Can Graph Foundation Models Generalize Over Architecture?

Benjamin Gutteridge, Michael Bronstein, Xiaowen Dong
Proceedings of GRaM: the Second Edition of the Workshop on Geometry-grounded Representation Learning and Generative Modeling, PMLR 326:294-320, 2026.

Abstract

Graph foundation models (GFMs) have recently attracted interest due to the promise of graph neural network (GNN) architectures that generalize zero-shot across graphs of arbitrary scales, feature dimensions, and domains. While existing work has demonstrated this ability empirically across diverse real-world benchmarks, these tasks share a crucial hidden limitation: they admit a narrow set of effective GNN architectures. In particular, current domain-agnostic GFMs rely on fixed architectural backbones, implicitly assuming that a single message-passing regime suffices across tasks. In this paper, we argue that architecture adaptivity is a necessary requirement for true GFMs. We show that existing approaches are non-robust to task-dependent architectural attributes and, as a case study, use range as a minimal and measurable axis along which this limitation becomes explicit. With theoretical analysis and controlled synthetic experiments, we demonstrate that fixed-backbone GFMs provably under-reach on tasks whose architectural requirements differ from those seen at training time. To address this issue, we introduce a framework that adapts effective GNN architecture at inference time by discovering and mixing task-specific linear graph operators, enabling zero-shot generalization across tasks with heterogeneous architectural requirements, without retraining. We validate our approach on arbitrary-range synthetic tasks and a suite of real-world benchmarks, demonstrating improved performance and robustness over existing domain-agnostic GFMs.

Cite this Paper

BibTeX
@InProceedings{pmlr-v326-gutteridge26a, title = {{C}an {G}raph {F}oundation {M}odels {G}eneralize {O}ver {A}rchitecture?}, author = {Gutteridge, Benjamin and Bronstein, Michael and Dong, Xiaowen}, booktitle = {Proceedings of GRaM: the Second Edition of the Workshop on Geometry-grounded Representation Learning and Generative Modeling}, pages = {294--320}, year = {2026}, editor = {Pouplin, Alison and Vadgama, Sharvaree and Bekkers, Erik and Kaba, Sékou-Oumar and Lawrence, Hannah and Lecha, Manuel and Baker, Elizabeth and Suk, Julian and Walters, Robin and Tomczak, Jakub and Jegelka, Stefanie}, volume = {326}, series = {Proceedings of Machine Learning Research}, month = {26 Apr}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v326/main/assets/gutteridge26a/gutteridge26a.pdf}, url = {https://proceedings.mlr.press/v326/gutteridge26a.html}, abstract = {Graph foundation models (GFMs) have recently attracted interest due to the promise of graph neural network (GNN) architectures that generalize zero-shot across graphs of arbitrary scales, feature dimensions, and domains. While existing work has demonstrated this ability empirically across diverse real-world benchmarks, these tasks share a crucial hidden limitation: they admit a narrow set of effective GNN architectures. In particular, current domain-agnostic GFMs rely on fixed architectural backbones, implicitly assuming that a single message-passing regime suffices across tasks. In this paper, we argue that architecture adaptivity is a necessary requirement for true GFMs. We show that existing approaches are non-robust to task-dependent architectural attributes and, as a case study, use range as a minimal and measurable axis along which this limitation becomes explicit. With theoretical analysis and controlled synthetic experiments, we demonstrate that fixed-backbone GFMs provably under-reach on tasks whose architectural requirements differ from those seen at training time. To address this issue, we introduce a framework that adapts effective GNN architecture at inference time by discovering and mixing task-specific linear graph operators, enabling zero-shot generalization across tasks with heterogeneous architectural requirements, without retraining. We validate our approach on arbitrary-range synthetic tasks and a suite of real-world benchmarks, demonstrating improved performance and robustness over existing domain-agnostic GFMs.} }
Endnote
%0 Conference Paper %T Can Graph Foundation Models Generalize Over Architecture? %A Benjamin Gutteridge %A Michael Bronstein %A Xiaowen Dong %B Proceedings of GRaM: the Second Edition of the Workshop on Geometry-grounded Representation Learning and Generative Modeling %C Proceedings of Machine Learning Research %D 2026 %E Alison Pouplin %E Sharvaree Vadgama %E Erik Bekkers %E Sékou-Oumar Kaba %E Hannah Lawrence %E Manuel Lecha %E Elizabeth Baker %E Julian Suk %E Robin Walters %E Jakub Tomczak %E Stefanie Jegelka %F pmlr-v326-gutteridge26a %I PMLR %P 294--320 %U https://proceedings.mlr.press/v326/gutteridge26a.html %V 326 %X Graph foundation models (GFMs) have recently attracted interest due to the promise of graph neural network (GNN) architectures that generalize zero-shot across graphs of arbitrary scales, feature dimensions, and domains. While existing work has demonstrated this ability empirically across diverse real-world benchmarks, these tasks share a crucial hidden limitation: they admit a narrow set of effective GNN architectures. In particular, current domain-agnostic GFMs rely on fixed architectural backbones, implicitly assuming that a single message-passing regime suffices across tasks. In this paper, we argue that architecture adaptivity is a necessary requirement for true GFMs. We show that existing approaches are non-robust to task-dependent architectural attributes and, as a case study, use range as a minimal and measurable axis along which this limitation becomes explicit. With theoretical analysis and controlled synthetic experiments, we demonstrate that fixed-backbone GFMs provably under-reach on tasks whose architectural requirements differ from those seen at training time. To address this issue, we introduce a framework that adapts effective GNN architecture at inference time by discovering and mixing task-specific linear graph operators, enabling zero-shot generalization across tasks with heterogeneous architectural requirements, without retraining. We validate our approach on arbitrary-range synthetic tasks and a suite of real-world benchmarks, demonstrating improved performance and robustness over existing domain-agnostic GFMs.
APA
Gutteridge, B., Bronstein, M. & Dong, X.. (2026). Can Graph Foundation Models Generalize Over Architecture?. Proceedings of GRaM: the Second Edition of the Workshop on Geometry-grounded Representation Learning and Generative Modeling, in Proceedings of Machine Learning Research 326:294-320 Available from https://proceedings.mlr.press/v326/gutteridge26a.html.

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