  In medical practice, treatments are selected based on the expected causal
effects on patient outcomes. Here, the gold standard for estimating causal
effects are randomized controlled trials; however, such trials are costly and
sometimes even unethical. Instead, medical practice is increasingly interested
in estimating causal effects among patient (sub)groups from electronic health
records, that is, observational data. In this paper, we aim at estimating the
average causal effect (ACE) from observational data (patient trajectories) that
are collected over time. For this, we propose DeepACE: an end-to-end deep
learning model. DeepACE leverages the iterative G-computation formula to adjust
for the bias induced by time-varying confounders. Moreover, we develop a novel
sequential targeting procedure which ensures that DeepACE has favorable
theoretical properties, i.e., is doubly robust and asymptotically efficient. To
the best of our knowledge, this is the first work that proposes an end-to-end
deep learning model tailored for estimating time-varying ACEs. We compare
DeepACE in an extensive number of experiments, confirming that it achieves
state-of-the-art performance. We further provide a case study for patients
suffering from low back pain to demonstrate that DeepACE generates important
and meaningful findings for clinical practice. Our work enables practitioners
to develop effective treatment recommendations based on population effects.
