# Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization?

arXiv: https://arxiv.org/abs/2512.08798 · HTML: https://mlsanity.com/paper/2512.08798/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 49 references that are in the map.
- First posted on arXiv 9 Dec 2025.

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

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (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)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [A decoder-only foundation model for time-series forecasting](https://mlsanity.com/paper/2310.10688/) (2023)
- [TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second](https://mlsanity.com/paper/2207.01848/) (2022)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (2020)
- [A critical look at the evaluation of GNNs under heterophily: Are we really making progress?](https://mlsanity.com/paper/2302.11640/) (2023)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [One for All: Towards Training One Graph Model for All Classification Tasks](https://mlsanity.com/paper/2310.00149/) (2023)
- [GraphGPT: Graph Instruction Tuning for Large Language Models](https://mlsanity.com/paper/2310.13023/) (2023)
- [Language is All a Graph Needs](https://mlsanity.com/paper/2308.07134/) (2023)
- [Sequential Modeling Enables Scalable Learning for Large Vision Models](https://mlsanity.com/paper/2312.00785/) (2023)
- [Exphormer: Sparse Transformers for Graphs](https://mlsanity.com/paper/2303.06147/) (2023)
- [Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning](https://mlsanity.com/paper/2305.19523/) (2023)
- [TiRex: Zero-Shot Forecasting Across Long and Short Horizons with Enhanced In-Context Learning](https://mlsanity.com/paper/2505.23719/) (2025)
- [GraphText: Graph Reasoning in Text Space](https://mlsanity.com/paper/2310.01089/) (2023)
- [GraphLLM: Boosting Graph Reasoning Ability of Large Language Model](https://mlsanity.com/paper/2310.05845/) (2023)
- [Moirai-MoE: Empowering Time Series Foundation Models with Sparse Mixture of Experts](https://mlsanity.com/paper/2410.10469/) (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)

## Built on by (most cited first, 10 of 10)

- [Beyond IID: How General Are Tabular Foundation Models, Really?](https://mlsanity.com/paper/2606.30410/) (2026)
- [TabPFN-3: Technical Report](https://mlsanity.com/paper/2605.13986/) (2026)
- [No Need to Train Your RDB Foundation Model](https://mlsanity.com/paper/2602.13697/) (2026)
- [Learning Posterior Predictive Distributions for Node Classification from Synthetic Graph Priors](https://mlsanity.com/paper/2604.19028/) (2026)
- [Fixed Aggregation Features Can Rival GNNs](https://mlsanity.com/paper/2601.19449/) (2026)
- [A Fair Evaluation of Graph Foundation Models for Node Property Prediction](https://mlsanity.com/paper/2606.24509/) (2026)
- [Surprisingly Simple and Effective Multi-Domain Graph Foundation Model through Graph-to-Table Alignment](https://mlsanity.com/paper/2607.11374/) (2026)
- [LoGIC: Budgeted Context Construction for Node-Level Graph In-Context Learning with Tabular Foundation Models](https://mlsanity.com/paper/2609.05955/) (2026)
- [GraphFAS: A Distributed System for Automated Graph Feature Generation and Selection in Industrial Transaction Networks](https://mlsanity.com/paper/2609.08970/) (2026)
- [Training Graph Foundation Models on The Web Graph](https://mlsanity.com/paper/2609.30894/) (2026)

## Abstract (arXiv)

Foundation models pretrained on large data have demonstrated remarkable zero-shot generalization capabilities across domains. Building on the success of TabPFN for tabular data and its recent extension to time series, we investigate whether graph node classification can be effectively reformulated as a tabular learning problem. We introduce TabPFN-GN, which transforms graph data into tabular features by extracting node attributes, structural properties, positional encodings, and optionally smoothed neighborhood features. This enables TabPFN to perform direct node classification without any graph-specific training or language model dependencies. Our experiments on 12 benchmark datasets reveal that TabPFN-GN achieves competitive performance with GNNs on homophilous graphs and consistently outperforms them on heterophilous graphs. These results demonstrate that principled feature engineering can bridge the gap between tabular and graph domains, providing a practical alternative to task-specific GNN training and LLM-dependent graph foundation models.