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+# 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
+```