Advanced Deep Learning for Medical Image Analysis

The application of deep learning is evolving, including in expert systems for healthcare, such as disease classification. Several challenges in the use of deep-learning algorithms in application to disease classification. The study aims to improve classification to address the problem. The thesis proposes a cost-sensitive imbalance training algorithm to address an unequal number of training examples, a two-stage Bayesian optimisation training algorithm and a dual-branch network to train a one-class classification scheme, further improving classification performance

Integrated Chest Image Analysis System "BU-MIA"

We introduce "BU-MIA," a Medical Image Analysis system that integrates various advanced chest image analysis methods for detection, estimation, segmentation, and registration. BU-MIA evaluates repeated computed tomography (CT) scans of the same patient to facilitate identification and evaluation of pulmonary nodules for interval growth. It provides a user-friendly graphical user interface with a number of interaction tools for development, evaluation, and validation of chest image analysis methods. The structures that BU-MIA processes include the thorax, lungs, and trachea, pulmonary structures, such as lobes, fissures, nodules, and vessels, and bones, such as sternum, vertebrae, and ribs

Parameter-efficient fine-tuning for medical image analysis:The missed opportunity

Foundation models have significantly advanced medical image analysis through the pre-train fine-tune paradigm. Among various fine-tuning algorithms, Parameter-Efficient Fine-Tuning (PEFT) is increasingly utilized for knowledge transfer across diverse tasks, including vision-language and text-to-image generation. However, its application in medical image analysis is relatively unexplored due to the lack of a structured benchmark for evaluating PEFT methods. This study fills this gap by evaluating 17 distinct PEFT algorithms across convolutional and transformer-based networks on image classification and text-to-image generation tasks using six medical datasets of varying size, modality, and complexity. Through a battery of over 700 controlled experiments, our findings demonstrate PEFT's effectiveness, particularly in low data regimes common in medical imaging, with performance gains of up to 22% in discriminative and generative tasks. These recommendations can assist the community in incorporating PEFT into their workflows and facilitate fair comparisons of future PEFT methods, ensuring alignment with advancements in other areas of machine learning and AI

Data efficient deep learning for medical image analysis: A survey

The rapid evolution of deep learning has significantly advanced the field of medical image analysis. However, despite these achievements, the further enhancement of deep learning models for medical image analysis faces a significant challenge due to the scarcity of large, well-annotated datasets. To address this issue, recent years have witnessed a growing emphasis on the development of data-efficient deep learning methods. This paper conducts a thorough review of data-efficient deep learning methods for medical image analysis. To this end, we categorize these methods based on the level of supervision they rely on, encompassing categories such as no supervision, inexact supervision, incomplete supervision, inaccurate supervision, and only limited supervision. We further divide these categories into finer subcategories. For example, we categorize inexact supervision into multiple instance learning and learning with weak annotations. Similarly, we categorize incomplete supervision into semi-supervised learning, active learning, and domain-adaptive learning and so on. Furthermore, we systematically summarize commonly used datasets for data efficient deep learning in medical image analysis and investigate future research directions to conclude this survey.Comment: Under Revie

Attention Mechanisms in Medical Image Segmentation: A Survey

Medical image segmentation plays an important role in computer-aided diagnosis. Attention mechanisms that distinguish important parts from irrelevant parts have been widely used in medical image segmentation tasks. This paper systematically reviews the basic principles of attention mechanisms and their applications in medical image segmentation. First, we review the basic concepts of attention mechanism and formulation. Second, we surveyed over 300 articles related to medical image segmentation, and divided them into two groups based on their attention mechanisms, non-Transformer attention and Transformer attention. In each group, we deeply analyze the attention mechanisms from three aspects based on the current literature work, i.e., the principle of the mechanism (what to use), implementation methods (how to use), and application tasks (where to use). We also thoroughly analyzed the advantages and limitations of their applications to different tasks. Finally, we summarize the current state of research and shortcomings in the field, and discuss the potential challenges in the future, including task specificity, robustness, standard evaluation, etc. We hope that this review can showcase the overall research context of traditional and Transformer attention methods, provide a clear reference for subsequent research, and inspire more advanced attention research, not only in medical image segmentation, but also in other image analysis scenarios.Comment: Submitted to Medical Image Analysis, survey paper, 34 pages, over 300 reference