3D Medical Image Lossless Compressor Using Deep Learning Approaches

The ever-increasing importance of accelerated information processing, communica-tion, and storing are major requirements within the big-data era revolution. With the extensive rise in data availability, handy information acquisition, and growing data rate, a critical challenge emerges in efficient handling. Even with advanced technical hardware developments and multiple Graphics Processing Units (GPUs) availability, this demand is still highly promoted to utilise these technologies effectively. Health-care systems are one of the domains yielding explosive data growth. Especially when considering their modern scanners abilities, which annually produce higher-resolution and more densely sampled medical images, with increasing requirements for massive storage capacity. The bottleneck in data transmission and storage would essentially be handled with an effective compression method. Since medical information is critical and imposes an influential role in diagnosis accuracy, it is strongly encouraged to guarantee exact reconstruction with no loss in quality, which is the main objective of any lossless compression algorithm. Given the revolutionary impact of Deep Learning (DL) methods in solving many tasks while achieving the state of the art results, includ-ing data compression, this opens tremendous opportunities for contributions. While considerable efforts have been made to address lossy performance using learning-based approaches, less attention was paid to address lossless compression. This PhD thesis investigates and proposes novel learning-based approaches for compressing 3D medical images losslessly.Firstly, we formulate the lossless compression task as a supervised sequential prediction problem, whereby a model learns a projection function to predict a target voxel given sequence of samples from its spatially surrounding voxels. Using such 3D local sampling information efficiently exploits spatial similarities and redundancies in a volumetric medical context by utilising such a prediction paradigm. The proposed NN-based data predictor is trained to minimise the differences with the original data values while the residual errors are encoded using arithmetic coding to allow lossless reconstruction.Following this, we explore the effectiveness of Recurrent Neural Networks (RNNs) as a 3D predictor for learning the mapping function from the spatial medical domain (16 bit-depths). We analyse Long Short-Term Memory (LSTM) models’ generalisabil-ity and robustness in capturing the 3D spatial dependencies of a voxel’s neighbourhood while utilising samples taken from various scanning settings. We evaluate our proposed MedZip models in compressing unseen Computerized Tomography (CT) and Magnetic Resonance Imaging (MRI) modalities losslessly, compared to other state-of-the-art lossless compression standards.This work investigates input configurations and sampling schemes for a many-to-one sequence prediction model, specifically for compressing 3D medical images (16 bit-depths) losslessly. The main objective is to determine the optimal practice for enabling the proposed LSTM model to achieve a high compression ratio and fast encoding-decoding performance. A solution for a non-deterministic environments problem was also proposed, allowing models to run in parallel form without much compression performance drop. Compared to well-known lossless codecs, experimental evaluations were carried out on datasets acquired by different hospitals, representing different body segments, and have distinct scanning modalities (i.e. CT and MRI).To conclude, we present a novel data-driven sampling scheme utilising weighted gradient scores for training LSTM prediction-based models. The objective is to determine whether some training samples are significantly more informative than others, specifically in medical domains where samples are available on a scale of billions. The effectiveness of models trained on the presented importance sampling scheme was evaluated compared to alternative strategies such as uniform, Gaussian, and sliced-based sampling

MiNL: Micro-images based Neural Representation for Light Fields

Traditional representations for light fields can be separated into two types: explicit representation and implicit representation. Unlike explicit representation that represents light fields as Sub-Aperture Images (SAIs) based arrays or Micro-Images (MIs) based lenslet images, implicit representation treats light fields as neural networks, which is inherently a continuous representation in contrast to discrete explicit representation. However, at present almost all the implicit representations for light fields utilize SAIs to train an MLP to learn a pixel-wise mapping from 4D spatial-angular coordinate to pixel colors, which is neither compact nor of low complexity. Instead, in this paper we propose MiNL, a novel MI-wise implicit neural representation for light fields that train an MLP + CNN to learn a mapping from 2D MI coordinates to MI colors. Given the micro-image's coordinate, MiNL outputs the corresponding micro-image's RGB values. Light field encoding in MiNL is just training a neural network to regress the micro-images and the decoding process is a simple feedforward operation. Compared with common pixel-wise implicit representation, MiNL is more compact and efficient that has faster decoding speed (\textbf{$\times$80$\sim$180} speed-up) as well as better visual quality (\textbf{1$\sim$4dB} PSNR improvement on average)

