PlainQAFact

PlainQAFact is a retrieval-augmented and question-answering (QA)-based factuality evaluation framework for assessing the factuality of biomedical plain language summarization tasks. PlainFact is a high-quality human-annotated dataset with fine-grained explanation (i.e., added information) annotations.

News

• (2025.03.11) PlainFact is now available on 🤗 Hugging Face: PlainFact for sentence-level data and PlainFact-summary for summary-level data.
• (2025.03.02) Pre-embedded vector bases of Textbooks and StatPearls can be downloaded here.
• (2025.03.01) 🚨🚨🚨 PlainQAFact is now on PyPI! Simply use pip install plainqafact to load our pipeline!
• (2025.02.24) Our PlainFact dataset can be downloaded here: PlainFact, including sentence-level and summary-level granularities.
  • Target_Sentence: The plain language sentence/summary.
  • Original_Abstract: The scientific abstract corresponding to each sentence/summary.
  • External: Whether the sentence includes information does not explicitly present in the scientific abstract. (yes: explanation, no: simplification)
  • We will release the full version of PlainFact soon (including Category and Relation information). Stay tuned!
• (2025.02.24) Our fine-tuned Question Generation model is available on 🤗 Hugging Face: QG model (or download it here)

NOTE: This repo is heavily relied on QAFactEval, QAEval, and MedRAG.

Overall Framework

Model Downloading

In PlainQAFact, we use pre-trained classifier to distinguish simplification and explanation sentences, Llama 3.1 8B Instruct for answer extraction, fine-tuned QG model, and the original question answering model from QAFactEval.

Download the pre-trained QA model and our pre-trained classifier through bash download_question_answering.sh.

Quickstart

conda create -n plainqafact python=3.9
pip install plainqafact

After installation, make sure you initialized git-lfs as required by MedRAG. Then, you can directly use PlainQAFact through:

from plainqafact import PlainQAFact

metric = PlainQAFact(
    cuda_device=0,
    classifier_type='learned',
    classifier_path='models/learned_classifier',
    llm_model_path='meta-llama/Llama-3.1-8B-Instruct',
    question_generation_model_path='uzw/bart-large-question-generation',
    qa_answering_model_dir='models/answering',
    knowledge_base='combined', # retrieve from both Textbooks and StatPearls KBs
    scoring_batch_size=1,
    answer_selection_strategy='llm-keywords'
)

# choice 1: interactively evaluate summaries
# summaries:
target_sentences = [
    "The study shows aspirin reduces heart attack risk.",
    "Patients with high blood pressure should exercise regularly."
]
# scientific abstracts:
abstracts = [
    "A comprehensive clinical trial demonstrated that daily aspirin administration significantly decreased the incidence of myocardial infarction in high-risk patients.",
    "Research indicates that regular physical activity is an effective intervention for managing hypertension in adult patients."
]

results = metric.evaluate(target_sentences, abstracts)

print(f"Explanation score (mean: {results['external_mean']:.4f}):", results['external_scores'])
print(f"Simplification score (mean: {results['internal_mean']:.4f}):", results['internal_scores'])
print(f"PlainQAFact score: {results['overall_mean']:.4f}")

Or you can evaluate a data file through:

from plainqafact import PlainQAFact

metric = PlainQAFact(
    cuda_device=0,
    classifier_type='learned',
    classifier_path='models/learned_classifier',
    llm_model_path='meta-llama/Llama-3.1-8B-Instruct',
    question_generation_model_path='uzw/bart-large-question-generation',
    qa_answering_model_dir='models/answering',
    knowledge_base='combined',
    scoring_batch_size=1,
    answer_selection_strategy='llm-keywords',
    target_sentence_col='Target_Sentence', # name of your summary's key (column)
    abstract_col='Original_Abstract', # name of your abstract's key (column)
    input_file_format='csv' # your input file format
)

