Biomedical Event Extraction as Multi-Turn Question Answering

Requirements

• python >= 3.7
• pip install -r requirements.txt

Download Files

Data

• Download Pathway Curation training, development and test sets from http://2013.bionlp-st.org/tasks/.
• Download GENIA11 training, development and test sets from http://weaver.nlplab.org/~bionlp-st/BioNLP-ST/downloads/downloads.shtml.

Miscellaneous

• Download pretrained SciBert checkpoint scibert-scivocab-uncased.
• Donwload pretrained models for Pathway Curation and GENIA from here. Extract and unzip the *.tar.gz files.

Training

Training can be conducted using the script scripts/train.sh. Change model directory model_dir and data directory data_dir to the respective locations in your systems. For further options, refer to the file /run/utils_io.py.

Predicting

Predictions can be conducted using the script scripts/predict.sh. Change model directory model_dir and data directory data_dir to the respective locations in your systems. Predictions in the BioNLP .a* format are written to the specified output folder predictions_dir. For further options, refer to the file /run/utils_io.py.

Disclaimer

Note, that this is highly experimental research code which is not suitable for production usage. We do not provide warranty of any kind. Use at your own risk.