Segmenting and Detecting Carotid Plaque Components in MRI

Cardiovascular diseases and stroke are currently the leading causes of death worldwide. Atherosclerotic plaque is a mostly asymptotic vascular disease, but rupture of an atherosclerotic plaque in the carotid artery could lead to stroke. Automated segmentation of plaque components could help improve risk assessment by producing fast and reliable results while saving costs. In this thesis two extensive comparisons have been made. First supervised classifiers are compared in the pixel-wise segmentation task of plaque components. In this comparison five conventional machine learning techniques and one deep learning architecture have been evaluated: linear and quadratic Bayes normal classifiers, linear logistic classifier, random forest and a U-net architecture. In the second comparison classifiers are evaluated in a detection task for their ability to learn with weakly labelled data. This is done within the multiple instance learning (MIL) framework. In addition to conventional multiple instance learning algorithms, a new MIL adaptation of the deep learning architecture, MIL U-net, is proposed and evaluated.In the pixel-wise segmentation tasks the U-net architecture was the best overall classifier after the addition of 93 extra training patients to the original 20 training patients. A good inter-rater agreement was found for the haemorrhage class (ICC = 0.684) and the calcification class (ICC = 0.627). In the detection task the supervised methods, trained with one-sided noise, outperformed multiple instance classifiers such as MIL-Boost and the proposed MIL U-net. In this task both random forest and the linear logistic classifier obtained a fair Cohen's kappa (0.419 and 0.445 respectively) for detection of calcification per slice. The same classifiers obtained good correlation (Cohen's kappa 0.717 and 0.666 respectively) for haemorrhage detection per slice.Mechanical Engineerin

GenNet framework: interpretable deep learning for predicting phenotypes from genetic data

Applying deep learning in population genomics is challenging because of computational issues and lack of interpretable models. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In this framework, interpretable and memory-efficient neural network architectures are constructed by embedding biologically knowledge from public databases, resulting in neural networks that contain only biologically plausible connections. We applied the framework to seventeen phenotypes and found well-replicated genes such as HERC2 and OCA2 for hair and eye color, and novel genes such as ZNF773 and PCNT for schizophrenia. Additionally, the framework identified ubiquitin mediated proteolysis, endocrine system and viral infectious diseases as most predictive biological pathways for schizophrenia. GenNet is a freely available, end-to-end deep learning framework that allows researchers to develop and use interpretable neural networks to obtain novel insights into the genetic architecture of complex traits and diseases.ImPhys/Medical ImagingImPhys/Computational ImagingApplied Science