# choice 2: directly evaluate a data file:
results = metric.evaluate_all(input_file='your_data.csv')

print(f"Explanation score (mean: {results['external_mean']:.4f}):", results['external_scores'])
print(f"Simplification score (mean: {results['internal_mean']:.4f}):", results['internal_scores'])
print(f"PlainQAFact score: {results['overall_mean']:.4f}")

Option 2: Install from source

Installation

• First, create a new conda env: conda create -n plainqafact python=3.9 and clone our repo.
• cd PlainQAFact
• Follow the instructions in MedRAG to install PyTorch and other required packages.
• Then, run the following command:

  conda install git
  pip install -r requirements.txt
  

• Finally, install the old tokenizer package through:

  pip install transformers_old_tokenizer-3.1.0-py3-none-any.whl
  

Running through our PlainFact dataset

Before running the following command, please download the question answering and learned classifier models through above instructions.

python3 run.py \
    --cuda_device 0 \
    --classifier_type learned \  # Options: 'learned', 'llama', 'gpt'
    --input_file data/summary_level.csv \ # path of the input dataset 
    --classifier_path path/to/learned_classifier \ # path of the classifier
    --llm_model_path meta-llama/Llama-3.1-8B-Instruct \ # path of the answer extractor
    --question_generation_model_path uzw/bart-large-question-generation \ # path of the question generation model
    --qa_answering_model_dir models/answering \ # path of the question answering model
    --knowledge_base combined \ # knowledge bases for retrieval, options: textbooks, statpearls, pubmed, wikipedia, combined
    --answer_selection_strategy llm-keywords  # Options: 'llm-keywords', 'gpt-keywords', 'none'

Running through your own data

Please modify the default_config.py file Line 17-19 to indicate the heading/key names of your dataset. We currently support .json, .txt, and .csv file.

python3 run.py \
    --cuda_device 0 \
    --classifier_type learned \
    --input_file your_own_data.json \
    --input_file_format json \
    --classifier_path path/to/learned_classifier \
    --llm_model_path meta-llama/Llama-3.1-8B-Instruct \
    --question_generation_model_path uzw/bart-large-question-generation \
    --qa_answering_model_dir models/answering \
    --knowledge_base textbooks \
    --answer_selection_strategy llm-keywords

Easily replace the pre-trained classifier to OpenAI models or your own

We provides options to easily replace our pre-trained classisifer tailored for the biomedical plain language summarization tasks to other tasks. You may simply set --classifier_type as gpt and provide your OpenAI API key in the default_config.py file Line 26 to run PlainQAFact.

python3 run.py \
    --cuda_device 0 \
    --classifier_type gpt \
    --input_file your_own_data.json \
    --input_file_format json \
    --llm_model_path meta-llama/Llama-3.1-8B-Instruct \
    --question_generation_model_path uzw/bart-large-question-generation \
    --qa_answering_model_dir models/answering \
    --knowledge_base textbooks \
    --answer_selection_strategy llm-keywords

Using other Knowledge Bases for retrieval

Currently, we only experiment with two KBs: Textbooks and StatPearls. You may want to use your customized KBs for more accurate retrieval. In PlainQAFact, we combine both Textbooks and StatPearls and concatenate with the scientific abstracts. Set --knowledge_base textbooks as combined to reproduce our results.

NOTE: Using Llama 3.1 8B model for both classification and answer extraction would take over 40 GB GPU memory. We recommend to use our pre-trained classifier or OpenAI models for classification if the GPU memory is limited.

Citation Information

For the use of PlainQAFact and PlainFact benchmark, please cite:

@misc{you2025plainqafactretrievalaugmentedfactualconsistency,
      title={PlainQAFact: Retrieval-augmented Factual Consistency Evaluation Metric for Biomedical Plain Language Summarization}, 
      author={Zhiwen You and Yue Guo},
      year={2025},
      eprint={2503.08890},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2503.08890}, 
}

Contact Information

If you have any questions, please email zhiweny2@illinois.edu.