Papers › BernGraph: Probabilistic Graph Neural Networks for EHR-based Medication Recommendations
BernGraph: Probabilistic Graph Neural Networks for EHR-based Medication Recommendations
Xihao Piao, Pei Gao, Zheng Chen, Lingwei Zhu, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun
The medical community believes binary medical event outcomes in EHR data contain sufficient information for making a sensible recommendation. However, there are two challenges to effectively utilizing such data: (1) modeling the relationship between massive 0,1 event outcomes is difficult, even with expert knowledge; (2) in practice, learning can be stalled by the binary values since the equally important 0 entries propagate no learning signals. Currently, there is a large gap between the assumed sufficient information and the reality that no promising results have been shown by utilizing solely the binary data: visiting or secondary information is often necessary to reach acceptable performance. In this paper, we attempt to build the first successful binary EHR data-oriented drug recommendation system by tackling the two difficulties, making sensible drug recommendations solely using the binary EHR medical records. To this end, we take a statistical perspective to view the EHR data as a sample from its cohorts and transform them into continuous Bernoulli probabilities. The transformed entries not only model a deterministic binary event with a distribution but also allow reflecting \emph{event-event} relationship by conditional probability. A graph neural network is learned on top of the transformation. It captures event-event correlations while emphasizing \emph{event-to-patient} features. Extensive results demonstrate that the proposed method achieves state-of-the-art performance on large-scale databases, outperforming baseline methods that use secondary information by a large margin. The source code is available at \url{https://github.com/chenzRG/BEHRMecom}
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Methods
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections