OpenMed-NER-OrganismDetect-PubMed-109M

What it does

This model detects species and organism names in English biomedical and clinical text, using a single 'Species' label. It reports an F1 score of 0.835 on the Species-800 test set, with 109 million parameters and a 512-token input limit.

Best for

• Species mentions in research papers
• Organism names in clinical notes
• Species extraction from PubMed abstracts

What it detects (1 labels)

• Species

Quality

Species Entity Recognition - Species names from the Species-800 dataset

Use it

pip install transformers torch

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