Patient Representation Transfer Learning from Clinical Notes based on Hierarchical Attention Network.

To explicitly learn patient representations from longitudinal clinical notes, we propose a hierarchical attention-based recurrent neural network (RNN) with greedy segmentation to distinguish between shorter and longer, more meaningful gaps between notes. The proposed model is evaluated for both a direct clinical prediction task (mortality) and as a transfer learning pre-training model to downstream evaluation (phenotype prediction of obesity and its comorbidities). Experimental results first show the proposed model with appropriate segmentation achieved the best performance on mortality prediction, indicating the effectiveness of hierarchical RNNs in dealing with longitudinal clinical text. Attention weights from the models highlight those parts of notes with the largest impact on mortality prediction and hopefully provide a degree of interpretability. Following the transfer learning approach, we also demonstrate the effectiveness and generalizability of pre-trained patient representations on target tasks of phenotyping. ©2020 AMIA - All rights reserved.