cxrfescore 0.2.3

Fact-level embedding metric for evaluating chest X-ray radiology report generation.

CXRFEScore

Fact-level embedding metric for evaluating chest X-ray radiology report generation.

CXRFEScore extracts factual statements from reports with a T5 fact extractor, embeds them with CXRFE (or compatible CXR-BERT models), and scores hypothesis/reference pairs via soft bipartite matching of fact embeddings.

Based on:

Messina et al., Extracting and Encoding: Leveraging Large Language Models and Medical Knowledge to Enhance Radiological Text Representation, Findings of ACL 2024.

Install

pip install cxrfescore

Optional visualization support:

pip install cxrfescore[viz]

Python: 3.10+

Runtime dependencies (installed automatically)

Package	Role
torch	Model inference
transformers	Load Hugging Face models
numpy	Arrays / aggregation
scikit-learn	Cosine similarity
nltk	Sentence splitting
tqdm	Progress bars
platformdirs	Default cache directory

Optional: matplotlib via cxrfescore[viz] for visualize_fact_similarity.

Additional requirements (not pip packages)

On first use the metric downloads:

• Encoder (default): pamessina/CXRFE
• Fact extractor: pamessina/T5FactExtractor
• NLTK punkt / punkt_tab (auto-downloaded)

Supported alternate encoders:

• microsoft/BiomedVLP-CXR-BERT-specialized
• microsoft/BiomedVLP-BioViL-T
• StanfordAIMI/SRR-BERT-Leaves (CLS embeddings only; label head unused)

A GPU is recommended but not required. CPU works and is slower.

Known-good stack from development: PyTorch 2.x + transformers 4.x / 5.x.

Quick start

from cxrfescore import CXRFEScore

metric = CXRFEScore(device="cuda")  # or "cpu"

hyps = [
    "There is a small right pleural effusion. The heart size is normal.",
]
refs = [
    "Small right pleural effusion. Normal heart size.",
]

result = metric(hyps, refs)
print(result["mean_similarity"])
print(result["per_pair_similarity"])

Extract facts or embeddings only

extract_facts treats each input string as a full report: sentence-split → T5 fact extraction → unique-fact aggregation (same pipeline as scoring).

facts_per_report = metric.extract_facts(hyps)
embeddings = metric.embed_facts(facts_per_report[0])  # shape (num_facts, dim)

Caching

With use_cache=True (default), results are kept in memory during the session:

• Sentence→facts: {cache_dir}/sent_to_facts.pkl (shared across encoders)
• Fact→embedding: {cache_dir}/embeddings/<encoder_name>/fact_to_embedding.pkl (per encoder)

Disk writes are not automatic. Call save_cache() explicitly after a large batch or at the end of a job:

metric = CXRFEScore(use_cache=True, cache_dir="/path/to/cache")
# ... score / extract / embed ...
metric.save_cache()

Disable with use_cache=False.

Inspect what is already on disk:

from cxrfescore import inspect_cache

inspect_cache()                 # default cache location
# or: metric.inspect_cache()    # uses this instance's cache_dir

Visualization

# requires: pip install cxrfescore[viz]
metric.visualize_fact_similarity(ref_report=refs[0], cand_report=hyps[0])

Examples

File	Purpose
examples/colab_smoke.md	Full Colab smoke + adversarial pairs
examples/minimal_cxrfe.md	Default CXRFE encoder
examples/minimal_cxr_bert_specialized.md	CXR-BERT specialized
examples/minimal_biovil_t.md	BioViL-T
examples/minimal_srr_bert_leaves.md	SRR-BERT-Leaves CLS
examples/minimal_extract_embed.md	extract_facts / embed_facts

Try it on Google Colab

After publishing, install in Colab (GPU runtime recommended):

!pip install cxrfescore

For a pre-release check against TestPyPI:

!pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ "cxrfescore==0.2.3"

Citation

If you use CXRFEScore, please cite:

Pablo Messina, Rene Vidal, Denis Parra, Alvaro Soto, and Vladimir Araujo. 2024. Extracting and Encoding: Leveraging Large Language Models and Medical Knowledge to Enhance Radiological Text Representation. In Findings of the Association for Computational Linguistics: ACL 2024, pages 3955–3986, Bangkok, Thailand. Association for Computational Linguistics.

@inproceedings{messina-etal-2024-extracting,
    title = "Extracting and Encoding: Leveraging Large Language Models and Medical Knowledge to Enhance Radiological Text Representation",
    author = "Messina, Pablo  and
      Vidal, Rene  and
      Parra, Denis  and
      Soto, Alvaro  and
      Araujo, Vladimir",
    editor = "Ku, Lun-Wei  and
      Martins, Andre  and
      Srikumar, Vivek",
    booktitle = "Findings of the Association for Computational Linguistics: ACL 2024",
    month = aug,
    year = "2024",
    address = "Bangkok, Thailand",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2024.findings-acl.236/",
    doi = "10.18653/v1/2024.findings-acl.236",
    pages = "3955--3986"
}

Paper: ACL Anthology · PDF · arXiv

Development

pip install -e ".[dev]"
pytest                          # unit + mocked tests (default)
pytest -m integration           # downloads HF models; needs network / GPU optional
python -m build

License

MIT