BiomedicalQA

This repository contains the code and preprocess datasets,for our participating model in BioASQ 8b challenge. We use BioSentVec, Scibert and Biobert language modelling representations for this task. The codebase was built on top of https://github.com/dmis-lab/bioasq-biobert

Usage

1. Setup Python paths

$ export PYTHONPATH=<repo_root_dir>

2. Install requirements

$ pip install -r requirements.txt

3. Train a model

Use the following comand to see the posible models and training configurations.

$ python TF_based/Yesno_BioQA.py --help

usage: training.py 

To level config for the BioBert project

optional arguments:

For instance, to train, execute the following:

$ python TF_based/Yesno_BioQA.py

4. Extract predictions from the test set using a trained model

python TF_based/Yesno_BioQA.py 

Running baselines

Please see the README file in the Baseline folder.

Running unit tests (NOT MANDATORY)

$ chmod +x run_tests.sh
$ ./run_tests.sh

Contributors

1. Karthick Gunasekaran

2. Vaishnavi

3. Kun Li