JointBioER

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Dependency package

JointBioER uses the following dependencies:

• Python 2.7
• keras 2.0.3
• Tensorflow 1.1.0
• numpy 1.12.1

Content

• JointBioER

  • DDI: the data and source code of our JointBioER on the DDI 2013 corpus
  • CPR: the data and source code of our JointBioER on the CPR corpus

• Pipeline

  • DDI
    • NER_DDI: NER of pipeline on the DDI 2013 corpus
    • RE_DDI: RE of pipeline on the DDI 2013 corpus
  • CPR
    • NER_CPR: NER of pipeline on the CPR corpus
    • RE_DDI: RE of pipeline on the CPR corpus

Train a pipeline model

To train a pipeline model, you need to train a NER model, and then train a RE model.

for example:

cd ./Pipeline/DDI/NER_DDI/src
python bilstm_crf_train.py
cd  ./Pipeline/DDI/RE_DDI/src
python bilstm_re_keras.py

Train a JointBioER model

Train our JointBioER model on the DDI 2013 corpus:

cd ./JointBioER/DDI/src
python bilstm_crf_train_ddi.py 

Train our JointBioER model on the CPR corpus:

cd ./JointBioER/CPR/src
python bilstm_crf_train_cpr.py