Impact of pre-analytical variables on deep learning accuracy in histopathology

Histopathology
Andrew D JonesHooman H Rashidi

Abstract

Machine learning (ML) binary classification in diagnostic histopathology is an area of intense investigation. Several assumptions, including training image quality/format and the number of training images required, appear to be similar in many studies irrespective of the paucity of supporting evidence. We empirically compared training image file type, training set size, and two common convolutional neural networks (CNNs) using transfer learning (ResNet50 and SqueezeNet). Thirty haematoxylin and eosin (H&E)-stained slides with carcinoma or normal tissue from three tissue types (breast, colon, and prostate) were photographed, generating 3000 partially overlapping images (1000 per tissue type). These lossless Portable Networks Graphics (PNGs) images were converted to lossy Joint Photographic Experts Group (JPG) images. Tissue type-specific binary classification ML models were developed by the use of all PNG or JPG images, and repeated with a subset of 500, 200, 100, 50, 30 and 10 images. Eleven models were generated for each tissue type, at each quantity of training images, for each file type, and for each CNN, resulting in 924 models. Internal accuracies and generalisation accuracies were compared. There was no meaningful signifi...Continue Reading

References

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Citations

May 8, 2020·NPJ Digital Medicine·Charlotte SyrykhPierre Brousset
Jun 21, 2019·Histopathology·Michael L Wilson, Kenneth A Fleming
Oct 27, 2020·Journal of Forensic Sciences·Jack GarlandRexson Tse
Nov 10, 2020·The Journal of Pathology·David J PapkeGeorge L Mutter
Feb 19, 2021·NPJ Digital Medicine·Charlotte SyrykhPierre Brousset
Apr 8, 2021·Physica Medica : PM : an International Journal Devoted to the Applications of Physics to Medicine and Biology : Official Journal of the Italian Association of Biomedical Physics (AIFB)·Luigi MancoLidia Strigari
May 21, 2021·Journal of Pathology Informatics·Elham Vali-BettsHooman H Rashidi
Jun 18, 2021·World Journal of Gastroenterology : WJG·Hiroshi Yoshida, Tomoharu Kiyuna
Nov 28, 2020·The American Journal of Pathology·Jerome Y ChengLiron Pantanowitz
Aug 24, 2021·Burns and Trauma·Francisco Serra E MouraChidi Ekwobi
Jan 26, 2021·Archives of Pathology & Laboratory Medicine·James H HarrisonMichelle N Stram
Jan 5, 2022·Journal of Neuropathology and Experimental Neurology·Mustafa N Shakir, Brittany N Dugger

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