tomolopolis / clinical_sum

Experiments for Estimating Redundancy in Clinical Texts

There are two notebooks:

1. PPL-Experiments: fine-tunes and estimates PPL (Entropy) for MIMIC-III (Full) & Stroke only, also KCH data (No data is stored in the notebook / this repo)

2. Redundnacy Exploration: Applies summarisation metrics over sequentially ordered notes of the same type, to then aggregate and compare average similarities between pairs of notes of different types

To reproduce results of the MIMIC-III experiments:

• Install the dependencies, (strongly recommend using a virtualenv / venv / conda env).

For example:

$ conda create -n clinc_redun python=3.7
$ conda activate clinc_redun
$ pip install -r requirements.txt

• Download / prepare MIMIC-III. Access available here
• Run each notebook

Data is all stored as indicated in ../data/