Machine Learning in Medical Image Analysis

Machine learning is playing a pivotal role in medical image analysis. Many algorithms based on machine learning have been applied in medical imaging to solve classification, detection, and segmentation problems. Particularly, with the wide application of deep learning approaches, the performance of medical image analysis has been significantly improved. In this thesis, we investigate machine learning methods for two key challenges in medical image analysis: The first one is segmentation of medical images. The second one is learning with weak supervision in the context of medical imaging. The first main contribution of the thesis is a series of novel approaches for image segmentation. First, we propose a framework based on multi-scale image patches and random forests to segment small vessel disease (SVD) lesions on computed tomography (CT) images. This framework is validated in terms of spatial similarity, estimated lesion volumes, visual score ratings and was compared with human experts. The results showed that the proposed framework performs as well as human experts. Second, we propose a generic convolutional neural network (CNN) architecture called the DRINet for medical image segmentation. The DRINet approach is robust in three different types of segmentation tasks, which are multi-class cerebrospinal fluid (CSF) segmentation on brain CT images, multi-organ segmentation on abdomen CT images, and multi-class tumour segmentation on brain magnetic resonance (MR) images. Finally, we propose a CNN-based framework to segment acute ischemic lesions on diffusion weighted (DW)-MR images, where the lesions are highly variable in terms of position, shape, and size. Promising results were achieved on a large clinical dataset. The second main contribution of the thesis is two novel strategies for learning with weak supervision. First, we propose a novel strategy called context restoration to make use of the images without annotations. The context restoration strategy is a proxy learning process based on the CNN, which extracts semantic features from images without using annotations. It was validated on classification, localization, and segmentation problems and was superior to existing strategies. Second, we propose a patch-based framework using multi-instance learning to distinguish normal and abnormal SVD on CT images, where there are only coarse-grained labels available. Our framework was observed to work better than classic methods and clinical practice.Open Acces

ORGAN LOCALIZATION AND DETECTION IN SOW’S USING MACHINE LEARNING AND DEEP LEARNING IN COMPUTER VISION

The objective of computer vision research is to endow computers with human-like perception to enable the capability to detect their surroundings, interpret the data they sense, take appropriate actions, and learn from their experiences to improve future performance. The area has progressed from using traditional pattern recognition and image processing technologies to advanced techniques in image understanding such as model-based and knowledge-based vision. In the past few years there has been a surge of interest in machine learning algorithms for computer vision-based applications. Machine learning technology has the potential to significantly contribute to the development of flexible and robust vision algorithms that will improve the performance of practical vision systems with a higher level of competence and greater generality. Additionally, the development of machine learning-based architectures has the potential to reduce system development time while simultaneously achieving the above-stated performance improvements. This work proposes the utilization of a computer vision-based approach that leverages machine and deep learning systems to aid the detection and identification of sow reproduction cycles by segmentation and object detection techniques. A lightweight machine learning system is proposed for object detection to address dataset collection issues in one of the most crucial and potentially lucrative farming applications. This technique was designed to detect the vulvae region in pre-estrous sows using a single thermal image. In the first experiment, the support vector machine (SVM) classifier was used after extracting features determined by 12 Gabor filters. The features are then concatenated with the features obtained from the Histogram of oriented gradients (HOG) to produce the results of the first experiment. In the second experiment, the number of distinct Gabor filters used was increased from 12 to 96. The system is trained on cropped image windows and uses the Gaussian pyramid technique to look for the vulva in the input image. The resulting process is shown to be lightweight, simple, and robust when applied to and evaluated on a large number of images. The results from extensive qualitative and quantitative testing experiments are included. The experimental results include false detection, missing detection and favorable detection rates. The results indicate state-of-the-art accuracy. Additionally, the project was expanded by utilizing the You Only Look Once (YOLO) deep learning Object Detection models for fast object detection. The results from object detection have been used to label images for segmentation. The bounding box from the detected area was systematically colored to achieve the segmented and labeled images. Then these segmented images are used as custom data to train U-Net segmentation. The first step involves building a machine learning model using Gabor filters and HOG for feature extraction and SVM for classification. The results discovered the deficiency of the model, therefore a second stage was suggested in which the dataset was trained using YOLOv3-dependent deep learning object detection. The resulting segmentation model is found to be the best choice to aid the process of vulva localization. Since the model depends on the original gray-scale image and the mask of the region of interest (ROI), a custom dataset containing these features was obtained, augmented, and used to train a U-Net segmentation model. The results of the final approach shows that the proposed system can segment sow\u27s vulva region even in low rank images and has an excellent performance efficiency. Furthermore, the resulting algorithm can be used to improve the automation of estrous detection by providing reliable ROI identification and segmentation and enabling beneficial temporal change detection and tracking in future efforts