JOINT CODING OF MULTIMODAL BIOMEDICAL IMAGES US ING CONVOLUTIONAL NEURAL NETWORKS

The massive volume of data generated daily by the gathering of medical images with different modalities might be difficult to store in medical facilities and share through communication networks. To alleviate this issue, efficient compression methods must be implemented to reduce the amount of storage and transmission resources required in such applications. However, since the preservation of all image details is highly important in the medical context, the use of lossless image compression algorithms is of utmost importance. This thesis presents the research results on a lossless compression scheme designed to encode both computerized tomography (CT) and positron emission tomography (PET). Different techniques, such as image-to-image translation, intra prediction, and inter prediction are used. Redundancies between both image modalities are also investigated. To perform the image-to-image translation approach, we resort to lossless compression of the original CT data and apply a cross-modality image translation generative adversarial network to obtain an estimation of the corresponding PET. Two approaches were implemented and evaluated to determine a PET residue that will be compressed along with the original CT. In the first method, the residue resulting from the differences between the original PET and its estimation is encoded, whereas in the second method, the residue is obtained using encoders inter-prediction coding tools. Thus, in alternative to compressing two independent picture modalities, i.e., both images of the original PET-CT pair solely the CT is independently encoded alongside with the PET residue, in the proposed method. Along with the proposed pipeline, a post-processing optimization algorithm that modifies the estimated PET image by altering the contrast and rescaling the image is implemented to maximize the compression efficiency. Four different versions (subsets) of a publicly available PET-CT pair dataset were tested. The first proposed subset was used to demonstrate that the concept developed in this work is capable of surpassing the traditional compression schemes. The obtained results showed gains of up to 8.9% using the HEVC. On the other side, JPEG2k proved not to be the most suitable as it failed to obtain good results, having reached only -9.1% compression gain. For the remaining (more challenging) subsets, the results reveal that the proposed refined post-processing scheme attains, when compared to conventional compression methods, up 6.33% compression gain using HEVC, and 7.78% using VVC

Image Analysis and Machine Learning in Agricultural Research

Agricultural research has been a focus for academia and industry to improve human well-being. Given the challenges in water scarcity, global warming, and increased prices of fertilizer, and fossil fuel, improving the efficiency of agricultural research has become even more critical. Data collection by humans presents several challenges including: 1) the subjectiveness and reproducibility when doing the visual evaluation, 2) safety when dealing with high toxicity chemicals or severe weather events, 3) mistakes cannot be avoided, and 4) low efficiency and speed. Image analysis and machine learning are more versatile and advantageous in evaluating different plant characteristics, and this could help with agricultural data collection. In the first chapter, information related to different types of imaging (e.g., RGB, multi/hyperspectral, and thermal imaging) was explored in detail for its advantages in different agriculture applications. The process of image analysis demonstrated how target features were extracted for analysis including shape, edge, texture, and color. After acquiring features information, machine learning can be used to automatically detect or predict features of interest such as disease severity. In the second chapter, case studies of different agricultural applications were demonstrated including: 1) leaf damage symptoms, 2) stress evaluation, 3) plant growth evaluation, 4) stand/insect counting, and 5) evaluation for produce quality. Case studies showed that the use of image analysis is often more advantageous than visual rating. Advantages of image analysis include increased objectivity, speed, and more reproducibly reliable results. In the third chapter, machine learning was explored using romaine lettuce images from RD4AG to automatically grade for bolting and compactness (two of the important parameters for lettuce quality). Although the accuracy is at 68.4 and 66.6% respectively, a much larger data base and many improvements are needed to increase the model accuracy and reliability. With the advancement in cameras, computers with high computing power, and the development of different algorithms, image analysis and machine learning have the potential to replace part of the labor and improve the current data collection procedure in agricultural research. Advisor: Gary L. Hei

Edge Intelligence : Empowering Intelligence to the Edge of Network

Edge intelligence refers to a set of connected systems and devices for data collection, caching, processing, and analysis proximity to where data are captured based on artificial intelligence. Edge intelligence aims at enhancing data processing and protects the privacy and security of the data and users. Although recently emerged, spanning the period from 2011 to now, this field of research has shown explosive growth over the past five years. In this article, we present a thorough and comprehensive survey of the literature surrounding edge intelligence. We first identify four fundamental components of edge intelligence, i.e., edge caching, edge training, edge inference, and edge offloading based on theoretical and practical results pertaining to proposed and deployed systems. We then aim for a systematic classification of the state of the solutions by examining research results and observations for each of the four components and present a taxonomy that includes practical problems, adopted techniques, and application goals. For each category, we elaborate, compare, and analyze the literature from the perspectives of adopted techniques, objectives, performance, advantages and drawbacks, and so on. This article provides a comprehensive survey of edge intelligence and its application areas. In addition, we summarize the development of the emerging research fields and the current state of the art and discuss the important open issues and possible theoretical and technical directions.Peer reviewe