This repository is for the Clinical Data Analysis tutorial using the OpenAI API.
It contains code and materials from the 3rd Genome Medicine Academy held in 2025 by the Korea Genome Organization (KOGO).
https://docs.google.com/presentation/d/1DiOlkh-lhqpQQmcHcn5c436wPVtsygQ_/
The tutorial consists of two main sessions:
Description: Leveraging OpenAI models to extract clinically relevant insights from free-text medical notes. Contact: Soungmun Kim (email)
Description: Leveraging OpenAI to learn low-dimensional gene representations from biomedical context.
Contact: Sungmin Kwon (email)
To run the tutorial notebooks, follow these steps:
- Click the green Code button (top right) and select Download ZIP.
- Unzip the downloaded file on your local computer.
- Go to Google Colab
- Click Open Colab button (top right)
- Choose the Upload tab and upload Tutorial 1 & Tutorial 2 notebook(.ipynb) files from the unzipped folder
- Session1/Tutorial1_ExtractInfo_ClinicalNotes.ipynb
- Session2/Tutorial2_GeneEmbeddings.ipynb
- Once uploaded, the notebook will open and is ready to run in Colab.
The API Key required for the practice can be found at the link below.
Note: This API Key is strictly for use during the KOGO workshop sessions only.