README.md

metadata

language: en
tags:
  - bert
  - medical
  - clinical
  - assertion
  - negation

Clinical Assertion / Negation Classification BERT

Model description

The model is introduced in the paper Assertion Detection in Clinical Notes: Medical Language Models to the Rescue? . It 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, AutoModel
tokenizer = AutoTokenizer.from_pretrained("bvanaken/clinical-assertion-negation-bert")
model = AutoModel.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, ABSENT or POSSIBLE. The entity in question is identified with the special token [entity] surrounding it.

Example input:

The patient recovered during the night and now denies any [entity] shortness of breath [entity].

Cite

@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"
}