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Paying Per-Label Attention for Multi-label Extraction from Radiology Reports

  • Patrick SchrempfEmail author
  • Hannah Watson
  • Shadia Mikhael
  • Maciej Pajak
  • Matúš Falis
  • Aneta Lisowska
  • Keith W. Muir
  • David Harris-Birtill
  • Alison Q. O’Neil
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 12446)

Abstract

Training medical image analysis models requires large amounts of expertly annotated data which is time-consuming and expensive to obtain. Images are often accompanied by free-text radiology reports which are a rich source of information. In this paper, we tackle the automated extraction of structured labels from head CT reports for imaging of suspected stroke patients, using deep learning. Firstly, we propose a set of 31 labels which correspond to radiographic findings (e.g. hyperdensity) and clinical impressions (e.g. haemorrhage) related to neurological abnormalities. Secondly, inspired by previous work, we extend existing state-of-the-art neural network models with a label-dependent attention mechanism. Using this mechanism and simple synthetic data augmentation, we are able to robustly extract many labels with a single model, classified according to the radiologist’s reporting (positive, uncertain, negative). This approach can be used in further research to effectively extract many labels from medical text.

Keywords

NLP Radiology report labelling BERT 

Notes

Acknowledgements

This work is part of the Industrial Centre for AI Research in digital Diagnostics (iCAIRD) which is funded by Innovate UK on behalf of UK Research and Innovation (UKRI) [project number: 104690]. We would like to thank the Glasgow Safe Haven for assistance in creating and providing this dataset. Thanks also to The Data Lab for support and funding.

Supplementary material

506088_1_En_29_MOESM1_ESM.pdf (150 kb)
Supplementary material 1 (pdf 149 KB)

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Patrick Schrempf
    • 1
    • 2
    Email author
  • Hannah Watson
    • 1
  • Shadia Mikhael
    • 1
  • Maciej Pajak
    • 1
  • Matúš Falis
    • 1
  • Aneta Lisowska
    • 1
  • Keith W. Muir
    • 3
  • David Harris-Birtill
    • 2
  • Alison Q. O’Neil
    • 1
    • 4
  1. 1.Canon Medical Research EuropeEdinburghUK
  2. 2.University of St AndrewsSt AndrewsUK
  3. 3.Institute of Neuroscience & PsychologyUniversity of GlasgowGlasgowUK
  4. 4.University of EdinburghEdinburghUK

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