrary dimensionality, into representations transferable to any downstream graph. By construction, SIGIL is equivariant to permutations of nodes, feature dimensions, and labels. Additionally, when the input features are one-hot indicators of discrete relations, SIGIL recovers and strictly generalizes existing foundation models for knowledge graph reasoning. A single SIGIL model, pretrained on one graph, delivers strong fully-inductive link prediction. Also, SIGIL can be used to implement existing knowledge graph foundation models. As such, SIGIL unifies several existing regimes in graph foundation model design under a single framework

Omer Yom-Tov, Avigdor Gal

Faculty of Data and Decision Sciences, Technion - Israel Institute of Technology Haifa, Israel

Graph Neural Networks Graph Representation Learning Graph Foundation Models

Jul 31, 2026cs.AI

Towards Multi-Label Graph Foundation Models: from Single-Vector Representation Learning to Multi-Semantic Basis Learning

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.

Dongxiao He, Jiayu Zhang, Jitao Zhao +2

Tianjin University Tianjin, China

Domain-Adversarial Learning Representation Learning Cross-Domain Transfer Learning Graph Foundation Models Node Classification

Jul 31, 2026cs.LG

Beyond Feature and Structure Alignment: Learning Transferable Propagation Knowledge for Graph Foundation Models

Graph Foundation Models (GFMs) have recently emerged as a promising paradigm for enabling knowledge transfer across diverse domains. Unlike traditional graph learning methods that are typically designed for in-domain settings, GFMs aim to learn transferable knowledge that can generalize to unseen graph domains. However, unlike language or visual data, graphs lack intrinsic and unified representation units, such as tokens in language and patches in vision, making it challenging to identify transferable knowledge units for building graph foundation models. Existing graph foundation models mainly focus on mitigating domain discrepancies through feature alignment and structure alignment, while overlooking the exploration of transferable knowledge units underlying graph data. Moreover, these methods generally rely on fixed propagation mechanisms during message passing, overlooking the heterogeneity in propagation patterns, as different edges may exhibit distinct propagation patterns for different feature dimensions. To address these limitations, we propose a Propagation-aware Graph Foundation Model (ProGFM), which regards the propagation relationships between edges and feature dimensions as transferable knowledge units. Through a propagation relationship prototype bank, ProGFM learns cross-domain transferable propagation knowledge, enabling adaptive information aggregation in unseen graph domains. Extensive experiments across various cross-domain transfer scenarios demonstrate that ProGFM possesses strong cross-domain knowledge transfer capability and exhibits superior generalization performance compared with existing methods.

Yi Wang, Jitao Zhao, Di Jin +1

Tianjin University Tianjin, China

Message Passing Neural Networks Cross-Domain Generalization Cross-Domain Transfer Learning Graph Foundation Models

Jul 30, 2026cs.LG

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

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.

Dongxiao He, Siqi Liu, Jitao Zhao +3

School of Computer Science and Technology Tianjin University Tianjin, China · School of Economics and Management Beijing University of Posts and Telecommunications Beijing, China

Cross-Domain Transfer Learning Graph Foundation Models Graph Transformer

Jul 29, 2026cs.LG

AgentGFM: A Graph Foundation Model with Node-Agent Information-Flow Control

Graph Foundation Models (GFMs) aim to learn transferable knowledge from multi-domain graphs and adapt to unseen scenarios. As a fundamental source of relational semantics in graphs, the transferability of topological patterns has long been central to GFM research. However, local structural patterns may vary across graphs and even among nodes within the same graph. Despite such structural variation, most existing GFMs rely on manually designed propagation schemes and apply them to new graphs largely unchanged. Such fixed schemes may not suit the diverse structural patterns of different nodes. This raises a key question: can each node autonomously determine how information should be propagated through the graph? We refer to this capability as information-flow control. Inspired by recent advances in agent technology, we formulate this problem as agent-based decision making and treat each node as an agent. Accordingly, we propose AgentGFM, in which all node agents follow a shared end-to-end trainable policy rather than using independent models. For adaptive information-flow control, each node interacts with the graph through a predict-act-observe-correct process. During the act stage, the node makes three decisions: source reception, signal-channel selection and gain-aware node-wise halting. The resulting observation is compared with the prediction and their discrepancy is used to correct the node state and guide subsequent interactions. Extensive experiments across node-level, graph-level and large-scale transfer scenarios demonstrate the effectiveness of AgentGFM across diverse graph topologies.

Jingbo Cui, Jitao Zhao, Di Jin +1

School of Computer Science and Technology, Tianjin University Tianjin, China

Graph Neural Networks Message Passing Neural Networks Agent-Based Modeling Transfer Learning Graph Foundation Models

Jul 28, 2026cs.AI

CHARM: A Multimodal Graph Foundation Model with Hierarchical Context Modeling for Zero-Shot Transfer

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.

