MED_NER - For chemical/ protein extraction

The repository is divided into two, pytorch/ contains updated code and the following README.md will explain steps to reproduce code + run. [The keras code is outdated and no readme is maintained for the same]

Running pytorch NER code

Setting up environment

To set up the environment, simply install pytorch/requirements.txt via pip in your virtual env.

pip install -r requirements.txt

Step 1 : Create Vocabulary

Move inside pytorch folder and run vocab.py, all necessary changes need to be made to config.json [no changes need to be made to any of the source files]

python vocab.py

Step 2 : Train a model

Training a model is via driver.py file and it also saves the best model. To change this behavior make necessary changes to the train() method.

python driver.py

Setting mode to train in config.json [Default] runs train loop from driver.py. To run model inference or test, change this json param to test.

TODO

1. Test method in driver [Possible bug in batch_iter]