Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives

Deep learning has demonstrated remarkable performance across various tasks in medical imaging. However, these approaches primarily focus on supervised learning, assuming that the training and testing data are drawn from the same distribution. Unfortunately, this assumption may not always hold true in practice. To address these issues, unsupervised domain adaptation (UDA) techniques have been developed to transfer knowledge from a labeled domain to a related but unlabeled domain. In recent years, significant advancements have been made in UDA, resulting in a wide range of methodologies, including feature alignment, image translation, self-supervision, and disentangled representation methods, among others. In this paper, we provide a comprehensive literature review of recent deep UDA approaches in medical imaging from a technical perspective. Specifically, we categorize current UDA research in medical imaging into six groups and further divide them into finer subcategories based on the different tasks they perform. We also discuss the respective datasets used in the studies to assess the divergence between the different domains. Finally, we discuss emerging areas and provide insights and discussions on future research directions to conclude this survey.Comment: Under Revie

Proceedings of the 17th Annual Conference of the European Association for Machine Translation

Proceedings of the 17th Annual Conference of the European Association for Machine Translation (EAMT

A review of technical factors to consider when designing neural networks for semantic segmentation of Earth Observation imagery

Semantic segmentation (classification) of Earth Observation imagery is a crucial task in remote sensing. This paper presents a comprehensive review of technical factors to consider when designing neural networks for this purpose. The review focuses on Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Generative Adversarial Networks (GANs), and transformer models, discussing prominent design patterns for these ANN families and their implications for semantic segmentation. Common pre-processing techniques for ensuring optimal data preparation are also covered. These include methods for image normalization and chipping, as well as strategies for addressing data imbalance in training samples, and techniques for overcoming limited data, including augmentation techniques, transfer learning, and domain adaptation. By encompassing both the technical aspects of neural network design and the data-related considerations, this review provides researchers and practitioners with a comprehensive and up-to-date understanding of the factors involved in designing effective neural networks for semantic segmentation of Earth Observation imagery.Comment: 145 pages with 32 figure

Recent Developments in Smart Healthcare

Medicine is undergoing a sector-wide transformation thanks to the advances in computing and networking technologies. Healthcare is changing from reactive and hospital-centered to preventive and personalized, from disease focused to well-being centered. In essence, the healthcare systems, as well as fundamental medicine research, are becoming smarter. We anticipate significant improvements in areas ranging from molecular genomics and proteomics to decision support for healthcare professionals through big data analytics, to support behavior changes through technology-enabled self-management, and social and motivational support. Furthermore, with smart technologies, healthcare delivery could also be made more efficient, higher quality, and lower cost. In this special issue, we received a total 45 submissions and accepted 19 outstanding papers that roughly span across several interesting topics on smart healthcare, including public health, health information technology (Health IT), and smart medicine

The Effectiveness of Transfer Learning Systems on Medical Images

Deep neural networks have revolutionized the performances of many machine learning tasks such as medical image classification and segmentation. Current deep learning (DL) algorithms, specifically convolutional neural networks are increasingly becoming the methodological choice for most medical image analysis. However, training these deep neural networks requires high computational resources and very large amounts of labeled data which is often expensive and laborious. Meanwhile, recent studies have shown the transfer learning (TL) paradigm as an attractive choice in providing promising solutions to challenges of shortage in the availability of labeled medical images. Accordingly, TL enables us to leverage the knowledge learned from related data to solve a new problem. The objective of this dissertation is to examine the effectiveness of TL systems on medical images. First, a comprehensive systematic literature review was performed to provide an up-to-date status of TL systems on medical images. Specifically, we proposed a novel conceptual framework to organize the review. Second, a novel DL network was pretrained on natural images and utilized to evaluate the effectiveness of TL on a very large medical image dataset, specifically Chest X-rays images. Lastly, domain adaptation using an autoencoder was evaluated on the medical image dataset and the results confirmed the effectiveness of TL through fine-tuning strategies. We make several contributions to TL systems on medical image analysis: Firstly, we present a novel survey of TL on medical images and propose a new conceptual framework to organize the findings. Secondly, we propose a novel DL architecture to improve learned representations of medical images while mitigating the problem of vanishing gradients. Additionally, we identified the optimal cut-off layer (OCL) that provided the best model performance. We found that the higher layers in the proposed deep model give a better feature representation of our medical image task. Finally, we analyzed the effect of domain adaptation by fine-tuning an autoencoder on our medical images and provide theoretical contributions on the application of the transductive TL approach. The contributions herein reveal several research gaps to motivate future research and contribute to the body of literature in this active research area of TL systems on medical image analysis

