Named entity recognition built on top of BERT and keras-bert.
bert (added as submodule to this project. FullTokenizer is used instead of keras-bert tokenizer)
keras-bert (https://pypi.org/project/keras-bert/)
Pretrained BERT model, e.g. from:
input data e.g. from:
Input data is expected to be in CONLL:ish format where Token and Tag are tab separated. First string on the line corresponds to Token and second string to Tag
Get submodules
git submodule init
git submodule update
Get pretrained models and data
./scripts/get-models.sh
./scripts/get-finer.sh
./scripts/get-turku-ner.sh
Run an experiment on FiNER news data (run-finer-news.sh trains, predict-finer-news.sh outputs predictions)
./scripts/run-finer-news.sh
./scripts/predict-finer-news.sh
python compare.py data/finer-news/test.tsv finer-news-predictions.tsv
Experiment on Turku NER corpus data (run-turku-ner.sh trains, predict-turku-ner.sh outputs predictions)
./scripts/run-turku-ner.sh
./scripts/predict-turku-ner.sh
python compare.py data/turku-ner/test.tsv turku-ner-predictions.tsv
If in a Slurm environment, edit scripts/slurm-run.sh to match your setup and create virtual environment, e.g.
module purge
module load tensorflow
python -m venv venv
source venv/bin/activate
pip install -r requirements.txt
then run
sbatch scripts/slurm-run.sh scripts/run-finer-news.sh
sbatch scripts/slurm-run.sh scripts/predict-finer-news.sh
python compare.py data/finer-news/test.tsv finer-news-predictions.tsv
and
sbatch scripts/slurm-run.sh scripts/run-turku-ner.sh
sbatch scripts/slurm-run.sh scripts/predict-turku-ner.sh
python compare.py data/turku-ner/test.tsv turku-ner-predictions.tsv
(the first jobs must finish before running the second ones.)
For parameter selection in a Slurm environment, try
./slurm/run-parameter-grid.sh
python3 slurm/select_params.py logs/*.out