arXiv subjects

Jong Chul Ye

Publications and source records attributed to Jong Chul Ye.

At least 217 records · Page 12Linked to original sources

arXiv2020

Unpaired Deep Learning for Accelerated MRI using Optimal Transport Driven CycleGAN

Recently, deep learning approaches for accelerated MRI have been extensively studied thanks to their high performance reconstruction in spite of significantly reduced runtime complexity. These neural networks are usually trained in a supervised manner, so matched pairs of subsampled and fully sampled k-space data are required. Unfortunately, it is often difficult to acquire matched fully sampled k-space data, since the acquisition of fully sampled k-space data requires long scan time and often leads to the change of the acquisition protocol. Therefore, unpaired deep learning without matched label data has become a very important research topic. In this paper, we propose an unpaired deep learning approach using a optimal transport driven cycle-consistent generative adversarial network (OT-cycleGAN) that employs a single pair of generator and discriminator. The proposed OT-cycleGAN architecture is rigorously derived from a dual formulation of the optimal transport formulation using a specially designed penalized least squares cost. The experimental results show that our method can reconstruct high resolution MR images from accelerated k- space data from both single and multiple coil acquisition, without requiring matched reference data.

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arXiv2020

AdaIN-Switchable CycleGAN for Efficient Unsupervised Low-Dose CT Denoising

Recently, deep learning approaches have been extensively studied for low-dose CT denoising thanks to its superior performance despite the fast computational time. In particular, cycleGAN has been demonstrated as a powerful unsupervised learning scheme to improve the low-dose CT image quality without requiring matched high-dose reference data. Unfortunately, one of the main limitations of the cycleGAN approach is that it requires two deep neural network generators at the training phase, although only one of them is used at the inference phase. The secondary auxiliary generator is needed to enforce the cycle-consistency, but the additional memory requirement and increases of the learnable parameters are the main huddles for cycleGAN training. To address this issue, here we propose a novel cycleGAN architecture using a single switchable generator. In particular, a single generator is implemented using adaptive instance normalization (AdaIN) layers so that the baseline generator converting a low-dose CT image to a routine-dose CT image can be switched to a generator converting high-dose to low-dose by simply changing the AdaIN code. Thanks to the shared baseline network, the additional memory requirement and weight increases are minimized, and the training can be done more stably even with small training data. Experimental results show that the proposed method outperforms the previous cycleGAN approaches while using only about half the parameters.

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arXiv2020

CycleMorph: Cycle Consistent Unsupervised Deformable Image Registration

Image registration is a fundamental task in medical image analysis. Recently, deep learning based image registration methods have been extensively investigated due to their excellent performance despite the ultra-fast computational time. However, the existing deep learning methods still have limitation in the preservation of original topology during the deformation with registration vector fields. To address this issues, here we present a cycle-consistent deformable image registration. The cycle consistency enhances image registration performance by providing an implicit regularization to preserve topology during the deformation. The proposed method is so flexible that can be applied for both 2D and 3D registration problems for various applications, and can be easily extended to multi-scale implementation to deal with the memory issues in large volume registration. Experimental results on various datasets from medical and non-medical applications demonstrate that the proposed method provides effective and accurate registration on diverse image pairs within a few seconds. Qualitative and quantitative evaluations on deformation fields also verify the effectiveness of the cycle consistency of the proposed method.

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arXiv2020

Two-Stage Deep Learning for Accelerated 3D Time-of-Flight MRA without Matched Training Data

Time-of-flight magnetic resonance angiography (TOF-MRA) is one of the most widely used non-contrast MR imaging methods to visualize blood vessels, but due to the 3-D volume acquisition highly accelerated acquisition is necessary. Accordingly, high quality reconstruction from undersampled TOF-MRA is an important research topic for deep learning. However, most existing deep learning works require matched reference data for supervised training, which are often difficult to obtain. By extending the recent theoretical understanding of cycleGAN from the optimal transport theory, here we propose a novel two-stage unsupervised deep learning approach, which is composed of the multi-coil reconstruction network along the coronal plane followed by a multi-planar refinement network along the axial plane. Specifically, the first network is trained in the square-root of sum of squares (SSoS) domain to achieve high quality parallel image reconstruction, whereas the second refinement network is designed to efficiently learn the characteristics of highly-activated blood flow using double-headed max-pool discriminator. Extensive experiments demonstrate that the proposed learning process without matched reference exceeds performance of state-of-the-art compressed sensing (CS)-based method and provides comparable or even better results than supervised learning approaches.

