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Estimating treatment effects from single-arm trials via latent-variable modeling

Manuel Haußmann · Tran Le · Viivi Halla-aho · Samu Kurki · Jussi Leinonen · Miika Koskinen · Samuel Kaski · Harri Lähdesmäki

MR1 & MR2 - Number 125
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Thu 2 May 8 a.m. PDT — 8:30 a.m. PDT


Randomized controlled trials (RCTs) are the accepted standard for treatment effect estimation but they can be infeasible due to ethical reasons and prohibitive costs. Single-arm trials, where all patients belong to the treatment group, can be a viable alternative but require access to an external control group. We propose an identifiable deep latent-variable model for this scenario that can also account for missing covariate observations by modeling their structured missingness patterns. Our method uses amortized variational inference to learn both group-specific and identifiable shared latent representations, which can subsequently be used for {\em (i)} patient matching if treatment outcomes are not available for the treatment group, or for {\em (ii)} direct treatment effect estimation assuming outcomes are available for both groups. We evaluate the model on a public benchmark as well as on a data set consisting of a published RCT study and real-world electronic health records. Compared to previous methods, our results show improved performance both for direct treatment effect estimation as well as for effect estimation via patient matching.

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