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An EHR foundation model pretrained on 4.5 million patients held its ranking across health systems it never saw, but its sensitivity at 95 percent specificity did not

AspireAI community · arXiv
TRACER is a decoder-based foundation model pretrained on more than 4.5 million patient sequences from four University of California health systems, then applied unchanged to more than 2 million patients from two systems excluded from both pretraining and downstream head training, across 16 incident diseases at one, two and five-year horizons. The authors argue that global metrics are the wrong summary for screening and instead report at the low false-positive rates screening actually runs at. At 95 percent specificity, flagged patients were up to eight times more likely to be diagnosed within a year than unselected patients, and the median C-index cost of moving to the external systems was only 0.041. But the operating-point numbers moved more than the global ones: for heart failure, AUROC went from 0.862 in-domain to 0.836 externally while sensitivity at 95 percent specificity fell 10.3 percentage points, and for the four rare cancers external sensitivity ranged from 14.9 to 56.5 percent at that threshold. The conclusion is that discrimination transfer does not imply detection transfer.
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One distance function matched sparse-autoencoder features across layers and compressed feature circuits into supernodes
Two sparse-autoencoder analyses have resisted scaling: matching semantically similar features across layers, and compressing large feature circuits into interpretable supernodes. This paper argues both are the same underlying problem, estimating semantic distances between SAE features that sit on different activation manifolds. Its representation treats each feature not as a single decoder vector but as an activation-weighted distribution over the hidden states expressing it, projects those distributions into a shared reference space, and compares them with Wasserstein distance. The representation is proved invariant to activation rescaling and stable under perturbation, and recovers true matches under finite-sample margin conditions. Empirically it outperformed decoder-vector and LLM-based baselines and captured subtle functional distinctions between related features, and it compressed large feature circuits into interpretable supernodes automatically. The limitation is that this is interpretability tooling: the paper demonstrates better feature matching and circuit compression, not that downstream interpretability claims become more accurate.
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