Deep Learning for 2D and 3D Scene Understanding

This thesis comprises a body of work that investigates the use of deep learning for 2D and 3D scene understanding. Although there has been significant progress made in computer vision using deep learning, a lot of that progress has been relative to performance benchmarks, and for static images; it is common to find that good performance on one benchmark does not necessarily mean good generalization to the kind of viewing conditions that might be encountered by an autonomous robot or agent. In this thesis, we address a variety of problems motivated by the desire to see deep learning algorithms generalize better to robotic vision scenarios. Specifically, we span topics of multi-object detection, unsupervised domain adaptation for semantic segmentation, video object segmentation, and semantic scene completion. First, most modern object detectors use a final post-processing step known as Non-maximum suppression (GreedyNMS). This suffers an inevitable trade-off between precision and recall in crowded scenes. To overcome this limitation, we propose a Pairwise-NMS to cure GreedyNMS. Specifically, a pairwise-relationship network that is based on deep learning is learned to predict if two overlapping proposal boxes contain two objects or zero/one object, which can handle multiple overlapping objects effectively. A common issue in training deep neural networks is the need for large training sets. One approach to this is to use simulated image and video data, but this suffers from a domain gap wherein the performance on real-world data is poor relative to performance on the simulation data. We target a few approaches to addressing so-called domain adaptation for semantic segmentation: (1) Single and multi-exemplars are employed for each class in order to cluster the per-pixel features in the embedding space; (2) Class-balanced self-training strategy is utilized for generating pseudo labels in the target domain; (3) Moreover, a convolutional adaptor is adopted to enforce the features in the source domain and target domain are closed with each other. Next, we tackle the video object segmentation by formulating it as a meta-learning problem, where the base learner aims to learn semantic scene understanding for general objects, and the meta learner quickly adapts the appearance of the target object with a few examples. Our proposed meta-learning method uses a closed-form optimizer, the so-called \ridge regression", which is conducive to fast and better training convergence. One-shot video object segmentation (OSVOS) has the limitation to \overemphasize" the generic semantic object information while \diluting" the instance cues of the object(s), which largely block the whole training process. Through adding a common module, video loss, which we formulate with various forms of constraints (including weighted BCE loss, high-dimensional triplet loss, as well as a novel mixed instance-aware video loss), to train the parent network, the network is then better prepared for the online fine-tuning. Next, we introduce a light-weight Dimensional Decomposition Residual network (DDR) for 3D dense prediction tasks. The novel factorized convolution layer is effective for reducing the network parameters, and the proposed multi-scale fusion mechanism for depth and color image can improve the completion and segmentation accuracy simultaneously. Moreover, we propose PALNet, a novel hybrid network for Semantic Scene Completion(SSC) based on single depth. PALNet utilizes a two-stream network to extract both 2D and 3D features from multi-stages using fine-grained depth information to eficiently capture the context, as well as the geometric cues of the scene. Position Aware Loss (PA-Loss) considers Local Geometric Anisotropy to determine the importance of different positions within the scene. It is beneficial for recovering key details like the boundaries of objects and the corners of the scene. Finally, we propose a 3D gated recurrent fusion network (GRFNet), which learns to adaptively select and fuse the relevant information from depth and RGB by making use of the gate and memory modules. Based on the single-stage fusion, we further propose a multi-stage fusion strategy, which could model the correlations among different stages within the network.Thesis (Ph.D.) -- University of Adelaide, School of Computer Science, 202

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.