Relational foundation models are increasingly pretrained on synthetic databases, yet downstream benchmarks reveal little about why one synthetic corpus produces a better model than another. In particular, strong performance may arise from realistic row-level statistics without the model ever learning to use relational structure. We study this as a data-attribution problem: which property of synthetic pretraining data induces relational computation? Using four Relational Transformer checkpoints trained with the same architecture, initialization, objective, and compute budget on corpora produced by four relational data generators, we trace a measurable property of the data to learned computation and downstream behavior. We hypothesize that relational mechanisms emerge when cross-table information is predictively necessary for the masked-cell pretraining objective. RelDiff exhibits by far the largest predictive gain from foreign-key-linked parents, and its corresponding model is uniquely sensitive to foreign-key interventions on unseen databases. This dependence survives a random-initialization control, grows monotonically with the fraction of corrupted links, and localizes to a serial cross-table pathway. Finally, disrupting the same mechanism during downstream inference removes RelDiff's advantage on relational tasks while leaving structure-insensitive models nearly unchanged. These results connect a property of synthetic training data to a learned mechanism and, through intervention, to downstream behavior.
Figures & tables
Corpus
Targets
Np/Nc
Row-only R2
Δparent
Δchild
RelDiff
48
30/22
0.022
+0.072 [+0.018,+0.091]
−0.001
GRDM
120
65/78
−0.011
−0.057[−0.076,−0.044]
−0.105
PluRel
113
84/71
0.166
+0.009 [+0.001,+0.022]
−0.000
RDB-PFN
120
72/68
0.436
+0.001 [−0.004,+0.009]
−0.005
Table 1: Predictive structure in the synthetic pretraining corpora. Row-only R2 measures target predictability without cross-table information. Δparent and Δchild measure the additional predictive value of FK-linked parent attributes and simple child aggregates, respectively. Np/Nc gives the number of target-column problems for which each relational feature set is available.
Model
L0
ΔLnbr
ΔLshuffle
ΔLremove
Rel. FK change
RelDiff
0.241
+0.127
+0.202
+0.197
+83.6%
GRDM
0.342
−0.002
+0.018
+0.034
+5.3%
PluRel
0.161
−0.000
+0.010
+0.019
+6.1%
RDB-PFN
0.208
+0.003
+0.007
+0.015
+3.4%
Random init
0.556
−0.025
+0.027
+0.057
+4.9%
Table 2: Functional reliance on relational structure on rel-stack . Entries are original masked-cell loss and absolute changes under three interventions. The final column reports the relative loss increase under full FK shuffling.
Figure 1: From data-side relational signal to model-side structural reliance. Left: median gain in held-out R2 obtained by adding FK-linked parent attributes to a row-only predictor; error bars are 95% bootstrap intervals. Right: increase in masked-cell reconstruction loss as an increasing fraction of rel-stack FK assignments is corrupted. RelDiff exhibits both the strongest parent-linked predictive signal and the steepest functional response to corruption.
Model
Original
ΔLnbr
ΔLshuffle
ΔLremove
RelDiff
0.339
+0.029
+0.069
+0.065
GRDM
0.350
+0.013
−0.005
−0.007
PluRel
0.339
+0.007
+0.009
+0.014
RDB-PFN
0.351
−0.002
+0.003
+0.007
Table 3: Structural reliance averaged over three real RelBench databases. Entries are mean original masked-cell loss and absolute changes under each intervention. The experiment uses a broader 27-batch probe suite than Table 2 .
Figure 2: Pathway-specific intervention localizes a serial cross-table computation. Neighbor attention aggregates linked children into a parent representation, which subsequently reaches the target through parent access in feat . Blocking parent access makes additional nbr ablation behaviorally redundant.
Figure 3: Behavioral importance of individual nbr attention heads. Individual head ablations reveal concentrated functional specialization in RelDiff. Its most important head accounts for approximately 39.5% of the positive head-attributable loss increase, compared with 12.5% under uniform contribution from eight heads.
Figure 4: Mean classification AUROC as a function of in-context length. Each point averages the six classification tasks. The 30k points incorporate the n=2048 re-evaluation of the two rare-label rel-stack tasks. Under the corrected evaluation all four checkpoints degrade from context 1,024 to 30k, with RelDiff showing the smallest decline.
