adverse-events

This repository contains the source code related to the manuscript "Preliminary Processing and Analysis of an Adverse Event Dataset for Detecting Sepsis-Related Events", presented at the IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2021).

A PDF of the published paper can be accessed here. See here to download the exact version of the source code used in the publication (v1.0).

Usage

1. Clone repo:

   git clone https://github.com/andreped/adverse-events.git

2. Create virtual environment, activate it, and install dependencies:

   cd adverse-events/python
   virtualenv -ppython3 venv --clear
   source venv/bin/activate
   pip install -r /path/to/requirements.txt

3. Create the project structure as defined below.

4. Run scripts for training and evaluating different classifier models:

   python main.py misc/default-params.ini

Different parameters relevant for the analysis, building of models, evaluation, plotting results, and similar, may be modified in the INI-file.

Project structure

└── adverse-events
    ├── python
    │   ├── multi-class
    │   ├── topic-analysis
    │   ├── utils
    │   └── ...
    ├── data
    │   ├── EQS_files
    │   ├── file-with-all-notes.csv
    │   └── file_with_annotated_notes.csv
    └── output
        ├── history
        ├── models
        └── figures

How to cite

If you use parts of the source code in your research, please, cite this publication:

@INPROCEEDINGS{yan2021sepsis,
    author={Yan, Melissa Y. and Høvik, Lise Husby and Pedersen, André and Gustad, Lise Tuset and Nytrø, Øystein},
    booktitle={2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
    title={Preliminary Processing and Analysis of an Adverse Event Dataset for Detecting Sepsis-Related Events},
    year={2021},
    pages={1605-1610},
    doi={10.1109/BIBM52615.2021.9669410}
}