检验表格型大模型在微生物组数据分布偏移下的鲁棒性,发现关键特征保留仍不足以保证稳定。
Are Tabular Foundation Models Robust to Realistic Query Distribution Shifts in Microbiome Data?

- 设计六组真实生物扰动测试,评估模型在支持-查询分布偏移下的表现
- 零值插补导致性能下降最严重,表明全局特征结构被破坏会破坏泛化能力
- 表格大模型对稀疏化更敏感,适合关注稳健性的科研人员参考
表格型基础模型(TFMs)在微生物组丰度数据上表现优异,但其在真实分布偏移下的鲁棒性尚未充分评估。本文构建了一个基准,基于六个涵盖四种疾病背景的肠道微生物组数据集,评估TFMs在生物启发式扰动下的表现。在上下文学习设置中,模型使用未扰动的支持集作为上下文,对扰动的查询样本进行评估。为隔离对‘捷径’特征的依赖,保留最具判别性的分类单元,并采用三种受控扰动策略:(i) 移除高丰度(无信息)分类单元,(ii) 通过增加零值比例实现稀疏化,(iii) 通过引入虚假非零值进行零值插补。结果表明,仅保护判别性特征不足以保证在支持-查询分布偏移下的稳定性:所有扰动均导致性能下降,其中零值插补最为有害,说明即使关键分类单元保留,全局特征结构被破坏仍会损害泛化能力。相对于经典随机森林基线,表格大模型对稀疏化更敏感,表明其对零膨胀类偏移更为脆弱。代码已公开于:https://github.com/UMMISCO/metagenomics-fm/。
原文摘要 · Abstract (English)
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/.
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