BCRE

This repository contains the models implemented for the Biomedical causal relationship extraction.

requirements

All the models are implemented using Python version 3.7+ with the libraries listed in requirement.txt . All the hyperparameters of the models can be changed inside the configure.yaml file.

Datasets

All the experiments have been condcating on two freely available datasets:

• Data used in Hahn-Powell, G., Bell, D., Valenzuela-Escárcega, M. A., & Surdeanu, M. (2016). This before that: Causal precedence in the biomedical domain. arXiv preprint arXiv:1606.08089. It is available here.
• BioCause (Biomedical Discourse Causality Corpus)

Codes

This repository consists of the codes for different tasks and models:

1. crossValidation
2. Fine tuning the BioBERT models
3. Random oversampling
4. Layer Visualization
5. ruleBased relation Extraction
6. etc.

Pretrained Word Embedding model

For the all implemented models, a pretarine biomedical word emebedding model is used. For the ElMo the option and weight files for the allennlp module must be downloaded first from here.