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This repository contains data and code for the paper"Comparing deep learning and concept extraction based methods for patient phenotyping".
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Patient Phenotyping

This repository contains the code and data for the paper "Comparing deep learning and concept extraction based methods for patient phenotyping".


In data/annotations.csv, you can find our annotations as well as unique identifiers for patient visits in MIMIC-III, namely the hospital admission ID, subject ID, and chart time. Due to HIPAA requirements, we cannot provide the text of the patients' discharge summary in this repository. With the information named above and access to MIMIC-III, it is easy to extract the text from the identifiers. We are in the process of submitting the annotations as a direct add-on to MIMIC-III to physionet which will make the linking-step obsolete. If you experience difficulties with the data, please contact us and we are happy to help!

In the following sections, we assume that annotations.csv is extended by an additional column named "text" that contains the discharge summary.

If you want to use the same word-embeddings we use, please download them here:


Here is how to run the code for baselines and deep learning components.


To run all the code on the same training and test splits, we provide preprocessing code in We assume that you ran word2vec on the extracted texts first and saved the resulting vectors in a file named "w2v.txt". If you need assistance or want to use our vectors, please contact us (as the file size is too large for this repository).

run it with the following command (with python 2.7):

python data/annotations.csv w2v.txt 

This will create one file data.h5 and one file data-nobatch.h5 in your main directory. Use the batched file for a speedup in the lua code, and the non-batched file for the baselines.


The code for baselines can be found in It is compatible with both python 2 and 3. To run it, simply enter

python --data data-nobatch.h5 --ngram 5

Convolutional Neural Net

We recommend that you have a GPU with a cuda installation. Otherwise, training might take a very long time! This code is based off of the following repository: You can find more information there!

Install Torch

From :

git clone
cd distro; bash install-deps;

Install Torch packages

luarocks install hdf5

Running the code

Please run the code with the following command:

th main.lua [OPTIONS]

You can find all options documented in the file itself. Important ones are "-gpuid" to set your GPU as well as "-label_index" to define which phenotype you want to detect. Here is the list that explains the indices:

1: cohort (is the patient frequent flier) 2: Obesity 3: Non Adherence 4: Developmental Delay Retardation 5: Advanced Heart Disease 6: Advanced Lung Disease 7: Schizophrenia and other Psychiatric Disorders 8: Alcohol Abuse 9: Other Substance Abuse 10: Chronic Pain Fibromyalgia 11: Chronic Neurological Dystrophies 12: Advanced Cancer 13: Depression 14: Dementia

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