Novel architecture for gated recurrent unit autoencoder trained on time series from electronic health records enables detection of ICU patient subgroups

Scientific Reports, vol. 13, pp. 4053

Abstract

Electronic health records (EHRs) are used in hospitals to store diagnoses, clinician notes, examinations, lab results, and interventions for each patient. Grouping patients into distinct subsets, for example, via clustering, may enable the discovery of unknown disease patterns or comorbidities, which could eventually lead to better treatment through personalized medicine. Patient data derived from EHRs is heterogeneous and temporally irregular. Therefore, traditional machine learning methods like PCA are ill-suited for analysis of EHR-derived patient data. We propose to address these issues with a new methodology based on training a gated recurrent unit (GRU) autoencoder directly on health record data. Our method learns a low-dimensional feature space by training on patient data time series, where the time of each data point is expressed explicitly. We use positional encodings for time, allowing our model to better handle the temporal irregularity of the data. We apply our method to data from the Medical Information Mart for Intensive Care (MIMIC-III). Using our data-derived feature space, we can cluster patients into groups representing major classes of disease patterns. Additionally, we show that our feature space exhibits a rich substructure at multiple scales.

Authors 5

1. Kilian Merkelbach Aachen JRC-COMBINE

   RWTH Aachen University

   Affiliation as printed

   JRC-COMBINE, RWTH Aachen University, MTZ, Pauwelsstrasse 19, Level 3, 52074, Aachen, Germany

2. Steffen Schaper

   Bayer (Germany)

   Affiliation as printed

   Pharmacometrics / Modeling and Simulation, Bayer AG - Pharmaceuticals, Leverkusen, Germany

3. Christian Diedrich

   Bayer (Germany)

   Affiliation as printed

   Pharmacometrics / Modeling and Simulation, Bayer AG - Pharmaceuticals, Leverkusen, Germany

4. Sebastian Johannes Fritsch Aachen Department of Intensive Care Medicine

   Forschungszentrum Jülich · Universitätsklinikum Aachen · Jülich Supercomputing Centre · RWTH Aachen University

   Affiliation as printed

   Department of Intensive Care Medicine, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany

   Juelich Supercomputing Centre, Forschungszentrum Juelich, Wilhelm-Johnen-Straße, 52428, Juelich, Germany

5. Andreas Schuppert corresponding Aachen JRC-COMBINE

   RWTH Aachen University

   Affiliation as printed

   JRC-COMBINE, RWTH Aachen University, MTZ, Pauwelsstrasse 19, Level 3, 52074, Aachen, Germany. schuppert@combine.rwth-aachen.de

   JRC-COMBINE, RWTH Aachen University, MTZ, Pauwelsstrasse 19, Level 3, 52074, Aachen, Germany