language: en
tags:
- bert
- medical
- clinical
- assertion
- negation
- text-classification
widget:
- text: Patient denies [entity] SOB [entity].
Clinical Assertion / Negation Classification BERT
Model description
The Clinical Assertion and Negation Classification BERT is introduced in the paper Assertion Detection in Clinical Notes: Medical Language Models to the Rescue? . The model helps structure information in clinical patient letters by classifying medical conditions mentioned in the letter into PRESENT, ABSENT and POSSIBLE.
The model is based on the ClinicalBERT - Bio + Discharge Summary BERT Model by Alsentzer et al. and fine-tuned on assertion data from the 2010 i2b2 challenge.
How to use the model
You can load the model via the transformers library:
from transformers import AutoTokenizer, AutoModelForSequenceClassification
tokenizer = AutoTokenizer.from_pretrained("bvanaken/clinical-assertion-negation-bert")
model = AutoModelForSequenceClassification.from_pretrained("bvanaken/clinical-assertion-negation-bert")
The model expects input in the form of spans/sentences with one marked entity to classify as PRESENT(0), ABSENT(1) or POSSIBLE(2). The entity in question is identified with the special token [entity] surrounding it.
Example input and inference:
input = "The patient recovered during the night and now denies any [entity] shortness of breath [entity]."
tokenized_input = tokenizer(input, return_tensors="pt")
output = model(**tokenized_input)
import numpy as np
predicted_label = np.argmax(output.logits.detach().numpy()) ## 1 == ABSENT
Cite
When working with the model, please cite our paper as follows:
@inproceedings{van-aken-2021-assertion,
title = "Assertion Detection in Clinical Notes: Medical Language Models to the Rescue?",
author = "van Aken, Betty and
Trajanovska, Ivana and
Siu, Amy and
Mayrdorfer, Manuel and
Budde, Klemens and
Loeser, Alexander",
booktitle = "Proceedings of the Second Workshop on Natural Language Processing for Medical Conversations",
year = "2021",
address = "Online",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2021.nlpmc-1.5",
doi = "10.18653/v1/2021.nlpmc-1.5"
}