OpenMed-NER-OncologyDetect-EuroMed-212M

What it does

This model performs named-entity recognition for oncology, identifying entities such as Cancer, Gene or gene product, and Tissue in English clinical and research documents. It reports an F1 score of 0.5 on the BioNLP 2013 Cancer Genetics test set, with a precision of 0.659 and recall of 0.403.

Best for

• Extracting cancer entities from clinical notes
• Mining biomedical literature for genetic entities
• Identifying pathological formations in research papers

What it detects (16 labels)

• Amino acid
• Anatomical system
• Cancer
• Cell
• Cellular component
• Developing anatomical structure
• Gene or gene product
• Immaterial anatomical entity
• Multi-tissue structure
• Organ
• Organism
• Organism subdivision
• Organism substance
• Pathological formation
• Simple chemical
• Tissue

Quality

Cancer Genetics - Cancer-related genetic entities

Use it

pip install transformers torch

from transformers import pipeline
ner = pipeline("token-classification", model="OpenMed/OpenMed-NER-OncologyDetect-EuroMed-212M", aggregation_strategy="simple")
print(ner("Patient prescribed 10 mg aspirin for hypertension."))

pip install --upgrade "openmed[onnx-runtime]"

from openmed import OnnxModel
model = OnnxModel.from_pretrained("OpenMed/OpenMed-NER-OncologyDetect-EuroMed-212M-v1-onnx-android")
for entity in model("The patient started imatinib after the consultation."):
    print(entity.to_dict())