Retrieval-aligned Tabular Foundation Models Enable Robust Clinical Risk Prediction in Electronic Health Records Under Real-world Constraints

Autoregressive foundation models for electronic health records can make predictions for diverse clinical tasks without finetuning. These methods work by generating possible "synthetic futures" for patients, and then inferring downstream predictions over these simulated trajectories. Despite their strong capabilities, these methods have several flaws. (1) Inference is extremely computationally expensive, as each prediction requires simulating many trajectories, each with many observations. (2) Their performance is noisy due to the variance inherent to simulation, which in particular reduces efficacy on rare events, which are often of high importance clinically. (3) They are not promptable, as their only input is the patient's medical history, requiring indirect aggregation at inference time. We introduce EveryQuery, a promptable foundation model for structured EHR data. Building on the insight that clinical prediction tasks can be written in a structured query language, EveryQuery takes a query as a prompt alongside the patient's history and estimates the outcome directly. This allows EveryQuery to make predictions across diverse clinical tasks, such as classification and survival modeling, without simulation or finetuning. Across three EHR datasets, EveryQuery outperforms a competitive autoregressive baseline on clinically relevant classification and time-to-event tasks, with mean AUROC gains of 14.3% and 12.7% on MIMIC-IV and a large academic medical center and comparable performance on the smaller NWICU dataset. Its advantage is largest for rare outcomes, and it requires 580x less inference compute.

Tabular data is the most common format in clinical practice, encompassing laboratory results, medication records, diagnostic codes, and patient demographics. As foundation models for tabular data have grown in number and variety, a practical question has become harder to answer: which model should a clinician or data scientist actually choose for a given task, and why? Existing surveys catalogue what these models can do, but they stop short of providing a structured way to compare them against the specific demands of a real application. We introduce \system{}, a comparative evaluation framework that scores and ranks tabular foundation models (TFMs) across six clinically meaningful dimensions: how well a model generalizes to new datasets, how effectively it protects patient privacy, how much data it needs to perform well, how it scales with growing datasets and feature spaces, how interpretable its predictions are to clinicians, and how fairly it performs across patient subgroups. Each dimension is broken down into measurable sub-components, and groups of sub-components can optionally be combined into supplementary compound scores, called super-metrics, that provide a diagnostic view of how a model performs across several dimensions simultaneously. To show how the framework works in practice, we apply it to two healthcare use cases, screening for iron deficiency and predicting heart failure, demonstrating how the same set of metrics leads to different model rankings depending on what matters most in each clinical context. We also provide a taxonomy of 45 TFMs organized by their underlying architecture, which serves as a reference for researchers and practitioners looking to navigate this rapidly expanding field.

Tabular foundation models (TFMs) achieve strong performance on health datasets, but their inference cost and infrastructure requirements limit practical use. We study whether their predictive behavior can be transferred to lightweight tabular models through knowledge distillation. Since in-context TFMs condition on the training set at inference time, naive distillation can introduce context leakage; we address this with stratified out-of-fold teacher labeling. Across $19$ healthcare datasets, $6$ TFM teachers, $4$ student families, and several multi-teacher ensembles, we find that distilled students retain at least $90\%$ of teacher AUC, outperforming teachers in some cases, while running at least $26\times$ faster on CPU and preserving calibration and fairness critical for health applications. Moreover, multi-teacher averaging does not consistently improve over the best single teacher. Leakage-aware distillation is thus a viable route for bringing TFM-quality predictions into inference-constrained health settings.