this-before-that

Causal precedence relations in the biomedical domain

Getting the corpus (and other resources)

To retrieve the annotated corpus, you will need git-lfs.

Once you've installed git-lfs, simply run this command:

git-lfs fetch

Running the sieve-based architecture (sans-lstm)

What you'll need...

1. Java 8
2. sbt

Running the LSTM

Installation: Using conda and Python 3.X

1. Fork and clone this repository

2. Install conda

3. Create a new conda environment using the environment.yml config:

conda env create -f environment.yml

The environment can be updated using the following command:

conda env update -f environment.yml

3. Activate the environment:

source activate bionlp

4. Test the installation:

python -c "import keras; print('Keras version: ', keras.__version__)"

GPU training

If you're training on an Ubuntu system with a CUDA card, you can run gpu_dependencies.sh to set things up.

Running the notebooks

jupyter notebook