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PAR-emrQA - Paragraph Segmentation of Two emrQA Subsets: Medication and Relations

This repository provides code for the Question-Answering and Paragraph Retrieval experiments in the BioNLP 2024 and Shared Tasks @ ACL 2024 paper: Paragraph Retrieval for Enhanced Question Answering in Clinical Documents

@inproceedings{lanz-pecina-2024-paragraph,
    title = "Paragraph Retrieval for Enhanced Question Answering in Clinical Documents",
    author = "Lanz, Vojtech and Pecina, Pavel",
    editor = "Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Miwa, Makoto  and
      Roberts, Kirk  and
      Tsujii, Junichi",
    booktitle = "Proceedings of the 23rd Workshop on Biomedical Natural Language Processing",
    month = aug,
    year = "2024",
    address = "Bangkok, Thailand",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2024.bionlp-1.48",
    pages = "580--590"
}

Experiments

  • Paragraph Retrieval (PR): Given a question and n paragraphs (i.e., report segmented into n paragraphs) as input, the objective is to rank the paragraphs based on the confidence that they contain relevant information. The task is evaluated using precision at top 1 (P@1), precision at top 2 (P@2), and precision at top 3 (P@3) paragraphs. Ground truth relevant paragraphs are those containing an answer evidence to a given question defined in the emrQA dataset.

  • Oracle Paragraph-driven Question Answering (Oracle-QA): Given a question and an Oracle paragraph (guaranteed to contain the answer), the objective is to identify and extract a minimal substring from the paragraph that precisely addresses or answers the given question. The task is evaluated using the official SQuAD metrics, which are F1 and Exact Match scores. We compare our predictions with the original form of the testing dataset generated by the filtration of Yue et al., i.e., with the dataset before the segmentation process.

  • Paragraph Retrieval–Question Answering (PR-QA): Given a question and n paragraphs (i.e., report segmented into n paragraphs), the goal is to identify and extract a substring from one of the paragraphs that precisely addresses or answers a given question. Evaluation of the task is based on the F1 and Exact Match scores in the same way as in the Oracle-QA task.

Setup

  1. Clone the repository

    git clone https://github.com/lanzv/PAR-emrQA

  2. and install all requirements

    pip install -r requirements.txt

  3. Download the emrQA dataset data.json (for instance here, but you need to register there first and sign the form and its conditions). Then, you can find the emrQA dataset under the Community Annotations Downloads. By default, the code works with the dataset of the following path:./data/data.json (but it is adaptable via script arguments).

  4. Download the BERT/LLMs models to the folder ../models/ (again, this is adaptable via script arguments) or just use huggingface model names.

Prepare emrQA medication and relations subsets (and split it into train/dev/test)

In order to filter, prepare, sample train set, and split the emrQA medication and relations subsets, call the prepare_datasets.py script:

python prepare_datasets.py --data_path ./data/data.json --target_dir ./processed_data --train_ratio 0.7 --dev_ratio 0.1 --topics medication relations --train_sample_ratios 0.2 0.05 --seed 54

For more info, check the prepare_datasets.py argument helps.

Run the Paragraph Retrieval - Question-Answering experiments

Run the experiment that segments prepared subsets into paragraphs, trains the given model and evaluate it on the Oracle-QA (gold paragraph is known), Paragraph Retrieval, and PRQA (gold paragraph is not known) tasks.

python run_experiment.py --train_path ./processed_data/medication-train.json --dev_path ./processed_data/medication-dev.json --test_path ./processed_data/medication-test.json --dataset_title medication --model_name BERTbase --model_path ../models/BERTbase --ft 100 --epochs 3 --seed 54

For more info, check the run_experiment.py argument helps.