Most of the Deep Neural Networks (DNNs) based CT image denoising literature shows that DNNs outperform traditional iterative methods in terms of metrics such as the RMSE, the PSNR and the SSIM. In many instances, using the same metrics, the DNN results from low-dose inputs are also shown to be comparable to their high-dose counterparts. However, these metrics do not reveal if the DNN results preserve the visibility of subtle lesions or if they alter the CT image properties such as the noise texture. Accordingly, in this work, we seek to examine the image quality of the DNN results from a holistic viewpoint for low-dose CT image denoising. First, we build a library of advanced DNN denoising architectures. This library is comprised of denoising architectures such as the DnCNN, U-Net, Red-Net, GAN, etc. Next, each network is modeled, as well as trained, such that it yields its best performance in terms of the PSNR and SSIM. As such, data inputs (e.g. training patch-size, reconstruction kernel) and numeric-optimizer inputs (e.g. minibatch size, learning rate, loss function) are accordingly tuned. Finally, outputs from thus trained networks are further subjected to a series of CT bench testing metrics such as the contrast-dependent MTF, the NPS and the HU accuracy. These metrics are employed to perform a more nuanced study of the resolution of the DNN outputs' low-contrast features, their noise textures, and their CT number accuracy to better understand the impact each DNN algorithm has on these underlying attributes of image quality.
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X-ray computed tomographic infrastructures are medical imaging modalities that rely on the acquisition of rays crossing examined objects while measuring their intensity decrease. Physical measurements are post-processed by mathematical reconstruction algorithms that may offer weaker or top-notch consistency guarantees on the computed volumetric field. Superior results are provided on the account of an abundance of low-noise measurements being supplied. Nonetheless, such a scanning process would expose the examined body to an undesirably large-intensity and long-lasting ionising radiation, imposing severe health risks. One main objective of the ongoing research is the reduction of the number of projections while keeping the quality performance stable. Due to the under-sampling, the noise occurring inherently because of photon-electron interactions is now supplemented by reconstruction artifacts. Recently, deep learning methods, especially fully convolutional networks have been extensively investigated and proven to be efficient in filtering such deviations. In this report algorithms are presented that take as input a slice of a low-quality reconstruction of the volume in question and aim to map it to the reconstruction that is considered ideal, the ground truth. Above that, the first system comprises two additional elements: firstly, it ensures the consistency with the measured sinogram, secondly it adheres to constraints proposed in classical compressive sampling theory. The second one, inspired by classical ways of solving the inverse problem of reconstruction, takes an iterative approach to regularise the hypothesis in the direction of the correct result.
With the rapid development of additive manufacturing, microstructures are attracting both academic and industrial interests. As an efficient way of analyzing the mechanical behaviors of microstructures, the homogenization method has been well studied in the literature. However, the classic homogenization method still faces challenges. Its computational cost is high for topological optimization that requires highly repeated calculation. The computation is more expensive when the microstructure is deformed from a regular cubic, causing changes for the virtual homogeneous material properties. To conquer this problem, we introduce a fine-designed 3D convolutional neural network (CNN), named DH-Net, to predict the homogenized properties of deformed microstructures. The novelty of DH-Net is that it predicts the local displacement rather than the homogenized properties. The macroscopic strains are considered as a constant in the loss function based on minimum potential energy. Thus DH-Net is label-free and more computation efficient than existing deep learning methods with the mean square loss function. We apply the shape-material transformation that a deformed microstructure with isotropic material can be bi-transformed into a regular structure with a transformed base material, such that the input with a CNN-friendly form feeds in DH-Net. DH-Net predicts homogenized properties with hundreds of acceleration compared to the standard homogenization method and even supports online computing. Moreover, it does not require a labeled dataset and thus can be much faster than current deep learning methods in training processing. DH-Net can predict both homogenized material properties and micro-mechanical properties, which is unavailable for existing DL methods. The generalization of DH-Net for different base materials and different types of microstructures is also taken into account.
Deep learning techniques have received much attention in the area of image denoising. However, there are substantial differences in the various types of deep learning methods dealing with image denoising. Specifically, discriminative learning based on deep learning can ably address the issue of Gaussian noise. Optimization models based on deep learning are effective in estimating the real noise. However, there has thus far been little related research to summarize the different deep learning techniques for image denoising. In this paper, we offer a comparative study of deep techniques in image denoising. We first classify the deep convolutional neural networks (CNNs) for additive white noisy images; the deep CNNs for real noisy images; the deep CNNs for blind denoising and the deep CNNs for hybrid noisy images, which represents the combination of noisy, blurred and low-resolution images. Then, we analyze the motivations and principles of the different types of deep learning methods. Next, we compare the state-of-the-art methods on public denoising datasets in terms of quantitative and qualitative analysis. Finally, we point out some potential challenges and directions of future research.
The rapid advancements in machine learning, graphics processing technologies and availability of medical imaging data has led to a rapid increase in use of machine learning models in the medical domain. This was exacerbated by the rapid advancements in convolutional neural network (CNN) based architectures, which were adopted by the medical imaging community to assist clinicians in disease diagnosis. Since the grand success of AlexNet in 2012, CNNs have been increasingly used in medical image analysis to improve the efficiency of human clinicians. In recent years, three-dimensional (3D) CNNs have been employed for analysis of medical images. In this paper, we trace the history of how the 3D CNN was developed from its machine learning roots, brief mathematical description of 3D CNN and the preprocessing steps required for medical images before feeding them to 3D CNNs. We review the significant research in the field of 3D medical imaging analysis using 3D CNNs (and its variants) in different medical areas such as classification, segmentation, detection, and localization. We conclude by discussing the challenges associated with the use of 3D CNNs in the medical imaging domain (and the use of deep learning models, in general) and possible future trends in the field.
Graph neural networks (GNNs) are effective machine learning models for various graph learning problems. Despite their empirical successes, the theoretical limitations of GNNs have been revealed recently. Consequently, many GNN models have been proposed to overcome these limitations. In this survey, we provide a comprehensive overview of the expressive power of GNNs and provably powerful variants of GNNs.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with arbitrary depth. Although the primitive GNNs have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on variants of graph neural networks such as graph convolutional network (GCN), graph attention network (GAT), gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.
We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to these existing approaches, while also supporting weaker supervision scenarios. Importantly, it can be trained purely from 2D images, without ground-truth pose annotations, and with a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach on synthetic data in various settings, showing that (i) it learns to disentangle shape from pose; (ii) using shading in the loss improves performance; (iii) our model is comparable or superior to state-of-the-art voxel-based approaches on quantitative metrics, while producing results that are visually more pleasing; (iv) it still performs well when given supervision weaker than in prior works.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
One of the most common tasks in medical imaging is semantic segmentation. Achieving this segmentation automatically has been an active area of research, but the task has been proven very challenging due to the large variation of anatomy across different patients. However, recent advances in deep learning have made it possible to significantly improve the performance of image recognition and semantic segmentation methods in the field of computer vision. Due to the data driven approaches of hierarchical feature learning in deep learning frameworks, these advances can be translated to medical images without much difficulty. Several variations of deep convolutional neural networks have been successfully applied to medical images. Especially fully convolutional architectures have been proven efficient for segmentation of 3D medical images. In this article, we describe how to build a 3D fully convolutional network (FCN) that can process 3D images in order to produce automatic semantic segmentations. The model is trained and evaluated on a clinical computed tomography (CT) dataset and shows state-of-the-art performance in multi-organ segmentation.
We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.
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