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Deep Learning to Predict Mortality Prior to Tracheostomy Decision in Adults with Respiratory Failure

This github repo represents the code base used to perform this study.

This code base relies on MIMIC-III for data substrate, as well as queries from the MIMIC-III Code Repository. Any SQL queries refer to MIMIC-III's postgres build.

To recreate the analysis:

  1. cohort/Cohort Selection.Rmd is used to generate the cohort from MIMIC-III flat files.
  • a MIMIC-III folder containing the database's flat files is required
  1. cohort/cohort.sql is used to perform more complex queries for MIMIC-III-derived data, including illness severity scores, mechanical ventilation status, etc.

  2. cohort/Clinical Tables.Rmd is used to generate the entire data set from the tables which are output from cohort.sql.

  3. modeling/Preprocessing for Modeling.ipynb is used to preprocess data (scaling, normalization) and perform the training/testing split.

  4. modeling/modelfinding_1yr_mort.ipynb and modeling/modelfinding_3mo_mort.ipynb are used to conduct a neural architecture search for their respective models.

  5. modeling/Model Evaluation.ipynb is used to analyze and visualize resulting model metrics.

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