Deep Learning Methods for Classification of Glioma and its Molecular Subtypes
Licentiate thesis, 2021
predict LGG molecular subtypes from magnetic resonance imaging (MRI) without taking biopsy. Accurate diagnosis prior to surgery would be important. Recently, non-invasive classification methods such as deep learning have shown promising outcome in prediction of glioma-subtypes based upon pre-operative brain scans. However, it needs large amount of annotated medical data on tumors. This thesis investigates methods on the problem of data scarcity, specifically for molecular LGG-subtypes.
The focus of this thesis is on two challenges for improving the classification performance of gliomas and its molecular subtypes using MRIs; data augmentation and domain mapping to overcome the lack of data and using data with unavailable GT annotation to tackle the issue of tedious task of manually marking tumor boundaries. Data augmentation includes generating synthetic MR images to enlarge the training data using Generative Adversarial Networks (GANs). Another type of GAN, CycleGAN, is used to enlarge the data size by mapping data from different domains to a target domain. A multi-stream Convolutional Autoencoder (CAE) classifier is proposed with a 2-stage training strategy. To enable MRI data to be used without tumor annotation, ellipse bounding box is proposed that gives comparable classification performance.
The thesis comprises of papers addressing the challenging problems of data scarcity and lacking of tumor annotation. These proposed methods can benefit the future research in bringing machine learning tools into clinical practice for non-invasive diagnostics that would assist surgeons and patients in the shared decision making process.
generative adversarial network
convolutional neural network
glioma subtype classification
Muhaddisa Barat Ali
Chalmers, Electrical Engineering, Signal Processing and Biomedical Engineering, Signal Processing
Domain Mapping and Deep Learning from Multiple MRI Clinical Datasets for Prediction of Molecular Subtypes in Low Grade Gliomas
Brain Sciences,; Vol. 10(2020)
Multi-stream Convolutional Autoencoder and 2D Generative Adversarial Network for Glioma Classification
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),; Vol. 11678 LNCS(2019)p. 234-245
Paper in proceeding
Prediction of Glioma-Subtypes: Comparison of Performance on a DL Classifier using Bounding Box Areas Versus Annotated Tumors, Muhaddisa Barat Ali, Irene Yu-Hua Gu , Alice Lidemar , Mitchel S. Berger , Georg Widhalm and Asgeir Store Jakola
Areas of Advance
Information and Communication Technology
Electrical Engineering, Electronic Engineering, Information Engineering
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 5067
Chalmers University of Technology
Opponent: Professor Atsuto Maki, KTH, Stockholm.