Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Deep learning in medical imaging and radiation therapy

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/1/mp13264_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/2/mp13264.pd

Deep Semantic Segmentation of Natural and Medical Images: A Review

The semantic image segmentation task consists of classifying each pixel of an image into an instance, where each instance corresponds to a class. This task is a part of the concept of scene understanding or better explaining the global context of an image. In the medical image analysis domain, image segmentation can be used for image-guided interventions, radiotherapy, or improved radiological diagnostics. In this review, we categorize the leading deep learning-based medical and non-medical image segmentation solutions into six main groups of deep architectural, data synthesis-based, loss function-based, sequenced models, weakly supervised, and multi-task methods and provide a comprehensive review of the contributions in each of these groups. Further, for each group, we analyze each variant of these groups and discuss the limitations of the current approaches and present potential future research directions for semantic image segmentation.Comment: 45 pages, 16 figures. Accepted for publication in Springer Artificial Intelligence Revie

TS-GCN: A novel tumor segmentation method integrating transformer and GCN

As one of the critical branches of medical image processing, the task of segmentation of breast cancer tumors is of great importance for planning surgical interventions, radiotherapy and chemotherapy. Breast cancer tumor segmentation faces several challenges, including the inherent complexity and heterogeneity of breast tissue, the presence of various imaging artifacts and noise in medical images, low contrast between the tumor region and healthy tissue, and inconsistent size of the tumor region. Furthermore, the existing segmentation methods may not fully capture the rich spatial and contextual information in small-sized regions in breast images, leading to suboptimal performance. In this paper, we propose a novel breast tumor segmentation method, called the transformer and graph convolutional neural (TS-GCN) network, for medical imaging analysis. Specifically, we designed a feature aggregation network to fuse the features extracted from the transformer, GCN and convolutional neural network (CNN) networks. The CNN extract network is designed for the image's local deep feature, and the transformer and GCN networks can better capture the spatial and context dependencies among pixels in images. By leveraging the strengths of three feature extraction networks, our method achieved superior segmentation performance on the BUSI dataset and dataset B. The TS-GCN showed the best performance on several indexes, with Acc of 0.9373, Dice of 0.9058, IoU of 0.7634, F1 score of 0.9338, and AUC of 0.9692, which outperforms other state-of-the-art methods. The research of this segmentation method provides a promising future for medical image analysis and diagnosis of other diseases

Extracting structured information from 2D images

Convolutional neural networks can handle an impressive array of supervised learning tasks while relying on a single backbone architecture, suggesting that one solution fits all vision problems. But for many tasks, we can directly make use of the problem structure within neural networks to deliver more accurate predictions. In this thesis, we propose novel deep learning components that exploit the structured output space of an increasingly complex set of problems. We start from Optical Character Recognition (OCR) in natural scenes and leverage the constraints imposed by a spatial outline of letters and language requirements. Conventional OCR systems do not work well in natural scenes due to distortions, blur, or letter variability. We introduce a new attention-based model, equipped with extra information about the neuron positions to guide its focus across characters sequentially. It beats the previous state-of-the-art benchmark by a significant margin. We then turn to dense labeling tasks employing encoder-decoder architectures. We start with an experimental study that documents the drastic impact that decoder design can have on task performance. Rather than optimizing one decoder per task separately, we propose new robust layers for the upsampling of high-dimensional encodings. We show that these better suit the structured per pixel output across the board of all tasks. Finally, we turn to the problem of urban scene understanding. There is an elaborate structure in both the input space (multi-view recordings, aerial and street-view scenes) and the output space (multiple fine-grained attributes for holistic building understanding). We design new models that benefit from a relatively simple cuboidal-like geometry of buildings to create a single unified representation from multiple views. To benchmark our model, we build a new multi-view large-scale dataset of buildings images and fine-grained attributes and show systematic improvements when compared to a broad range of strong CNN-based baselines

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