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Generative Adversarial Networks to enhance decision support in digital pathology
Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning.
2019 (English)Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
Abstract [en]

Histopathological evaluation and Gleason grading on Hematoxylin and Eosin(H&E) stained specimens is the clinical standard in grading prostate cancer. Recently, deep learning models have been trained to assist pathologists in detecting prostate cancer. However, these predictions could be improved further regarding variations in morphology, staining and differences across scanners. An approach to tackle such problems is to employ conditional GANs for style transfer. A total of 52 prostatectomies from 48 patients were scanned with two different scanners. Data was split into 40 images for training and 12 images for testing and all images were divided into overlapping 256x256 patches. A segmentation model was trained using images from scanner A, and the model was tested on images from both scanner A and B. Next, GANs were trained to perform style transfer from scanner A to scanner B. The training was performed using unpaired training images and different types of Unsupervised Image to Image Translation GANs (CycleGAN and UNIT). Beside the common CycleGAN architecture, a modified version was also tested, adding Kullback Leibler (KL) divergence in the loss function. Then, the segmentation model was tested on the augmented images from scanner B.The models were evaluated on 2,000 randomly selected patches of 256x256 pixels from 10 prostatectomies. The resulting predictions were evaluated both qualitatively and quantitatively. All proposed methods outperformed in AUC, in the best case the improvement was of 16%. However, only CycleGAN trained on a large dataset demonstrated to be capable to improve the segmentation tool performance, preserving tissue morphology and obtaining higher results in all the evaluation measurements. All the models were analyzed and, finally, the significance of the difference between the segmentation model performance on style transferred images and on untransferred images was assessed, using statistical tests.

Place, publisher, year, edition, pages
2019. , p. 69
Keywords [en]
Generative Adversarial Networks, Digital Pathology, CycleGAN, Style Transfer
National Category
Probability Theory and Statistics Medical Image Processing Other Engineering and Technologies not elsewhere specified
Identifiers
URN: urn:nbn:se:liu:diva-158486ISRN: LIU-IDA/STAT-A–19/007–SEOAI: oai:DiVA.org:liu-158486DiVA, id: diva2:1333801
External cooperation
ContextVision
Subject / course
Statistics
Presentation
2019-06-04, 14:30 (English)
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Available from: 2019-08-08 Created: 2019-07-01 Last updated: 2019-08-08Bibliographically approved

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Master Thesis(6238 kB)23 downloads
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De Biase, Alessia
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CiteExportLink to record
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