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arXiv2020

OT-driven Multi-Domain Unsupervised Ultrasound Image Artifact Removal using a Single CNN

Ultrasound imaging (US) often suffers from distinct image artifacts from various sources. Classic approaches for solving these problems are usually model-based iterative approaches that have been developed specifically for each type of artifact, which are often computationally intensive. Recently, deep learning approaches have been proposed as computationally efficient and high performance alternatives. Unfortunately, in the current deep learning approaches, a dedicated neural network should be trained with matched training data for each specific artifact type. This poses a fundamental limitation in the practical use of deep learning for US, since large number of models should be stored to deal with various US image artifacts. Inspired by the recent success of multi-domain image transfer, here we propose a novel, unsupervised, deep learning approach in which a single neural network can be used to deal with different types of US artifacts simply by changing a mask vector that switches between different target domains. Our algorithm is rigorously derived using an optimal transport (OT) theory for cascaded probability measures. Experimental results using phantom and in vivo data demonstrate that the proposed method can generate high quality image by removing distinct artifacts, which are comparable to those obtained by separately trained multiple neural networks.

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arXiv2020

CycleGAN with a Blur Kernel for Deconvolution Microscopy: Optimal Transport Geometry

Deconvolution microscopy has been extensively used to improve the resolution of the wide-field fluorescent microscopy, but the performance of classical approaches critically depends on the accuracy of a model and optimization algorithms. Recently, the convolutional neural network (CNN) approaches have been studied as a fast and high performance alternative. Unfortunately, the CNN approaches usually require matched high resolution images for supervised training. In this paper, we present a novel unsupervised cycle-consistent generative adversarial network (cycleGAN) with a linear blur kernel, which can be used for both blind- and non-blind image deconvolution. In contrast to the conventional cycleGAN approaches that require two deep generators, the proposed cycleGAN approach needs only a single deep generator and a linear blur kernel, which significantly improves the robustness and efficiency of network training. We show that the proposed architecture is indeed a dual formulation of an optimal transport problem that uses a special form of the penalized least squares cost as a transport cost. Experimental results using simulated and real experimental data confirm the efficacy of the algorithm.

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arXiv2020

Unsupervised CT Metal Artifact Learning using Attention-guided beta-CycleGAN

Metal artifact reduction (MAR) is one of the most important research topics in computed tomography (CT). With the advance of deep learning technology for image reconstruction,various deep learning methods have been also suggested for metal artifact removal, among which supervised learning methods are most popular. However, matched non-metal and metal image pairs are difficult to obtain in real CT acquisition. Recently, a promising unsupervised learning for MAR was proposed using feature disentanglement, but the resulting network architecture is complication and difficult to handle large size clinical images. To address this, here we propose a much simpler and much effective unsupervised MAR method for CT. The proposed method is based on a novel beta-cycleGAN architecture derived from the optimal transport theory for appropriate feature space disentanglement. Another important contribution is to show that attention mechanism is the key element to effectively remove the metal artifacts. Specifically, by adding the convolutional block attention module (CBAM) layers with a proper disentanglement parameter, experimental results confirm that we can get more improved MAR that preserves the detailed texture of the original image.

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arXiv2020

Pushing the Limit of Unsupervised Learning for Ultrasound Image Artifact Removal

Ultrasound (US) imaging is a fast and non-invasive imaging modality which is widely used for real-time clinical imaging applications without concerning about radiation hazard. Unfortunately, it often suffers from poor visual quality from various origins, such as speckle noises, blurring, multi-line acquisition (MLA), limited RF channels, small number of view angles for the case of plane wave imaging, etc. Classical methods to deal with these problems include image-domain signal processing approaches using various adaptive filtering and model-based approaches. Recently, deep learning approaches have been successfully used for ultrasound imaging field. However, one of the limitations of these approaches is that paired high quality images for supervised training are difficult to obtain in many practical applications. In this paper, inspired by the recent theory of unsupervised learning using optimal transport driven cycleGAN (OT-cycleGAN), we investigate applicability of unsupervised deep learning for US artifact removal problems without matched reference data. Experimental results for various tasks such as deconvolution, speckle removal, limited data artifact removal, etc. confirmed that our unsupervised learning method provides comparable results to supervised learning for many practical applications.

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arXiv2020

Differentiated Backprojection Domain Deep Learning for Conebeam Artifact Removal

Conebeam CT using a circular trajectory is quite often used for various applications due to its relative simple geometry. For conebeam geometry, Feldkamp, Davis and Kress algorithm is regarded as the standard reconstruction method, but this algorithm suffers from so-called conebeam artifacts as the cone angle increases. Various model-based iterative reconstruction methods have been developed to reduce the cone-beam artifacts, but these algorithms usually require multiple applications of computational expensive forward and backprojections. In this paper, we develop a novel deep learning approach for accurate conebeam artifact removal. In particular, our deep network, designed on the differentiated backprojection domain, performs a data-driven inversion of an ill-posed deconvolution problem associated with the Hilbert transform. The reconstruction results along the coronal and sagittal directions are then combined using a spectral blending technique to minimize the spectral leakage. Experimental results show that our method outperforms the existing iterative methods despite significantly reduced runtime complexity.

