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

arXiv: https://arxiv.org/abs/2606.24995 · HTML: https://mlsanity.com/paper/2606.24995/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 24 references that are in the map.
- First posted on arXiv 23 Jun 2026.

## Builds on (most cited first, 14 of 14)

- [Explaining and Harnessing Adversarial Examples](https://mlsanity.com/paper/1412.6572/) (2014)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [A Baseline for Detecting Misclassified and Out-of-Distribution Examples in Neural Networks](https://mlsanity.com/paper/1610.02136/) (2016)
- [TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second](https://mlsanity.com/paper/2207.01848/) (2022)
- [OpenML: networked science in machine learning](https://mlsanity.com/paper/1407.7722/) (2014)
- [Transformers Can Do Bayesian Inference](https://mlsanity.com/paper/2112.10510/) (2021)
- [TabICL: A Tabular Foundation Model for In-Context Learning on Large Data](https://mlsanity.com/paper/2502.05564/) (2025)
- [TabICLv2: A better, faster, scalable, and open tabular foundation model](https://mlsanity.com/paper/2602.11139/) (2026)
- [TabPFN-2.5: Advancing the State of the Art in Tabular Foundation Models](https://mlsanity.com/paper/2511.08667/) (2025)
- [TabDPT: Scaling Tabular Foundation Models on Real Data](https://mlsanity.com/paper/2410.18164/) (2024)
- [Large Scale Transfer Learning for Tabular Data via Language Modeling](https://mlsanity.com/paper/2406.12031/) (2024)
- [ConTextTab: A Semantics-Aware Tabular In-Context Learner](https://mlsanity.com/paper/2506.10707/) (2025)
- [TabPFN-Wide: Continued Pre-Training for Extreme Feature Counts](https://mlsanity.com/paper/2510.06162/) (2025)
- [TabFlex: Scaling Tabular Learning to Millions with Linear Attention](https://mlsanity.com/paper/2506.05584/) (2025)

## Abstract (arXiv)

Tabular foundation models (TFMs) achieve strong performance on microbiome abundance data, yet their robustness under realistic distribution shift remains poorly characterized. We introduce a benchmark that evaluates the robustness of TFMs to biologically inspired perturbations across six gut microbiome datasets spanning four disease contexts. In this in-context learning setting, models receive unperturbed support sets as context and are evaluated on perturbed query samples. To isolate robustness beyond "shortcut" features, we preserve the most discriminative taxa and apply three controlled perturbation strategies: (i) removal of high-abundance (uninformative) taxa, (ii) sparsification via increased zero-inflation, and (iii) zero-imputation via spurious non-zero injections. Our results show that protecting discriminative features is insufficient to guarantee stability under support-query shift: across datasets, all perturbations degrade model performance, with zero-imputation consistently the most harmful, indicating that corrupting global feature structure can break generalization even when key taxa are retained. Sparsification disproportionately affects TFMs relative to a classical random forest baseline, suggesting greater sensitivity to zero-inflation-type shifts. The code is publicly available at: https://github.com/UMMISCO/metagenomics-fm/.