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

arXiv: https://arxiv.org/abs/2609.20419 · HTML: https://mlsanity.com/paper/2609.20419/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 53 references that are in the map.
- First posted on arXiv 17 Sep 2026.

## Builds on (most cited first, 30 of 41)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances](https://mlsanity.com/paper/1306.0895/) (2013)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)
- [Scaling Graph Neural Networks with Approximate PageRank](https://mlsanity.com/paper/2007.01570/) (2020)
- [Optimal Transport for structured data with application on graphs](https://mlsanity.com/paper/1805.09114/) (2018)
- [Understanding Attention and Generalization in Graph Neural Networks](https://mlsanity.com/paper/1905.02850/) (2019)
- [Gromov-Wasserstein Learning for Graph Matching and Node Embedding](https://mlsanity.com/paper/1901.06003/) (2019)
- [Graph Foundation Models: Concepts, Opportunities and Challenges](https://mlsanity.com/paper/2310.11829/) (2023)
- [Position: Graph Foundation Models are Already Here](https://mlsanity.com/paper/2402.02216/) (2024)
- [All in One and One for All: A Simple yet Effective Method towards Cross-domain Graph Pretraining](https://mlsanity.com/paper/2402.09834/) (2024)
- [SAMGPT: Text-free Graph Foundation Model for Multi-domain Pre-training and Cross-domain Adaptation](https://mlsanity.com/paper/2502.05424/) (2025)
- [Multi-Domain Graph Foundation Models: Robust Knowledge Transfer via Topology Alignment](https://mlsanity.com/paper/2502.02017/) (2025)
- [Simple and Asymmetric Graph Contrastive Learning without Augmentations](https://mlsanity.com/paper/2310.18884/) (2023)

## Built on by (most cited first, 1 of 1)

- [Spectral Reversal: Counteracting Singular Value Bias for Graph Prompting](https://mlsanity.com/paper/2609.32143/) (2026)

## Abstract (arXiv)

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.