Measuring uncertainty in human visual segmentation

Segmenting visual stimuli into distinct groups of features and visual objects is central to visual function. Classical psychophysical methods have helped uncover many rules of human perceptual segmentation, and recent progress in machine learning has produced successful algorithms. Yet, the computational logic of human segmentation remains unclear, partially because we lack well-controlled paradigms to measure perceptual segmentation maps and compare models quantitatively. Here we propose a new, integrated approach: given an image, we measure multiple pixel-based same--different judgments and perform model--based reconstruction of the underlying segmentation map. The reconstruction is robust to several experimental manipulations and captures the variability of individual participants. We demonstrate the validity of the approach on human segmentation of natural images and composite textures. We show that image uncertainty affects measured human variability, and it influences how participants weigh different visual features. Because any putative segmentation algorithm can be inserted to perform the reconstruction, our paradigm affords quantitative tests of theories of perception as well as new benchmarks for segmentation algorithms.Comment: 27 pages, 9 figures, 4 appendix, 3 figures in appendi

Morphological segmentation analysis and texture-based support vector machines classification on mice liver fibrosis microscopic images

Background To reduce the intensity of the work of doctors, pre-classification work needs to be issued. In this paper, a novel and related liver microscopic image classification analysis method is proposed. Objective For quantitative analysis, segmentation is carried out to extract the quantitative information of special organisms in the image for further diagnosis, lesion localization, learning and treating anatomical abnormalities and computer-guided surgery. Methods in the current work, entropy based features of microscopic fibrosis mice’ liver images were analyzed using fuzzy c-cluster, k-means and watershed algorithms based on distance transformations and gradient. A morphological segmentation based on a local threshold was deployed to determine the fibrosis areas of images. Results the segmented target region using the proposed method achieved high effective microscopy fibrosis images segmenting of mice liver in terms of the running time, dice ratio and precision. The image classification experiments were conducted using Gray Level Co-occurrence Matrix (GLCM). The best classification model derived from the established characteristics was GLCM which performed the highest accuracy of classification using a developed Support Vector Machine (SVM). The training model using 11 features was found to be as accurate when only trained by 8 GLCMs. Conclusion The research illustrated the proposed method is a new feasible research approach for microscopy mice liver image segmentation and classification using intelligent image analysis techniques. It is also reported that the average computational time of the proposed approach was only 2.335 seconds, which outperformed other segmentation algorithms with 0.8125 dice ratio and 0.5253 precision

Probabilistic framework for image understanding applications using Bayesian Networks

Machine learning algorithms have been successfully utilized in various systems/devices. They have the ability to improve the usability/quality of such systems in terms of intelligent user interface, fast performance, and more importantly, high accuracy. In this research, machine learning techniques are used in the field of image understanding, which is a common research area between image analysis and computer vision, to involve higher processing level of a target image to make sense of the scene captured in it. A general probabilistic framework for image understanding where topics associated with (i) collection of images to generate a comprehensive and valid database, (ii) generation of an unbiased ground-truth for the aforesaid database, (iii) selection of classification features and elimination of the redundant ones, and (iv) usage of such information to test a new sample set, are discussed. Two research projects have been developed as examples of the general image understanding framework; identification of region(s) of interest, and image segmentation evaluation. These techniques, in addition to others, are combined in an object-oriented rendering system for printing applications. The discussion included in this doctoral dissertation explores the means for developing such a system from an image understanding/ processing aspect. It is worth noticing that this work does not aim to develop a printing system. It is only proposed to add some essential features for current printing pipelines to achieve better visual quality while printing images/photos. Hence, we assume that image regions have been successfully extracted from the printed document. These images are used as input to the proposed object-oriented rendering algorithm where methodologies for color image segmentation, region-of-interest identification and semantic features extraction are employed. Probabilistic approaches based on Bayesian statistics have been utilized to develop the proposed image understanding techniques

Diff-CAPTCHA: An Image-based CAPTCHA with Security Enhanced by Denoising Diffusion Model

To enhance the security of text CAPTCHAs, various methods have been employed, such as adding the interference lines on the text, randomly distorting the characters, and overlapping multiple characters. These methods partly increase the difficulty of automated segmentation and recognition attacks. However, facing the rapid development of the end-to-end breaking algorithms, their security has been greatly weakened. The diffusion model is a novel image generation model that can generate the text images with deep fusion of characters and background images. In this paper, an image-click CAPTCHA scheme called Diff-CAPTCHA is proposed based on denoising diffusion models. The background image and characters of the CAPTCHA are treated as a whole to guide the generation process of a diffusion model, thus weakening the character features available for machine learning, enhancing the diversity of character features in the CAPTCHA, and increasing the difficulty of breaking algorithms. To evaluate the security of Diff-CAPTCHA, this paper develops several attack methods, including end-to-end attacks based on Faster R-CNN and two-stage attacks, and Diff-CAPTCHA is compared with three baseline schemes, including commercial CAPTCHA scheme and security-enhanced CAPTCHA scheme based on style transfer. The experimental results show that diffusion models can effectively enhance CAPTCHA security while maintaining good usability in human testing