Tailoring automated data augmentation to H&E-stained histopathologyDownload PDF

Feb 09, 2021 (edited Feb 22, 2021)MIDL 2021 Conference SubmissionReaders: Everyone
  • Keywords: computational pathology, data augmentation, autoML, domain shift
  • TL;DR: We propose a method to tailor automated data augmentation framework RandAugment to H&E stained histopathology.
  • Abstract: Convolutional neural networks (CNN) are sensitive to domain shifts, which can result in poor generalization. In medical imaging, data acquisition conditions differ among institutions, which leads to variations in image properties and thus domain shift. Stain variation in histopathological slides is a prominent example. Data augmentation is one way to make CNNs robust to varying forms of domain shift, but requires extensive hyperparameter tuning. Due to the large search space, this is cumbersome and often leads to sub-optimal generalization performance. In this work, we focus on automated and computationally efficient data augmentation policy selection for histopathological slides. Building upon the RandAugment framework, we introduce several domain-specific modifications relevant to histopathological images, increasing generalizability. We test these modifications on H\&E-stained histopathology slides from Camelyon17 dataset. Our proposed framework outperforms the state-of-the-art manually engineered data augmentation strategy, achieving an area under the ROC curve of 0.964 compared to 0.958, respectively.
  • Registration: I acknowledge that publication of this at MIDL and in the proceedings requires at least one of the authors to register and present the work during the conference.
  • Source Code Url: https://github.com/DIAGNijmegen/pathology-he-auto-augment
  • Authorship: I confirm that I am the author of this work and that it has not been submitted to another publication before.
  • Data Set Url: https://camelyon17.grand-challenge.org/
  • Paper Type: validation/application paper
  • Source Latex: zip
  • Primary Subject Area: Application: Histopathology
  • Secondary Subject Area: Transfer Learning and Domain Adaptation
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