Usage

Installation

To use EHRmonize, first install it using pip:

$ pip install ehrmonize

Using EHRmonize

To harmonize EHR data and retrieve generic drug names, you can use the EHRmonize class and its methods. Below is an example of how to set up and use EHRmonize:

from ehrmonize import EHRmonize
import pandas as pd
data = pd.read_csv("hf://datasets/AIWongLab/ehrmonize/ehrmonize.csv")

shots = [
     "An input drugname 'vancocin' would be classified as 'vancomycin'.",
]

ehrm = EHRmonize(
   model_id='gpt-4o',
   temperature=0.1,
   max_tokens=64,
   openai_api_key=userdata.get('OPENAI_API_KEY'), # defined via secrets
   )

 ehrm.config_prompting(
   n_shots=1,
 )

 ehrm.set_task(
   task='task_generic_route',
   possible_shots=shots,
 )

data['predicted_generic'] = ehrm.predict(
   input=data['drug'],
   progress_bar=True
)

# display the original drug name, labeled generic name, and predicted generic name
display(data[['drug', 'generic_name', 'predicted_generic']])