Clinical Relation Extration with Transformers
Aim
This package is developed for researchers easily to use state-of-the-art transformers models for extracting relations from clinical notes. No prior knowledge of transformers is required. We handle the whole process from data preprocessing to training to prediction.
Dependency
The package is built on top of the Transformers developed by the HuggingFace. We have the requirement.txt to specify the packages required to run the project.
Background
Our training strategy is inspired by the paper: https://arxiv.org/abs/1906.03158 We only support train-dev mode, but you can do 5-fold CV.
Available models
- BERT
- XLNet
- RoBERTa
- ALBERT
- DeBERTa
- Longformer
We will keep adding new models.
usage and example
- data format
see sample_data dir (train.tsv and test.tsv) for the train and test data format
The sample data is a small subset of the data prepared from the 2018 umass made1.0 challenge corpus
# data format: tsv file with 8 columns:
1. relation_type: adverse
2. sentence_1: ALLERGIES : [s1] Penicillin [e1] .
3. sentence_2: [s2] ALLERGIES [e2] : Penicillin .
4. entity_type_1: Drug
5. entity_type_2: ADE
6. entity_id_1: T1
7. entity_id2: T2
8. file_id: 13_10
note:
1) the entity between [s1][e1] is the first entity in a relation; the second entity in the relation is inbetween [s2][e2]
2) even the two entities in the same sentenc, we still require to put them separately
3) in the test.tsv, you can set all labels to neg or no_relation or whatever, because we will not use the label anyway
4) We recommend to evaluate the test performance in a separate process based on prediction. (see **post-processing**)
5) We recommend using official evaluation scripts to do evaluation to make sure the results reported are reliable.
- preprocess data (see the preprocess.ipynb script for more details on usage)
we did not provide a script for training and test data generation
we have a jupyter notebook with preprocessing 2018 n2c2 data as an example
you can follow our example to generate your own dataset
- special tags
we use 4 special tags to identify two entities in a relation
# the defaults tags we defined in the repo are
EN1_START = "[s1]"
EN1_END = "[e1]"
EN2_START = "[s2]"
EN2_END = "[e2]"
If you need to customize these tags, you can change them in
config.py
- training
please refer to the wiki page for all details of the parameters flag details
export CUDA_VISIBLE_DEVICES=1
data_dir=./sample_data
nmd=./new_modelzw
pof=./predictions.txt
log=./log.txt
# NOTE: we have more options available, you can check our wiki for more information
python ./src/relation_extraction.py \
--model_type bert \
--data_format_mode 0 \
--classification_scheme 1 \
--pretrained_model bert-base-uncased \
--data_dir $data_dir \
--new_model_dir $nmd \
--predict_output_file $pof \
--overwrite_model_dir \
--seed 13 \
--max_seq_length 256 \
--cache_data \
--do_train \
--do_lower_case \
--train_batch_size 4 \
--eval_batch_size 4 \
--learning_rate 1e-5 \
--num_train_epochs 3 \
--gradient_accumulation_steps 1 \
--do_warmup \
--warmup_ratio 0.1 \
--weight_decay 0 \
--max_num_checkpoints 1 \
--log_file $log \
- prediction
export CUDA_VISIBLE_DEVICES=1
data_dir=./sample_data
nmd=./new_model
pof=./predictions.txt
log=./log.txt
# we have to set data_dir, new_model_dir, model_type, log_file, and eval_batch_size, data_format_mode
python ./src/relation_extraction.py \
--model_type bert \
--data_format_mode 0 \
--classification_scheme 1 \
--pretrained_model bert-base-uncased \
--data_dir $data_dir \
--new_model_dir $nmd \
--predict_output_file $pof \
--overwrite_model_dir \
--seed 13 \
--max_seq_length 256 \
--cache_data \
--do_predict \
--do_lower_case \
--eval_batch_size 4 \
--log_file $log \
- post-processing (we only support transformation to brat format)
# see --help for more information
data_dir=./sample_data
pof=./predictions.txt
python src/data_processing/post_processing.py \
--mode mul \
--predict_result_file $pof \
--entity_data_dir ./test_data_entity_only \
--test_data_file ${data_dir}/test.tsv \
--brat_result_output_dir ./brat_output
Using json file for experiment config instead of commend line
- to simplify using the package, we support using json file for configuration
- using json, you can define all parameters in a separate json file instead of input via commend line
- config_experiment_sample.json is a sample json file you can follow to develop yours
- to run experiment with json config, you need to follow run_json.sh
export CUDA_VISIBLE_DEVICES=1
python ./src/relation_extraction_json.py \
--config_json "./config_experiment_sample.json"
Baseline (baseline directory)
- We also implemented some baselines for relation extraction using machine learning approaches
- baseline is for comparison only
- baseline based on SVM
- features extracted may not optimize for each dataset (cover most commonly used lexical and semantic features)
- see baseline/run.sh for example
Issues
raise an issue if you have problems.
Citation
please cite our paper:
# We have a preprint at
https://arxiv.org/abs/2107.08957
Clinical Pre-trained Transformer Models
We have a series transformer models pre-trained on MIMIC-III. You can find them here:
- https://transformer-models.s3.amazonaws.com/mimiciii_albert_10e_128b.zip
- https://transformer-models.s3.amazonaws.com/mimiciii_bert_10e_128b.zip
- https://transformer-models.s3.amazonaws.com/mimiciii_electra_5e_128b.zip
- https://transformer-models.s3.amazonaws.com/mimiciii_roberta_10e_128b.zip
- https://transformer-models.s3.amazonaws.com/mimiciii_xlnet_5e_128b.zip
- https://transformer-models.s3.amazonaws.com/mimiciii_deberta_10e_128b.tar.gz
- https://transformer-models.s3.amazonaws.com/mimiciii_longformer_5e_128b.zip
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