Relation Extraction from Biomedical and ClinicalText: Unified Multitask Learning Framework
Requirements
python 3.7
Please run the following command from the directory.
pip install -r requirements.txt
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Please download the pre-trained word embedding from here and put it in the directory data.
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Download all the dataset AiMED, BioInfer, i2b2 2010clinical information challenge and Semeval 2013 DDIExtraction challenge dataset.
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Split the data into train and test set and places them under the directory "data".
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The dataset files should be in the following file name structure:
<dataset_name>-<fold_number>.train
<dataset_name>-<fold_number>.test
E.g. aimed-2.train, aimed-2.test
An example of the sample file is given in the directory "data" with the name “sample-data.txt”
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Go the “src” directory.
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Run the following command:
python main.py
If you are using this code then please cite our paper:
@ARTICLE{9178986,
author={Yadav, Shweta and Ramesh, Srivastsa and Saha, Sriparna and Ekbal, Asif},
journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
title={Relation Extraction from Biomedical and Clinical Text: Unified Multitask Learning Framework},
year={2020},
volume={},
number={},
pages={1-1},
doi={10.1109/TCBB.2020.3020016}}
This code is distributed under the CC BY-NC-SA license.