Ankang Yang, Jitao Zhao, Di Jin +2

School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University · Data Science Program, Columbian College of Arts and Sciences, The George Washington University

Transfer Learning Graph Foundation Models Multimodal Graph Learning LLMs for Graph Learning

Jul 27, 2026cs.LG

MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning

Predicting the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small molecules remains a major challenge in drug discovery. Here, we present MEGA-CL, a foundation graph neural network framework for universal molecular ADMET prediction. MEGA-CL integrates self-supervised contrastive learning with a multi-head external attention mechanism and an enhanced message-passing architecture, enabling simultaneous modeling of local chemical substructures and global inter-graph relationships while mitigating over-smoothing effects commonly observed in deep graph networks. Across 13 benchmark datasets and 21 downstream ADMET tasks, MEGA-CL consistently outperforms state-of-the-art baseline models. In particular, the framework demonstrates robust performance on challenging regression tasks, including clearance (CL) and steady-state volume of distribution (VDss), while maintaining strong generalization ability in independent external validation. Clinically relevant predictive accuracy was achieved, with more than 75% of predictions falling within a 3-fold error range. In an external evaluation on 18 novel compounds derived from recently approved FDA drugs, over 50% of human liver microsome clearance (HLMC) predictions were within a 2-fold error range. To further assess its practical applicability, MEGA-CL was prospectively evaluated on three preclinical drug candidates using in vitro hepatic microsomal metabolism assays and CYP450 inhibition assays guided by model predictions. The predicted HLMC values for all candidates were within 2.5-fold of the experimentally measured values, and 73.3% of CYP450 inhibition endpoints (11/15) were correctly classified. These results demonstrate the potential of MEGA-CL as a generalizable framework for accelerating in silico ADMET evaluation and early-stage drug candidate optimization.

Tinghui Jin, Kedu Jin, Ying Li +8

School of Science, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China · 2Sir Run Run Hospital, Nanjing Medical University, Nanjing, China · 3Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China

Graph SSL Graph Foundation Models Molecular Property Prediction

Jul 20, 2026cs.AI

Attacking Graph Foundation Models Through Their Shared Representation

A graph foundation model generalizes across graph domains by mapping every input into one shared representation before any task reasoning. We call this map the alignment layer, the component that separates a graph foundation model from a graph neural network, and we show it is a distinct attack surface that prior work has not studied. We attack it at inference time, with no access to training, on six public models spanning spectral tokenizers, text embedding spaces, and a discrete codebook. A directed representation-space perturbation collapses every model, but at a budget comparable to the representation norm a plain graph network also needs, with one exception: OpenGraph, whose spectral tokenizer collapses at a fifth of that budget, an alignment-specific fragility a plain network does not share and which a same-representation control traces to the tokenizer rather than the decoder. A realizable input-space attack that edits edges, features, or text removes at least half the correct predictions on three of the six models at peak. How much of this fragility an input-access attacker realizes tracks how directly the decoder reads the representation, and not the clean accuracy a task leaves; we measure this carrier gain structurally from the decoder's local Lipschitz sensitivity, and report clean-accuracy headroom as a within-model ordering heuristic that does not survive on realizable attacks.

Pankaj Kumar, Subhankar Mishra

1National Institute of Science Education and Research · 2An OCC of Homi Bhabha National Institute

Adversarial Attacks Graph Foundation Models

Jul 20, 2026cs.LG

A Weisfeiler-Leman Characterization of Global-Attention Graph Transformers for Mixed-Integer Linear Programs

Graph foundation models (GFMs) with global attention are increasingly used to represent mixed-integer linear programs (MILPs), aiming to capture structure beyond the locality of standard graph neural networks. We study their expressive power through graph isomorphism testing, asking which MILP instances they map to identical representations. We prove that a broad class of hierarchical graph transformers combining global linear attention, edge-weighted cross-attention, and bipartite message passing is bounded by the one-dimensional Weisfeiler-Leman (1-WL) test: under any parameter setting, 1-WL-equivalent MILP graphs receive identical graph embeddings. Our compositional proof shows that each architectural component is a symmetric multiset function and thus preserves 1-WL equivalence. We validate this characterization across ten diverse graph encoders, including Graphormer-, GraphGPS-, Set-Transformer-, and Gasse-style models. Across model capacities, graph scales, and pooling operators, every tested encoder maps 1-WL-equivalent non-isomorphic graph pairs to numerically identical embeddings. Consequently, graph invariants that vary within a 1-WL equivalence class cannot be recovered from these representations. We further show that expressiveness beyond 1-WL arises from input encoding rather than attention: random-walk positional encodings separate the constructed pairs, while additional constructions expose the limits of this remedy. These results characterize the expressive power of global-attention GFMs and provide an encoder-agnostic diagnostic for detecting 1-WL-induced representation equivalence.

