Explainable Prediction of Medical Codes from Clinical Text
James Mullenbach, Sarah Wiegreffe, Jon Duke, Jimeng Sun, Jacob Eisenstein
Abstract
Clinical notes are text documents that are created by clinicians for each patient encounter. They are typically accompanied by medical codes, which describe the diagnosis and treatment. Annotating these codes is labor intensive and error prone; furthermore, the connection between the codes and the text is not annotated, obscuring the reasons and details behind specific diagnoses and treatments. We present an attentional convolutional network that predicts medical codes from clinical text. Our method aggregates information across the document using a convolutional neural network, and uses an attention mechanism to select the most relevant segments for each of the thousands of possible codes. The method is accurate, achieving precision@8 of 0.71 and a Micro-F1 of 0.54, which are both better than the prior state of the art. Furthermore, through an interpretability evaluation by a physician, we show that the attention mechanism identifies meaningful explanations for each code assignment.- Anthology ID:
- N18-1100
- Volume:
- Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)
- Month:
- June
- Year:
- 2018
- Address:
- New Orleans, Louisiana
- Editors:
- Marilyn Walker, Heng Ji, Amanda Stent
- Venue:
- NAACL
- SIG:
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 1101–1111
- Language:
- URL:
- https://aclanthology.org/N18-1100
- DOI:
- 10.18653/v1/N18-1100
- Cite (ACL):
- James Mullenbach, Sarah Wiegreffe, Jon Duke, Jimeng Sun, and Jacob Eisenstein. 2018. Explainable Prediction of Medical Codes from Clinical Text. In Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers), pages 1101–1111, New Orleans, Louisiana. Association for Computational Linguistics.
- Cite (Informal):
- Explainable Prediction of Medical Codes from Clinical Text (Mullenbach et al., NAACL 2018)
- PDF:
- https://preview.aclanthology.org/nschneid-patch-4/N18-1100.pdf
- Code
- jamesmullenbach/caml-mimic + additional community code
- Data
- MIMIC-III