Enformer: An encoder-decoder generative model to enhance prediction of disease outcomes using electronic health records

Deep learning transformer-based models using longitudinal electronic health records (EHRs) have shown a great success in prediction of clinical diseases or outcomes. Pretraining on a large dataset can help such models map the input space better and boost their performance on relevant tasks through finetuning with limited data. In this study, we present Enformer, a generative encoder-decoder model with transformer that was pretrained using a new pretraining objective - predicting all diseases and outcomes of a patient at a future visit from previous visits. Enformer’s encoder-decoder framework, paired with the novel pretraining objective, helped it achieve the new state-of-the-art (SOTA) performance on multiple clinical prediction tasks. Comparing with the previous SOTA model, Enformer improved area under the precision–recall curve (AUPRC) by 2% (p<0.001) for pancreatic cancer onset and by 24% (p<0.001) for intentional self-harm in patients with PTSD. The high performance in predicting intentional self-harm shows the potential of Enformer in building effective clinical intervention systems. Enformer is also generalizable and can be easily finetuned for clinical prediction tasks with limited data.