Novel Deep Learning Models for Medical Imaging Analysis

abstract: Deep learning is a sub-field of machine learning in which models are developed to imitate the workings of the human brain in processing data and creating patterns for decision making. This dissertation is focused on developing deep learning models for medical imaging analysis of different modalities for different tasks including detection, segmentation and classification. Imaging modalities including digital mammography (DM), magnetic resonance imaging (MRI), positron emission tomography (PET) and computed tomography (CT) are studied in the dissertation for various medical applications. The first phase of the research is to develop a novel shallow-deep convolutional neural network (SD-CNN) model for improved breast cancer diagnosis. This model takes one type of medical image as input and synthesizes different modalities for additional feature sources; both original image and synthetic image are used for feature generation. This proposed architecture is validated in the application of breast cancer diagnosis and proved to be outperforming the competing models. Motivated by the success from the first phase, the second phase focuses on improving medical imaging synthesis performance with advanced deep learning architecture. A new architecture named deep residual inception encoder-decoder network (RIED-Net) is proposed. RIED-Net has the advantages of preserving pixel-level information and cross-modality feature transferring. The applicability of RIED-Net is validated in breast cancer diagnosis and Alzheimer’s disease (AD) staging. Recognizing medical imaging research often has multiples inter-related tasks, namely, detection, segmentation and classification, my third phase of the research is to develop a multi-task deep learning model. Specifically, a feature transfer enabled multi-task deep learning model (FT-MTL-Net) is proposed to transfer high-resolution features from segmentation task to low-resolution feature-based classification task. The application of FT-MTL-Net on breast cancer detection, segmentation and classification using DM images is studied. As a continuing effort on exploring the transfer learning in deep models for medical application, the last phase is to develop a deep learning model for both feature transfer and knowledge from pre-training age prediction task to new domain of Mild cognitive impairment (MCI) to AD conversion prediction task. It is validated in the application of predicting MCI patients’ conversion to AD with 3D MRI images.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201

Epithelium detection and cervical intraepithelial neoplasia classification in digitized histology images

“Cervical cancer is one of the most deadly cancers faced by women. It is the second leading cause of cancer death in women aged 20 to 39 years. In order to detect cancer at early stages, pathologists analyze the epithelium region from the cervical histology images. These histology images have a pre-cervical cancer condition called cervical intraepithelial neoplasia (CIN) determined by pathologists. This study deals with automating the process of epithelium detection and epithelium CIN classification in digitized histology images. For epithelium detection, the objective is to detect epithelium regions in microscopy images from non-epithelium regions and background. convolutional neural networks, both shallow and deep networks are used for epithelium detection. The highest epithelium detection accuracy of 98.84% is obtained using transfer learning on VGG-19 architecture, pre-trained on the ImageNet dataset. For CIN classification, the epithelium region is divided into 5 segments along the medial axis and patches from each segment were used for training the deep learning model. Vertical segment level classification probabilities from deep learning model are obtained and further classified using SVM, LDA, MLP, logistic and RF classifiers. The highest image level accuracy obtained is 77.27% for MLP classifier using voting”--Abstract, page iii

Two-Stream Convolutional Networks for Action Recognition in Videos

We investigate architectures of discriminatively trained deep Convolutional Networks (ConvNets) for action recognition in video. The challenge is to capture the complementary information on appearance from still frames and motion between frames. We also aim to generalise the best performing hand-crafted features within a data-driven learning framework. Our contribution is three-fold. First, we propose a two-stream ConvNet architecture which incorporates spatial and temporal networks. Second, we demonstrate that a ConvNet trained on multi-frame dense optical flow is able to achieve very good performance in spite of limited training data. Finally, we show that multi-task learning, applied to two different action classification datasets, can be used to increase the amount of training data and improve the performance on both. Our architecture is trained and evaluated on the standard video actions benchmarks of UCF-101 and HMDB-51, where it is competitive with the state of the art. It also exceeds by a large margin previous attempts to use deep nets for video classification