Collaborative Hypergraph Neural Network for Sequential Diagnosis Prediction

Codes for paper: Collaborative Hypergraph Neural Network for Sequential Diagnosis Prediction

Requirements

pip install -r requirements.txt

1. Prepare the datasets

(1) Download the MIMIC-III and MIMIC-IV datasets

The original datasets can be downloaded from the following URLs.

Go to https://mimic.physionet.org/ for access. Once you have the authority for the dataset, download the dataset and extract the csv files to data/mimic3/raw/ and data/mimic4/raw/ in this project.

After the datasets are downloaded, please put each of them into a specified directory of the project.

Folder Specification

data/
- mimic3
  - encoded
  - parsed
  - raw
  - standard
- mimic4
  - encoded
  - parsed
  - raw
  - standard
- params
  - mimic3
  - mimic4
- icd9.txt
raw
- mimic3
  - ADMISSIONS.csv
  - DIAGNOSES_ICD.csv
  - PRESCRIPTIONS.csv
  - PATIENTS.csv
  - NOTEEVENTS.csv
- mimic4
  - admissions.csv
  - diagnoses_ics.csv
  - prescriptions.csv
  - patient.csv
  - noteevents.csv

(2) Preprocess datasets

python run_preprocess.py

2. Configuration

Please see train.py for detailed configurations.

3. Train model

You can train the model with the following command:

```bash
python train.py
```

Acknowledgement

If this work is useful in your research, please cite our paper.

HELJJ / CHLN