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https://github.com/sempwn/medical-text-nlp
Tutorial for applying machine learning to text data within healthcare
https://github.com/sempwn/medical-text-nlp
Last synced: 3 months ago
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Tutorial for applying machine learning to text data within healthcare
- Host: GitHub
- URL: https://github.com/sempwn/medical-text-nlp
- Owner: sempwn
- License: mit
- Created: 2019-04-18T16:43:03.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2023-05-12T18:19:45.000Z (over 1 year ago)
- Last Synced: 2024-10-12T01:22:13.859Z (4 months ago)
- Language: Jupyter Notebook
- Size: 5.38 MB
- Stars: 11
- Watchers: 1
- Forks: 8
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# medical-text-nlp
[](https://mybinder.org/v2/gh/sempwn/medical-text-nlp/HEAD?labpath=slides%2Fnlp_overview_slides.ipynb)
[](https://colab.research.google.com/github/sempwn/medical-text-nlp/blob/master/slides/nlp_overview_slides.ipynb)
Tutorial for applying machine learning to text data within healthcare
## Getting started
These instructions will get you a copy of the notebook up and running on your local machine.
### Prerequisites
The easiest way to get up and running is to install [Anaconda](https://www.anaconda.com/download/_), which provides `python`, numerous scientific libraries as well as `jupyter`. Once [Anaconda](https://www.anaconda.com/download/) is installed, navigate to directory for this repository and run `jupyter` via the command line (using the example directory `/Projects/medical-text-nlp/`):
```bash
cd /Projects/medical-text-nlp/
jupyter notebook
```
You can also launch `jupyter` through the [Anaconda Navigator](https://www.anaconda.com/distribution/#feature-desktop-gui).
### Installing
The repository requires the following libraries to be installed via the command-line or within a `conda` terminal
```bash
conda install scikit-learn
conda install pandas
conda install -c anaconda nltk
conda install -c conda-forge wordcloud
```
### Opening notebook
Once the jupyter session is running navigate to the notebook [tutorial.ipynb](nbs/tutorial.ipynb)
### (Optional) setting up using docker
For enhanced replicability a [Docker environment](https://docs.docker.com/get-started/) is also provided with the repo, along with a [requirements.txt](requirements.txt) file specifying the Python libraries required. In order to set up the project within this framework run through the following steps
Install [Docker Desktop](https://www.docker.com/products/docker-desktop)
Build the container by running the following command
```docker build --pull --rm -f "Dockerfile.dockerfile" -t medicaltextnlp:latest "."```
Run docker
```docker run --rm -d -p 8888:8888/tcp medicaltextnlp:latest```
Navigate to the following in a web browser
```http://localhost:8888/```
You will need an access token which can be found in the terminal logs. For more information read the [Jupyter Docker Stacks](https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html) docs.
## License
This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details