Md Abrar Jahin, Craig A. Knoblock, Jay Pujara

University of Southern California, Los Angeles, CA 90089, USA · USC Information Sciences Institute, Marina del Rey, CA 90292, USA

Mixed-Integer Linear Programming GNN Expressivity Graph Foundation Models Graph Transformer

Jul 19, 2026cs.LG

Node4All: Learning Node Representation Beyond Datasets

Node representation learning has advanced rapidly, yet most existing methods rely on per-dataset training and hyperparameter tuning. This dataset-specific optimization comes from the difficulty of designing reusable graph models that generalize across diverse graph datasets. In this work, we introduce Node4All, a node representation learner applicable to arbitrary graph datasets without any dataset-specific optimization. Node4All is built on two complementary ideas. At the architectural level, we introduce the Channel Graph Transformer (CGT), which enables a single fixed parameterization to process arbitrary graph datasets. At the learning level, we propose a self-supervised learning based on a series of synthetic graphs. Together, these components enable generalization beyond individual datasets, which is infeasible with existing architectures and learning frameworks. We extensively evaluate Node4All on node classification across 25 benchmarks against 21 baselines, covering both supervised and self-supervised methods. Despite all baselines being trained and optimized for each dataset, a single Node4All, applied uniformly across the datasets, achieves a competitive ranking of 5th among 21 baselines. Moreover, Node4All supports one-shot and in-context learning with an appropriate predictor and outperforms recent graph foundation models (GFMs) in these settings. These results demonstrate that Node4All not only achieves reusability across arbitrary graph datasets, but also remains an effective solution in practice. Code and model checkpoints are available in https://github.com/dooho00/node4all.

Dooho Lee, Jaemin Yoo

KAIST · Daejeon, Republic of Korea · Seoul National University +1

Graph Representation Learning Graph SSL Domain Generalization Graph Foundation Models Graph Transformer

Jul 17, 2026cs.LG

Toward Federated Multimodal Graph Foundation Models: A Topology-Aware Multimodal Alignment Framework

Multimodal-attributed graphs (MAGs), whose nodes carry modalities such as images and text alongside topological structure, now pervade applications including social platforms, e-commerce, and biomedical networks, offering richer semantic signals than single-modality graphs. In practice, such graphs are fragmented across privacy-restricted silos owned by different platforms and institutions, so learning a broadly transferable model over them demands collaborative training that never exposes raw data. This places the task at the intersection of multimodal graph learning and federated learning, yet existing methods cover only one side of it. To address the challenges from these two perspectives, we propose FedGAMMA, casting federated multimodal graph foundation learning as a two-stage semantic-structural alignment problem of federated pre-training and prompt-based fine-tuning. During pre-training, a shared-private semantic enhancer disentangles cross-modal commonality from modality-specific information, aligning it through optimal transport, a topology-aware graph fusion module decouples semantic and structural views via semantic residual graphs and dual positional encodings, and a dual-channel affinity-aware aggregation mechanism estimates client similarity from feature and graph centroids without exposing raw data. During fine-tuning, FedGAMMA adapts the pretrained encoder through lightweight graph-aware prompts, a shared prompt pool with controlled exploration, and channel-wise prompt synchronization. Experiments on twelve multimodal graph datasets show FedGAMMA consistently surpassing a broad range of baselines across downstream tasks, with gains of up to 12.96%. FedGAMMA further outperforms competitive baselines accross multi-domain datasets on multiple tasks with up to 5.71% under few-shot learning scenario.

Xunkai Li, Guohao Fu, Yuming Ai +4

Beijing Institute of Technology, Beijing, 100811, China

Multimodal Federated Learning Cross-Modal Alignment Multimodal Pretraining Federated Graph Learning Prompt Tuning Graph Foundation Models+1

