heljj / chln

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.