bio-ee-baseline

here is a repo about biomedical event extraction. here is a pytorch version of DUT-LiuYang/biomedical-event-trigger-extraction.

Paper: Li L, Liu Y. Exploiting argument information to improve biomedical event trigger identification via recurrent neural networks and supervised attention mechanisms[C]//2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017: 565-568.

biomedical datasets

you can use TEES to get BioNLP[09-13] datasets which format are xml.

surprise! I found a fantastic biomedical github repo bigscience-workshop/biomedical

BigBIO (BigScience Biomedical) is an open library of biomedical dataloaders built using Huggingface's (🤗)

Prerequisites

First, I get PudMed abstracts data by crawling PudMed E-utilizes api 👍 . here is my spider code.

In paper, author use GDep parser for dependency parses, but I can't get this software. In this repo, so we use stanford CoreNLP for dependency parses and apply its result to train dependency-base word embedding.(word2vecf code from BIU-NLP/word2vecf, a kind of a variant of word2vec)

Usage

preprocess stage:

cd data
./preprocess.sh GE09

After running this command, you will get output.conf in your root directory.

train stage:

python main.py

test stage(TBD):

python test.py