A pre-registered test against known true risk found tabular foundation models are not a shortcut to calibrated clinical prediction, and neither is Firth logistic regression
AspireAI community · arXiv
Whether a tabular foundation model's predicted risks are correctly calibrated cannot be settled on real clinical data, because true risk is unknown there. This study pre-registered a simulation where the true risk is known, then compared TabPFN-3.5, TabICLv2 and Mitra-v2 against Firth logistic regression with intercept correction across 58 scenarios and 1,000 random designs, followed by four real clinical datasets. The foundation models' calibration slope matched Firth's within the pre-registered margin in 36 or 37 of 48 core scenarios and was better only at a sample size of 200 with a 3 percent event rate. The more sobering number is that even 3,000 patients often were not enough: with Firth, TabPFN-3.5 or Mitra-v2, between 63 and 83 percent of samples gave risks close to the truth at 10 and 30 percent event rates, and 35 to 50 percent at 3 percent, while TabICLv2 did worse at 8 to 39 percent and 1 to 3 percent. On real data no model resisted a change in event rate between populations, though recalibrating on 500 local patients largely repaired it.
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