  Objective: We investigate whether deep learning techniques for natural
language processing (NLP) can be used efficiently for patient phenotyping.
Patient phenotyping is a classification task for determining whether a patient
has a medical condition, and is a crucial part of secondary analysis of
healthcare data. We assess the performance of deep learning algorithms and
compare them with classical NLP approaches.
  Materials and Methods: We compare convolutional neural networks (CNNs),
n-gram models, and approaches based on cTAKES that extract pre-defined medical
concepts from clinical notes and use them to predict patient phenotypes. The
performance is tested on 10 different phenotyping tasks using 1,610 discharge
summaries extracted from the MIMIC-III database.
  Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The
average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our
model having an F1-score up to 37 points higher than alternative approaches. We
additionally assess the interpretability of our model by presenting a method
that extracts the most salient phrases for a particular prediction.
  Conclusion: We show that NLP methods based on deep learning improve the
performance of patient phenotyping. Our CNN-based algorithm automatically
learns the phrases associated with each patient phenotype. As such, it reduces
the annotation complexity for clinical domain experts, who are normally
required to develop task-specific annotation rules and identify relevant
phrases. Our method performs well in terms of both performance and
interpretability, which indicates that deep learning is an effective approach
to patient phenotyping based on clinicians' notes.
