Medical image retrieval and automatic annotation: VPA-SABANCI at ImageCLEF 2009

Advances in the medical imaging technology has lead to an exponential growth in the number of digital images that needs to be acquired, analyzed, classified, stored and retrieved in medical centers. As a result, medical image classification and retrieval has recently gained high interest in the scientific community. Despite several attempts, such as the yearly-held ImageCLEF Medical Image Annotation Competition, the proposed solutions are still far from being su±ciently accurate for real-life implementations. In this paper we summarize the technical details of our experiments for the ImageCLEF 2009 medical image annotation task. We use a direct and two hierarchical classification schemes that employ support vector machines and local binary patterns, which are recently developed low-cost texture descriptors. The direct scheme employs a single SVM to automatically annotate X-ray images. The two proposed hierarchi-cal schemes divide the classification task into sub-problems. The first hierarchical scheme exploits ensemble SVMs trained on IRMA sub-codes. The second learns from subgroups of data defined by frequency of classes. Our experiments show that hier-archical annotation of images by training individual SVMs over each IRMA sub-code dominates its rivals in annotation accuracy with increased process time relative to the direct scheme

MIRACLE’s Naive Approach to Medical Images Annotation

One of the proposed tasks of the ImageCLEF 2005 campaign has been an Automatic Annotation Task. The objective is to provide the classification of a given set of 1,000 previously unseen medical (radiological) images according to 57 predefined categories covering different medical pathologies. 9,000 classified training images are given which can be used in any way to train a classifier. The Automatic Annotation task uses no textual information, but image-content information only. This paper describes our participation in the automatic annotation task of ImageCLEF 2005

Task Decomposition and Synchronization for Semantic Biomedical Image Segmentation

Semantic segmentation is essentially important to biomedical image analysis. Many recent works mainly focus on integrating the Fully Convolutional Network (FCN) architecture with sophisticated convolution implementation and deep supervision. In this paper, we propose to decompose the single segmentation task into three subsequent sub-tasks, including (1) pixel-wise image segmentation, (2) prediction of the class labels of the objects within the image, and (3) classification of the scene the image belonging to. While these three sub-tasks are trained to optimize their individual loss functions of different perceptual levels, we propose to let them interact by the task-task context ensemble. Moreover, we propose a novel sync-regularization to penalize the deviation between the outputs of the pixel-wise segmentation and the class prediction tasks. These effective regularizations help FCN utilize context information comprehensively and attain accurate semantic segmentation, even though the number of the images for training may be limited in many biomedical applications. We have successfully applied our framework to three diverse 2D/3D medical image datasets, including Robotic Scene Segmentation Challenge 18 (ROBOT18), Brain Tumor Segmentation Challenge 18 (BRATS18), and Retinal Fundus Glaucoma Challenge (REFUGE18). We have achieved top-tier performance in all three challenges.Comment: IEEE Transactions on Medical Imagin

From Fully-Supervised, Single-Task to Scarcely-Supervised, Multi-Task Deep Learning for Medical Image Analysis

Image analysis based on machine learning has gained prominence with the advent of deep learning, particularly in medical imaging. To be effective in addressing challenging image analysis tasks, however, conventional deep neural networks require large corpora of annotated training data, which are unfortunately scarce in the medical domain, thus often rendering fully-supervised learning strategies ineffective.This thesis devises for use in a variety of medical image analysis applications a series of novel deep learning methods, ranging from fully-supervised, single-task learning to scarcely-supervised, multi-task learning that makes efficient use of annotated training data. Specifically, its main contributions include (1) fully-supervised, single-task learning for the segmentation of pulmonary lobes from chest CT scans and the analysis of scoliosis from spine X-ray images; (2) supervised, single-task, domain-generalized pulmonary segmentation in chest X-ray images and retinal vasculature segmentation in fundoscopic images; (3) largely-unsupervised, multiple-task learning via deep generative modeling for the joint synthesis and classification of medical image data; and (4) partly-supervised, multiple-task learning for the combined segmentation and classification of chest and spine X-ray images

Serial dependence in a simulated clinical visual search task.

In everyday life, we continuously search for and classify objects in the environment around us. This kind of visual search is extremely important when performed by radiologists in cancer image interpretation and officers in airport security screening. During these tasks, observers often examine large numbers of uncorrelated images (tumor x-rays, checkpoint x-rays, etc.) one after another. An underlying assumption of such tasks is that search and recognition are independent of our past experience. Here, we simulated a visual search task reminiscent of medical image search and found that shape classification performance was strongly impaired by recent visual experience, biasing classification errors 7% more towards the previous image content. This perceptual attraction exhibited the three main tuning characteristics of Continuity Fields: serial dependence extended over 12 seconds back in time (temporal tuning), it occurred only between similar tumor-like shapes (feature tuning), and only within a limited spatial region (spatial tuning). Taken together, these results demonstrate that serial dependence influences shape perception and occurs in visual search tasks. They also raise the possibility of a detrimental impact of serial dependence in clinical and practically relevant settings, such as medical image perception