Are Tabular Foundation Models Robust to Realistic Query Distribution Shifts in Microbiome Data?

Tabular Foundation Models (TFMs) have emerged as novel approaches for tabular predictive tasks, demonstrating competitive predictive performance to ensemble tree-based models. Most TFMs are trained and evaluated on independent and identically distributed data, but this assumption changes in real-world scenarios due to distribution shifts, which compromise the robustness of models. Limited research has been conducted of TFMs under distribution shifts. We present an empirical evaluation of Out-Of-Distribution (OOD) performance of nine TFMs, spanning diverse pre-training strategies and architectures: TabPFNv2, TabPFNv2.5, TabPFNv2.6, TabPFNv3, TabICL, TabICLv2, Mitra, LimiX and TabFM. Three real-world datasets from the TableShift study were considered (HELOC, Voting, Childhood Lead), covering label, socioeconomic, and geographic shift types. Our results show that all evaluated TFMs degrade systematically under distribution shift regardless of pre-training strategy, with shift gaps ranging from 0.003 to 0.060 depending on shift type. The relationship between in-distribution and OOD predictive performance documented for classical tabular models extends into TFMs. We also identified a scalability gap, as high-performing models demand significant memory and computational resources beyond what standard deployment infrastructure can support. This study extends existing benchmarks for OOD in tabular data, providing evidence to support their adoption in high-stakes domains characterized by structural distribution shifts.

Tabular foundation models with different architectures converge in accuracy across a range of classification and regression tasks. This raises questions a leaderboard cannot answer: (i) whether the models execute the same in-context algorithm, (ii) where row, column, and class-permutation invariances originate, and (iii) how robust they are under perturbations engineered against the inferred mechanism. We characterize all three. The model families realize qualitatively distinct similarity-based readouts: from an attention-weighted vote over context labels to a class-conditional mean readout, each confirmed by causal intervention. We find that the representation collapse highlighted in prior work is not a practical concern for them. Each model's permutation invariances trace to specific positional parameters whose removal preserves accuracy and makes approximate invariance exact. Perturbations engineered against each readout reproduce predicted failure modes; hub and rank attacks isolate them from refit baselines. Together these results give a mechanistic account of contemporary tabular foundation models and identify which inductive biases govern both their accuracy and characteristic failures.

Transformer-based tabular foundation models (TFMs) dominate small to medium tabular predictive benchmark tasks, yet their inference mechanisms remain largely unexplored. We present the first large-scale mechanistic study of layerwise dynamics in 6 state-of-the-art tabular in-context learning models. We explore how predictions emerge across depth, identify distinct stages of inference and reveal latent-space dynamics that differ from those of language models. Our findings indicate substantial depthwise redundancy across multiple models, suggesting iterative refinement with overlapping computations during inference stages. Guided by these insights, we design a proof-of-concept, looped single-layer model that uses only 20% of the original model's parameters while achieving comparable performance. The code is available at https://github.com/amirbalef/is_one_layer_enough.