Image Quality Assessment for Population Cardiac MRI: From Detection to Synthesis

Cardiac magnetic resonance (CMR) images play a growing role in diagnostic imaging of cardiovascular diseases. Left Ventricular (LV) cardiac anatomy and function are widely used for diagnosis and monitoring disease progression in cardiology and to assess the patient's response to cardiac surgery and interventional procedures. For population imaging studies, CMR is arguably the most comprehensive imaging modality for non-invasive and non-ionising imaging of the heart and great vessels and, hence, most suited for population imaging cohorts. Due to insufficient radiographer's experience in planning a scan, natural cardiac muscle contraction, breathing motion, and imperfect triggering, CMR can display incomplete LV coverage, which hampers quantitative LV characterization and diagnostic accuracy. To tackle this limitation and enhance the accuracy and robustness of the automated cardiac volume and functional assessment, this thesis focuses on the development and application of state-of-the-art deep learning (DL) techniques in cardiac imaging. Specifically, we propose new image feature representation types that are learnt with DL models and aimed at highlighting the CMR image quality cross-dataset. These representations are also intended to estimate the CMR image quality for better interpretation and analysis. Moreover, we investigate how quantitative analysis can benefit when these learnt image representations are used in image synthesis. Specifically, a 3D fisher discriminative representation is introduced to identify CMR image quality in the UK Biobank cardiac data. Additionally, a novel adversarial learning (AL) framework is introduced for the cross-dataset CMR image quality assessment and we show that the common representations learnt by AL can be useful and informative for cross-dataset CMR image analysis. Moreover, we utilize the dataset invariance (DI) representations for CMR volumes interpolation by introducing a novel generative adversarial nets (GANs) based image synthesis framework, which enhance the CMR image quality cross-dataset

An original framework for understanding human actions and body language by using deep neural networks

The evolution of both fields of Computer Vision (CV) and Artificial Neural Networks (ANNs) has allowed the development of efficient automatic systems for the analysis of people's behaviour. By studying hand movements it is possible to recognize gestures, often used by people to communicate information in a non-verbal way. These gestures can also be used to control or interact with devices without physically touching them. In particular, sign language and semaphoric hand gestures are the two foremost areas of interest due to their importance in Human-Human Communication (HHC) and Human-Computer Interaction (HCI), respectively. While the processing of body movements play a key role in the action recognition and affective computing fields. The former is essential to understand how people act in an environment, while the latter tries to interpret people's emotions based on their poses and movements; both are essential tasks in many computer vision applications, including event recognition, and video surveillance. In this Ph.D. thesis, an original framework for understanding Actions and body language is presented. The framework is composed of three main modules: in the first one, a Long Short Term Memory Recurrent Neural Networks (LSTM-RNNs) based method for the Recognition of Sign Language and Semaphoric Hand Gestures is proposed; the second module presents a solution based on 2D skeleton and two-branch stacked LSTM-RNNs for action recognition in video sequences; finally, in the last module, a solution for basic non-acted emotion recognition by using 3D skeleton and Deep Neural Networks (DNNs) is provided. The performances of RNN-LSTMs are explored in depth, due to their ability to model the long term contextual information of temporal sequences, making them suitable for analysing body movements. All the modules were tested by using challenging datasets, well known in the state of the art, showing remarkable results compared to the current literature methods

Computational Approaches to Drug Profiling and Drug-Protein Interactions

Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

Image recognition, semantic segmentation and photo adjustment using deep neural networks

Deep Neural Networks (DNNs) have proven to be effective models for solving various problems in computer vision. Multi-Layer Perceptron Networks, Convolutional Neural Networks and Recurrent Neural Networks are representative examples of DNNs in the setting of supervised learning. The key ingredients in the successful development of DNN-based models include but not limited to task-specific designs of network architecture, discriminative feature representation learning and scalable training algorithms. In this thesis, we describe a collection of DNN-based models to address three challenging computer vision tasks, namely large-scale visual recognition, image semantic segmentation and automatic photo adjustment. For each task, the network architecture is carefully designed on the basis of the nature of the task. For large-scale visual recognition, we design a hierarchical Convolutional Neural Network to fully exploit a semantic hierarchy among visual categories. The resulting model can be deemed as an ensemble of specialized classifiers. We improve state-of-the-art results at an affordable increase of the computational cost. For image semantic segmentation, we integrate convolutional layers with novel spatially recurrent layers for incorporating global contexts into the prediction process. The resulting hybrid network is capable of learning improved feature representations, which lead to more accurate region recognition and boundary localization. Combined with a post-processing step involving a fully-connected conditional random field, our hybrid network achieves new state-of-the-art results on a large benchmark dataset. For automatic photo adjustment, we take a data-driven approach to learn the underlying color transforms from manually enhanced examples. We formulate the learning problem as a regression task, which can be approached with a Multi-Layer Perceptron network. We concatenate global contextual features, local contextual features as well as pixel-wise features and feed them into the deep network. State-of-the-art results are achieved on datasets with both global and local stylized adjustments

Diagnosis of Neurodegenerative Diseases using Deep Learning

Automated disease classification systems can assist radiologists by reducing workload while initiating therapy to slow disease progression and improve patients’ quality of life. With significant advances in machine learning (ML) and medical scanning over the last decade, medical image analysis has experienced a paradigm change. Deep learning (DL) employing magnetic resonance imaging (MRI) has become a prominent method for computer-assisted systems because of its ability to extract high-level features via local connection, weight sharing, and spatial invariance. Nonetheless, there are several important research challenges when advancing toward clinical application, and these problems inspire the contributions presented throughout this thesis. This research develops a framework for the classification of neurodegenerative diseases using DL techniques and MRI. The presented thesis involves three evolution stages. The first stage is the development of a robust and reproducible 2D classification system with high generalisation performance for Alzheimer’s disease (AD), mild cognitive impairment (MCI), and Parkinson’s disease (PD) using deep convolutional neural networks (CNN). The next phase of the first stage extends this framework and demonstrates its use on different datasets while quantifying the effect of a highly observed phenomenon called data leakage in the literature. Key contributions of the thesis presented in this stage are a thorough analysis of the literature, a discussion on the potential flaws of the selected studies, and the development of an open-source evaluation system for neurodegenerative disease classification using structural MRI. The second stage aims to overcome the problems stem from investigating 3D data with 2D models. With this goal, a 3D CNN-based diagnostic framework is developed for classifying AD and PD patients from healthy controls using T1-weighted brain MRI data. The last stage includes two phases with a focus on AD and MCI diagnosis. The first phase proposes a new autoencoder-based deep neural network structure by integrating supervised prediction and unsupervised representation. The second phase introduces the final contribution of the thesis which is a novel ensemble approach that may also be used to predict diseases other than neurodegenerative ones (e.g., tuberculosis (TB)) using a modality apart from MRI