alsmadi/ehr-data-analysis

• Organization

  • There are two directories, each correspond to a simulation in the experiments section of the paper: sim_class_1 (linear decision boundary) and sim_class_2 (quadratic decision boundary).
  • Each directory has three sub directories: code, data, and qsub.
  • Directory 'code' has files of all the R source code that was used in the analysis.
  • Directory 'data' has (if any) simulated data that was used in the analysis. This directory may be empty or absent.
  • Directory 'qsub' has SGE files (.q) that were used to submit jobs on a SGE cluster.

• Files

  • 'sim_data_corr.R' contains the code to simulate and partition the data for classification in first simulation.
  • 'sim_data_nolin_corr.R' contains the code to simulate and partition the data for classification in second simulation.
  • 'sim_data_nonlin_corr_reg.R' contains the code to simulate and partition the data for regression in second simulation.
  • 'analyze_result_class.R' contains the code for analyzing the results for classification of GP with the SE kernel, logistic regression and ridge regression and lasso regression with and without SE kernel-based covariates, SVM and KRR with spectrum and boundrange kernels, and competing methods and making tables.
  • 'analyze_result_reg.R' contains the code for analyzing the results for regression of GP with the SE kernel, logistic regression and ridge regression and lasso regression with and without SE kernel-based covariates, SVM and KRR with spectrum and boundrange kernels, and competing methods and making tables.
  • 'gp_logistic.R' contains the code for the GP classification with the SE kernel.
  • 'submit.R' contains the code for the R code for submitting a job on the cluster. The files in 'qsub' directory use this file for running simulations.

• Citation: If you use the code, then please cite the following paper:

  • Sanvesh Srivastava, Zongyi Xu, Yunyi Li, Nick Street, and Stephanie Gilbertson-White (2020+). Gaussian Process Regression and Classification using International Disease Classification Codes as Covariates. Submitted to Biometrics.

• Contact: Please email Sanvesh Srivastava ([email protected]) if you have any questions related to the code.

• Acknowledgment Office of Naval Research (ONR-BAA N000141812741) and the National Science Foundation (DMS-1854667/1854662).

• NOTE: We are unable to provide the code for real data analysis due to privacy concerns.