Jul 15, 2026cs.LG

MxGPS: Multiplex Graph Transformers for a Power Grid Foundation Model

Single-task fine-tuning of graph neural networks (GNNs) for power grid problems exhibits a systematic failure mode: models that achieve the lowest in-distribution error degrade the most under topology shift. We term this topology overfitting: the tendency of task-specific gradient signals to encode relational structure particular to the training topologies rather than the underlying physics, causing models to fail on unseen grids despite strong in-distribution performance. To expose and address this failure mode, we introduce MxGPS (Multiplex GPS), a multiplex graph transformer that runs K task-specialised GPS branches over a shared node encoder, jointly trained on Static State Estimation (SSE) and AC Power Flow (PF) via a self-supervised pre-training and multi-task fine-tuning protocol, with a cross-branch attention module evaluated in ablation. The joint SSE+PF objective forces the shared encoder to simultaneously satisfy complementary gradient signals, preventing it from overfitting to topology-specific relational structure. Under a 3-fold sliding-window cross-validation spanning four unseen topologies (14-, 24-, 162-, and 300-bus), MxGPS attains 0% boundary violation rate (BVR) on all four zero-shot Power Flow topologies. Critically, models with substantially lower in-distribution PF error degrade by 190% to 1400% under topology shift, whereas MxGPS degrades by only 39%, an inversion that directly implicates topology overfitting as the failure mechanism rather than insufficient model capacity. With only 1.6M parameters (12x fewer than the GridFM reference baseline), MxGPS demonstrates that multi-task joint training is a principled and parameter-efficient mechanism for topology-agnostic generalisation in power grid foundation models.

Charilaos Papaioannou, Ioannis Tsantilas, Dimitris Giannakakos +9

Multi-Task Learning Graph Foundation Models Graph Transformer Power Systems

Jul 13, 2026cs.LG

Surprisingly Simple and Effective Multi-Domain Graph Foundation Model through Graph-to-Table Alignment

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.

Chunyu Hu, Tianyin Liao, Ge Lan +4

Nankai University · Tsinghua University · Beihang University

Tabular Foundation Models Graph Representation Learning Graph Foundation Models

Jul 11, 2026cs.AI

GRATE: Temporal Extensions for Inductive KG Foundation Models via Gated Rotary Attention

Knowledge graph foundation models such as Ultra and Trix achieve strong inductive transfer by learning relation-graph representations that generalise to unseen entities and relations. Extending this transferability to temporal knowledge graphs (TKGs) remains challenging: existing temporal models tie their parameters to dataset-specific entities, relations, or timestamps and are not designed to transfer to TKGs with disjoint vocabularies. We propose GRATE (Gated Rotary Attention for Temporal Encoding), an entity-side message function that adds no learnable parameters and encodes time through relative time differences by rotating each edge message according to its time gap to the query and applying a query-conditioned gate to select temporally relevant signals. GRATE integrates into NBFNet-style KG foundation models while preserving structural transferability. Existing TKG benchmarks evaluate within shared train/test vocabularies and cannot directly test cross-dataset temporal transfer; we therefore construct GDELTIndT and WIKIIndT, inductive transfer benchmark suites with disjoint entities, relations, and timestamps spanning both interpolation and extrapolation. Across these benchmarks and held-out forecasting datasets, a single jointly pretrained GRATE checkpoint improves over the static base model in most settings.

Jiaxin Pan, Osama Mohammed, Daniel Hernández +1

Analytic Computing, Institute for Artificial Intelligence, University of Stuttgart, Stuttgart, Germany · University of Southampton, Southampton, United Kingdom.

Temporal Link Prediction Graph Foundation Models Temporal Attention KG Completion Temporal KGs

Jul 7, 2026cs.LG

Canopy: A Heterograph Foundation Model for Metabolic Engineering

Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering. Existing computational approaches either rely on stoichiometric constraint-based models that cannot learn from experimental data, or apply tabular machine learning to hand-crafted features that discard the relational structure of biological knowledge. We present Canopy, a heterogeneous graph foundation model that integrates ten public and proprietary data sources into a unified knowledge graph (KG) of 6.9M nodes across 13 types and 34 edge types, covering genes, proteins, metabolites, reactions, pathways, strains, and fermentation experiments. Node features are encoded through domain-specific foundation models (ESM-2 for protein sequences, MoLFormer for chemical SMILES, and PubMedBERT for biomedical text), yielding a multi-modal representation within a single graph. We pretrain a Heterogeneous Graph Transformer (HGT) augmented with SignNet positional encodings, Jumping Knowledge aggregation, and virtual nodes using four self-supervised objectives (link prediction, masked node modelling, distance prediction, and contrastive experiment clustering), balanced via learned homoscedastic uncertainty weighting. On the downstream task of fermentation titer prediction, frozen Canopy embeddings achieve

R^{2} = 0.41

with a lightweight probe, outperforming tabular baselines (best

R^{2} = 0.24

) and homogeneous GNN variants.

Jake Bowden, Laurence Legon, Satnam Surae

Twig Bio, London, United Kingdom

Heterogeneous GNNs Graph SSL Graph Foundation Models Multimodal Graph Learning Biomedical KGs