detecting-health-advice: A Python repository from junwang4

This is a collaborative project with the School of Information at Syracuse University. Health and medical researchers often give clinical and policy recommendations to inform health practice and public health policy. However, no current health information system supports the direct retrieval of health advice. This study fills the gap by developing and validating an NLP-based prediction model for identifying health advice in research publications.

How to cite

Li, Y., Wang, J. and Yu, B (2021). Detecting Health Advice in Medical Research Literature. EMNLP'2021. 7th-11th November 2021. Online and in the Dominican Republic.

@inproceedings{li2021EMNLPHealthAdvice,
  title={Detecting Health Advice in Medical Research Literature},
  author={Li, Yingya and Wang, Jun and Yu, Bei},
  booktitle={Proceedings of EMNLP'2021},
  year={2021},
}

NOTE: Our running environment is

Ubuntu: 16.04 / PyTorch: 1.8.2 / CUDA: 10.1 / GPU: TITAN Xp

STEP 1. Prerequisite

Install bert-sklearn -- a scikit-learn wrapper to finetune BERT model based on the Huggingface's pytorch transformer.

git clone -b master https://github.com/charles9n/bert-sklearn
cd bert-sklearn
pip install .

Install package fire (for use with command line interfaces)

pip install fire

STEP 2. Get the repo, including code and data

git clone https://github.com/junwang4/detecting-health-advice
cd detecting-health-advice

STEP 3. Model evaluation

cd code

NOTE: Check Makefile for quick access to the following commands

3.1 To evaluate the performance of the model, say, 5-fold cross-validation

First, generate a prediction file as the result of training and testing each of the 5 folds

python run.py advice_classifier --task=train_KFold_model

This will take as input the annotated dataset data/annotations_structured_abstract.csv, and assemble the prediction results from each fold into code/working/pred/[TAG]_train_K5_epochs3.csv Also, 5 fine-tuned BERT models will be saved at code/working/model/[TAG]_K5_epochs3_[fold].bin

Second, display the evaluation results

python run.py advice_classifier --task=evaluate_and_error_analysis

Result (after assembling results from the K=5 runs):

              precision    recall  f1-score   support

           0      0.963     0.951     0.957      3575
           1      0.908     0.922     0.915      1482
           2      0.917     0.941     0.928       925

    accuracy                          0.942      5982
   macro avg      0.929     0.938     0.933      5982

3.2 Apply the above fine-tuned models to the unseen sentences

For the unstructured abstracts:

python run.py advice_classifier --task=apply_trained_model_to_discussion_sentences

For the discussion/conclusion sections:

python run.py advice_classifier --task=apply_trained_model_to_unstructured_abstract_sentences

3.3 Postprocess the above results with filtering rules

For the unstructured abstracts:

python run.py advice_classifier --task=postprocessing_filter_for_unstructured_abstracts

For the discussion/conclusion sections:

python run.py advice_classifier --task=postprocessing_filter_for_discussions

STEP 4. A data and feature augmentation approach for predicting discussion sentences

This is an approach of augmenting training data with part of annotated discussion sentences, and then applying the trained model to the remaining discussion sentences. First, we split the discussion sentences into K groups (grouped by paper ID). When running evaluation on group k (k=1,2,...K), the training data consists of all structured abstract sentences and the discussion sentences from the remaining K-1 groups (except group k). The newly constructed text will take the following form:

section name [SEP] citation mentioned [SEP] past tense [SEP] The original sentence

Specifically, for structured abstract sentences:

structured abstract [SEP] [SEP] [SEP] The original sentence

And for discussion sentences:

discussion [SEP] No [SEP] Yes [SEP] The original sentence

Run the following commands

python run.py augmented_advice_classifier --task=train_KFold_model --feature_section=1 --feature_citation=1 --feature_past_tense=1
python run.py augmented_advice_classifier --task=evaluate_and_error_analysis --feature_section=1 --feature_citation=1 --feature_past_tense=1

Result (after assembling results from the K=5 runs):

              precision    recall  f1-score   support

           0      0.991     0.990     0.990      3635
           1      0.827     0.883     0.854       162
           2      0.892     0.859     0.875       135

    accuracy                          0.981      3932
   macro avg      0.903     0.911     0.907      3932