OpenMed-NER-PharmaDetect-PubMed-109M

What it does

This model detects the single entity type "Chemical or drug" in English clinical notes, research papers, and healthcare documents. It is a 109M-parameter BERT model based on BiomedBERT, reporting an F1 score of 0.956 on the BC5CDR chemicals test set.

Best for

• Medication extraction from patient records
• Drug mentions in research literature
• Chemical entity lists from clinical notes

What it detects (1 labels)

• Chemical or drug

Quality

Chemical Entity Recognition - Chemical entities from the BC5CDR dataset

Use it

pip install transformers torch

from transformers import pipeline
ner = pipeline("token-classification", model="OpenMed/OpenMed-NER-PharmaDetect-PubMed-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-PharmaDetect-PubMed-109M-v1-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-PharmaDetect-PubMed-109M", config=OpenMedConfig(backend="mlx"))
for e in result.entities:
    print(e.label, e.text)