bvanaken's picture
Update README.md
62c409a
|
raw
history blame
2.5 kB
metadata
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"
}