michelole / n2c2

Supporting code for participation at the 2018 n2c2 Shared-Task

National NLP Clinical Challenges (n2c2)

A repository containing support code and resources developed at the Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria) for participation at the 2018 n2c2 Shared-Task Track 1 organized by the Department of Biomedical Informatics at the Harvard Medical School.

Citing

If you use data or code in your work, please cite our JAMIA paper:

@article{oleynik2019evaluating,
  title={Evaluating shallow and deep learning strategies for the 2018 n2c2 shared-task on clinical text classification},
  author={Michel Oleynik and Amila Kugic and Zdenko Kasáč and Markus Kreuzthaler},
  journal={Journal of the American Medical Informatics Association},
  publisher={Oxford University Press},
  year={2019}
}

Also of interest:

• Our n2c2 presentation slides

Code Dependencies

• JDK8+
• python3 (to run official evaluation scripts)
• make (to compile fastText)
• gcc/clang (to compile fastText)