Deep Learning Methods for Classification of Gliomas and Their Molecular Subtypes, From Central Learning to Federated Learning

• The most common type of brain cancer in adults are gliomas. Under the updated 2016 World Health Organization (WHO) tumor classification in central nervous system (CNS), identification of molecular subtypes of gliomas is important. For low grade gliomas (LGGs), prediction of molecular subtypes by observing magnetic resonance imaging (MRI) scans might be difficult without taking biopsy. With the development of machine learning (ML) methods such as deep learning (DL), molecular based classification methods have shown promising results from MRI scans that may assist clinicians for prognosis and deciding on a treatment strategy. However, DL requires large amount of training datasets with tumor class labels and tumor boundary annotations. Manual annotation of tumor boundary is a time consuming and expensive process. The thesis is based on the work developed in five papers on gliomas and their molecular subtypes. We propose novel methods that provide improved performance.  The proposed methods consist of a multi-stream convolutional autoencoder (CAE)-based classifier, a deep convolutional generative adversarial network (DCGAN) to enlarge the training dataset, a CycleGAN to handle domain shift, a novel federated learning (FL) scheme to allow local client-based training with dataset protection, and employing bounding boxes to MRIs when tumor boundary annotations are not available. Experimental results showed that DCGAN generated MRIs have enlarged the original training dataset size and have improved the classification performance on test sets. CycleGAN showed good domain adaptation on multiple source datasets and improved the classification performance. The proposed FL scheme showed a slightly degraded performance as compare to that of central learning (CL) approach while protecting dataset privacy. Using tumor bounding boxes showed to be an alternative approach to tumor boundary annotation for tumor classification and segmentation, with a trade-off between a slight decrease in performance and saving time in manual marking by clinicians. The proposed methods may benefit the future research in bringing DL tools into clinical practice for assisting tumor diagnosis and help the decision making process.

Ämnesord

NATURVETENSKAP  -- Data- och informationsvetenskap -- Datorteknik (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Computer Engineering (hsv//eng)

NATURVETENSKAP  -- Data- och informationsvetenskap -- Människa-datorinteraktion (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Human Computer Interaction (hsv//eng)

NATURVETENSKAP  -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Computer Sciences (hsv//eng)

NATURVETENSKAP  -- Data- och informationsvetenskap -- Datorseende och robotik (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Computer Vision and Robotics (hsv//eng)

MEDICIN OCH HÄLSOVETENSKAP  -- Klinisk medicin -- Cancer och onkologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Clinical Medicine -- Cancer and Oncology (hsv//eng)

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Annan elektroteknik och elektronik (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Other Electrical Engineering, Electronic Engineering, Information Engineering (hsv//eng)

Nyckelord

glioma subtype classification

convolutional autoencoder

convolutional NN

multi-stream U-Net.

CycleGAN

1p/19q codeletion

federated learning

IDH mutation

generative adversarial network

Deep learning

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