OpenMed-NER-AnatomyDetect-PubMed-v2-109M

What it does

This model identifies Anatomy entities, such as anatomical structures and body parts, in English clinical notes and biomedical literature. It reports an F1 score of 0.9 on the AnatEM benchmark, with 109M parameters and a 512-token input limit.

Best for

• Anatomical entity extraction from medical records
• Biomedical literature mining for anatomy mentions
• Clinical text annotation for research

What it detects (1 labels)

• Anatomy

Quality

Anatomical Entity Recognition - Anatomical structures and body parts

Use it

pip install transformers torch

from transformers import pipeline
ner = pipeline("token-classification", model="OpenMed/OpenMed-NER-AnatomyDetect-PubMed-v2-109M", 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-AnatomyDetect-PubMed-v2-109M-onnx-android")
for entity in model("The patient started imatinib after the consultation."):
    print(entity.to_dict())

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-NER-AnatomyDetect-PubMed-v2-109M", config=OpenMedConfig(backend="mlx"))
for e in result.entities:
    print(e.label, e.text)