Context
Model
Original
FK shuffled
Nbr ablated
ΔFK
Δnbr
30k
RelDiff
0.865
0.579
0.624
−0.286
−0.241
30k
GRDM
0.520
0.622
0.537
+0.102
+0.018
30k
PluRel
0.652
0.650
0.636
−0.003
−0.017
30k
RDB-PFN
0.642
0.643
0.634
+0.001
−0.008
1,024
RelDiff
0.847
0.718
0.728
−0.129
−0.119
1,024
GRDM
0.609
0.618
0.622
+0.009
+0.013
Table 4: Downstream intervention on rel-stack user-engagement. Entries are AUROC on identical examples under standard inference, FK shuffling, and internal nbr ablation. The 30k evaluation uses n=2048 examples (60 positives). ΔFK and Δnbr are changes relative to original inference.
Appendix figures & tables9 assets
Supplementary material from the paper’s appendix.
Appendix
Generator
Reference data
Relational structure
Value generation
RelDiff
Yes
fitted to reference FK graph
joint graph-conditioned diffusion
GRDM
Yes
reference structure / degree statistics
graph-conditional diffusion
PluRel
No
procedural relational sampler
conditional causal mechanisms
RDB-PFN
No
hand-designed relational prior
SCM-style synthetic prior
Appendix
Table 5: Summary of the four synthetic pretraining generators. “Reference-conditioned” denotes generation tied to the schema or relational structure of an existing database; “reference-free” denotes generation from a synthetic prior.
Corpus
Numerical
Text / categorical
Boolean
RelDiff
512
234
0
GRDM
518
0
0
PluRel
1132
0
518
RDB-PFN
1081
0
0
Appendix
Table 6: Column-type census in the available synthetic corpora. Counts are over the sampled databases used in the audit. The available GRDM export contains no preserved text/categorical columns: string and datetime fields are represented numerically.
Figure 5: Task-level relational predictive gains. Each point corresponds to one target-column prediction problem. RelDiff exhibits substantially larger gains from linked-parent attributes, whereas the simple child aggregates considered here provide little additional predictive signal.
Corpus
Feature
Table
Cross-table
RelDiff
1.10
0.57
1.04
GRDM
0.69
0.43
0.71
PluRel
0.79
0.34
0.85
RDB-PFN
0.82
0.16
0.81
Appendix
Table 7: Diversity of the generated corpora. Values are mean pairwise embedding distances along feature-, table-, and cross-table axes. RelDiff has the largest measured diversity, but the ordering of the remaining corpora does not reproduce the ordering of functional relational reliance.
Figure 6: Output diversity measured directly in the generated databases. RelDiff has the largest diversity on all three axes, but diversity alone does not reproduce the ordering of functional relational reliance.
Model
Encoders
Col
Feat
Nbr
FFN
GRDM
4.386
3.440
4.047
3.129
3.525
PluRel
2.345
2.893
2.636
2.198
2.504
RDB-PFN
2.311
3.142
2.455
2.142
2.445
RelDiff
3.690
3.025
3.315
3.622
3.089
Appendix
Table 8: Per-parameter checkpoint deviation by RT component. Entries are RMS deviations from the four-checkpoint mean, multiplied by 103 . Among the attention streams, RelDiff has its largest deviation in nbr , whereas GRDM has its largest deviation in feat .
Figure 7: Checkpoint deviation by attention stream and depth. Weight-space differences identify components that were affected differently during pretraining. Functional importance is established separately by intervention.
Checkpoint pair
Early CKA
Late CKA
GRDM / RelDiff
0.944
0.824
PluRel / RelDiff
0.944
0.810
GRDM / PluRel
0.938
0.718
PluRel / RDB-PFN
0.909
0.707
RDB-PFN / RelDiff
0.870
0.587
GRDM / RDB-PFN
0.808
0.406
Appendix
Table 9: Pairwise linear CKA on identical real-data inputs. Early and late values average blocks 0–5 and 6–11, respectively.
