# A Fair Benchmarking of Deep Relational Database Learning Models

arXiv: https://arxiv.org/abs/2607.03659 · HTML: https://mlsanity.com/paper/2607.03659/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 25 references that are in the map.
- First posted on arXiv 4 Jul 2026.

## Builds on (most cited first, 18 of 18)

- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Revisiting Deep Learning Models for Tabular Data](https://mlsanity.com/paper/2106.11959/) (2021)
- [Tabular Data: Deep Learning is Not All You Need](https://mlsanity.com/paper/2106.03253/) (2021)
- [Deep Neural Networks and Tabular Data: A Survey](https://mlsanity.com/paper/2110.01889/) (2021)
- [Nomic Embed: Training a Reproducible Long Context Text Embedder](https://mlsanity.com/paper/2402.01613/) (2024)
- [MiniLMv2: Multi-Head Self-Attention Relation Distillation for Compressing Pretrained Transformers](https://mlsanity.com/paper/2012.15828/) (2020)
- [Why do tree-based models still outperform deep learning on tabular data?](https://mlsanity.com/paper/2207.08815/) (2022)
- [RelBench: A Benchmark for Deep Learning on Relational Databases](https://mlsanity.com/paper/2407.20060/) (2024)
- [Better by Default: Strong Pre-Tuned MLPs and Boosted Trees on Tabular Data](https://mlsanity.com/paper/2407.04491/) (2024)
- [Relational Deep Learning: Graph Representation Learning on Relational Databases](https://mlsanity.com/paper/2312.04615/) (2023)
- [Supervised Learning on Relational Databases with Graph Neural Networks](https://mlsanity.com/paper/2002.02046/) (2020)
- [RelGNN: Composite Message Passing for Relational Deep Learning](https://mlsanity.com/paper/2502.06784/) (2025)
- [Griffin: Towards a Graph-Centric Relational Database Foundation Model](https://mlsanity.com/paper/2505.05568/) (2025)
- [A Closer Look at TabPFN v2: Understanding Its Strengths and Extending Its Capabilities](https://mlsanity.com/paper/2502.17361/) (2025)
- [Relational Transformer: Toward Zero-Shot Foundation Models for Relational Data](https://mlsanity.com/paper/2510.06377/) (2025)
- [Relational Graph Transformer](https://mlsanity.com/paper/2505.10960/) (2025)
- [Attention versus Contrastive Learning of Tabular Data -- A Data-centric Benchmarking](https://mlsanity.com/paper/2401.04266/) (2024)
- [Transformers Meet Relational Databases](https://mlsanity.com/paper/2412.05218/) (2024)

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

- [Advancing Open and Reproducible Relational Learning: RelArena-α, TabPFN-Rel and RPI](https://mlsanity.com/paper/2608.16319/) (2026)

## Abstract (arXiv)

Relational databases (RDBs) are the primary data infrastructure in many enterprises, yet recent deep learning methods designed for RDBs have been evaluated under inconsistent experimental protocols, making fair comparison difficult. We present one of the first systematic benchmarking studies of recently released deep learning methods for RDBs, evaluating them across five relational databases, with one classification and one regression task for each. We refactor all deep RDB models to allow the full range of experimental procedures to be applied consistently across all methods. Our findings indicate that the relational transformer (RT) approach delivers the strongest overall performance on both classification and regression tasks compared to the state-of-the-art graph-based modeling and learning of RDBs. Even for single-table learning tasks, deep learning methods designed for RDBs outperform the leading tabular foundation model, TabPFN 2.5. Extending learning from a single table (hop = 0) to multiple tables (hop = 1, 2) by connecting neighboring tables in relational databases enhances performance, but the additional benefit from higher hops diminishes as computational overhead grows. Deep RDB learning methods have the potential to challenge state-of-the-art tabular foundation models, especially on large-scale enterprise data. The source code for this benchmarking study is publicly available.