OpenMed-ZeroShot-NER-Oncology-Medium-209M

What it does

This model detects 16 cancer-related entity types, such as genes, cells, and tissues, in English clinical and research text. It is based on GLiNER and reports an F1 of 0.876 on the BioNLP 2013 Cancer Genetics test set.

Best for

• Cancer pathway curation from literature
• Driver gene analysis in tumor biology
• Precision oncology literature mining

What it detects (16 labels)

Trained on the label below; you can pass any other label names at inference time.

• 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 gliner

from gliner import GLiNER
model = GLiNER.from_pretrained("OpenMed/OpenMed-ZeroShot-NER-Oncology-Medium-209M")
print(model.predict_entities("Patient with type 2 diabetes and hypertension.", ["disease"]))

pip install "openmed[mlx]"

from openmed import analyze_text
from openmed.core.config import OpenMedConfig
result = analyze_text("Patient started imatinib in March.", model_name="OpenMed/OpenMed-ZeroShot-NER-Oncology-Medium-209M", config=OpenMedConfig(backend="mlx"))
for e in result.entities:
    print(e.label, e.text)