# Tasks on Medical Data

Developed by Keen (keen.you@yale.edu) Fall 2021

## /tasks

These tasks are included in the wrapper function subdirectory, check [here](https://github.com/IreneZihuiLi/EHRKit-LILY/tree/main/wrapper_functions) for more comprehensive usage descriptions.

The /tasks directory contains code for tasks that utilize MIMIC data. Tasks including named entity recognition, abbreviation detection, entity linking, hyponym detection, and translation. 

The /tasks/utils subdirectory contains helper functions for various tasks including selecting medical notes from csv file using row\_id or subject\_id, vectorize notes, and segmenting notes into sentences. Additional tasks including document clustering and retrieving similar documents.

## /non_mimic

The /non\_mimic directory contains tasks that utilize medical data that is not MIMIC. Tasks including de-identification, inference, and question answering.

## Getting Started with Collated Tasks

#### Clone repo & prepare data

```

git clone https://github.com/Yale-LILY/EHRKit.git --depth=1

cd EHRKit/

cd tutorials

mkdir data

mkdir data/mimic_data

cp /data/corpora/mimic/NOTEEVENTS.csv ./data/mimic_data/.

```

#### Create virtual environment

```

python3 -m venv task_virenv/

source task_virenv/bin/activate

```

#### Install packages

```

pip install pip==21.3.1

pip install -U spacy

pip install scispacy

pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz

pip install pandas==1.1.5

pip install numpy==1.19.5

pip install transformers==4.12.3

pip install torch==1.10.0

pip install torchvision==0.11.1

pip install sentencepiece==0.1.96

pip install sklearn

pip install PyRuSH

pip install stanza==1.3.0

```