Model
Normalized entropy
Top-1 mass
RelDiff
0.843
0.396
GRDM
0.858
0.394
RDB-PFN
0.890
0.361
PluRel
0.898
0.361
Appendix
Table 10: Within-neighborhood attention statistics. Lower normalized entropy indicates more selective attention among the FK-linked cells permitted by the architectural mask.
Relational Databases (RDBs) are the backbone of modern business, yet they lack foundation models comparable to those in text or vision. A key obstacle is that high-quality RDBs are private, scarce, and structurally heterogeneous, making internet-scale pre-training infeasible. To overcome this data scarcity, we introduce RDB-PFN, the first relational foundation model trained purely via synthetic data. Inspired by Prior-Data Fitted Networks (PFNs), where synthetic data generated from Structural Causal Models (SCMs) enables reasoning on single tables, we design a Relational Prior Generator to create an infinite stream of diverse RDBs from scratch. Pre-training on over 2 million synthetic single-table and relational tasks, RDB-PFN learns to adapt to any new database instantly via genuine in-context learning. Experiments show that RDB-PFN achieves strong few-shot performance on 19 real-world relational prediction tasks, outperforming state-of-the-art tabular foundation models evaluated on the same DFS-linearized inputs, while using a lightweight architecture and fast inference. The code is available at https://github.com/MuLabPKU/RDBPFN.
Yanbo Wang, Jiaxuan You, Chuan Shi +1
Institute for Artificial Intelligence, Peking University · University of Illinois at Urbana-Champaign · Institute of Computing Technology, Beijing University of Post and Telecommunication +1
Relational Prior-Data Fitted Networks (PFNs) such as RDB-PFN approximate Bayesian inference over multi-table relational databases by pretraining on millions of synthetic tasks. We investigate three intertwined questions about this paradigm. First, can a structurally different synthetic generator PluRel substitute for RDB-PFN's prior? Second, how much does the order in which synthetic data is presented to the PFN affect downstream performance? Third, how much relational reasoning can a PFN acquire from single-table synthetic pretraining alone, before any relational data is introduced? Using PluRel as the sole synthetic data source across all experiments, we find: (i) a progressive single-table curriculum that gradually widens schema complexity from 7 to 17 columns reaches 0.703 average ROC-AUC on the 23-task tabular benchmark using only approximately 13,300 synthetic tables (approximately 45x fewer single-table datasets than RDB-PFN's reported warm-up recipe), while the same data trained all-at-once collapses to 0.541 ROC-AUC; (ii) a relational curriculum trained from scratch on only approximately 5,500 PluRel databases reaches 0.638 average ROC-AUC on the 19-task RelBench/4DBInfer benchmark, recovering 88% of RDB-PFN's reported performance with approximately 220x less relational synthetic data; and (iii) the single-table curriculum model, evaluated directly on the relational benchmark without any relational adaptation, achieves 0.631, nearly matching the dedicated relational pipeline. Together, these findings suggest that curriculum design and synthetic data diversity may matter more for relational PFN pretraining than the specific relational generator or raw synthetic scale alone.
Relational Foundation Models (RFMs) facilitate data-driven decision-making by learning from complex multi-table databases. However, the diverse relational databases needed to train such models are rarely public due to privacy constraints. While there are methods to generate synthetic tabular data of arbitrary size, incorporating schema structure and primary-foreign key connectivity for multi-table generation remains challenging. Here we introduce PLUREL, a framework to synthesize multi-tabular relational databases from scratch. In a step-by-step fashion, PLUREL models (1) schemas with directed graphs, (2) inter-table primary-foreign key connectivity with bipartite graphs, and, (3) feature distributions in tables via conditional causal mechanisms. The design space across these stages supports the synthesis of a wide range of diverse databases, while being computationally lightweight. Using PLUREL, we observe for the first time that (1) RFM pretraining loss exhibits power-law scaling with the number of synthetic databases and total pretraining tokens, (2) scaling the number of synthetic databases improves generalization to real databases, and (3) synthetic pretraining yields strong base models for continued pretraining on real databases. Overall, our framework and results position synthetic data scaling as a promising paradigm for RFMs.
Vignesh Kothapalli, Rishabh Ranjan, Valter Hudovernik +4