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arXiv2020

Understanding Graph Isomorphism Network for rs-fMRI Functional Connectivity Analysis

Graph neural networks (GNN) rely on graph operations that include neural network training for various graph related tasks. Recently, several attempts have been made to apply the GNNs to functional magnetic resonance image (fMRI) data. Despite recent progresses, a common limitation is its difficulty to explain the classification results in a neuroscientifically explainable way. Here, we develop a framework for analyzing the fMRI data using the Graph Isomorphism Network (GIN), which was recently proposed as a powerful GNN for graph classification. One of the important contributions of this paper is the observation that the GIN is a dual representation of convolutional neural network (CNN) in the graph space where the shift operation is defined using the adjacency matrix. This understanding enables us to exploit CNN-based saliency map techniques for the GNN, which we tailor to the proposed GIN with one-hot encoding, to visualize the important regions of the brain. We validate our proposed framework using large-scale resting-state fMRI (rs-fMRI) data for classifying the sex of the subject based on the graph structure of the brain. The experiment was consistent with our expectation such that the obtained saliency map show high correspondence with previous neuroimaging evidences related to sex differences.

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arXiv2020

Deep Learning COVID-19 Features on CXR using Limited Training Data Sets

Under the global pandemic of COVID-19, the use of artificial intelligence to analyze chest X-ray (CXR) image for COVID-19 diagnosis and patient triage is becoming important. Unfortunately, due to the emergent nature of the COVID-19 pandemic, a systematic collection of the CXR data set for deep neural network training is difficult. To address this problem, here we propose a patch-based convolutional neural network approach with a relatively small number of trainable parameters for COVID-19 diagnosis. The proposed method is inspired by our statistical analysis of the potential imaging biomarkers of the CXR radiographs. Experimental results show that our method achieves state-of-the-art performance and provides clinically interpretable saliency maps, which are useful for COVID-19 diagnosis and patient triage.

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arXiv2020

NTIRE 2020 Challenge on Perceptual Extreme Super-Resolution: Methods and Results

This paper reviews the NTIRE 2020 challenge on perceptual extreme super-resolution with focus on proposed solutions and results. The challenge task was to super-resolve an input image with a magnification factor 16 based on a set of prior examples of low and corresponding high resolution images. The goal is to obtain a network design capable to produce high resolution results with the best perceptual quality and similar to the ground truth. The track had 280 registered participants, and 19 teams submitted the final results. They gauge the state-of-the-art in single image super-resolution.

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arXiv2020

Unsupervised Deep Learning for MR Angiography with Flexible Temporal Resolution

Time-resolved MR angiography (tMRA) has been widely used for dynamic contrast enhanced MRI (DCE-MRI) due to its highly accelerated acquisition. In tMRA, the periphery of the k-space data are sparsely sampled so that neighbouring frames can be merged to construct one temporal frame. However, this view-sharing scheme fundamentally limits the temporal resolution, and it is not possible to change the view-sharing number to achieve different spatio-temporal resolution trade-off. Although many deep learning approaches have been recently proposed for MR reconstruction from sparse samples, the existing approaches usually require matched fully sampled k-space reference data for supervised training, which is not suitable for tMRA. This is because high spatio-temporal resolution ground-truth images are not available for tMRA. To address this problem, here we propose a novel unsupervised deep learning using optimal transport driven cycle-consistent generative adversarial network (cycleGAN). In contrast to the conventional cycleGAN with two pairs of generator and discriminator, the new architecture requires just a single pair of generator and discriminator, which makes the training much simpler and improves the performance. Reconstruction results using in vivo tMRA data set confirm that the proposed method can immediately generate high quality reconstruction results at various choices of view-sharing numbers, allowing us to exploit better trade-off between spatial and temporal resolution in time-resolved MR angiography.

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arXiv2020

Geometric Approaches to Increase the Expressivity of Deep Neural Networks for MR Reconstruction

Recently, deep learning approaches have been extensively investigated to reconstruct images from accelerated magnetic resonance image (MRI) acquisition. Although these approaches provide significant performance gain compared to compressed sensing MRI (CS-MRI), it is not clear how to choose a suitable network architecture to balance the trade-off between network complexity and performance. Recently, it was shown that an encoder-decoder convolutional neural network (CNN) can be interpreted as a piecewise linear basis-like representation, whose specific representation is determined by the ReLU activation patterns for a given input image. Thus, the expressivity or the representation power is determined by the number of piecewise linear regions. As an extension of this geometric understanding, this paper proposes a systematic geometric approach using bootstrapping and subnetwork aggregation using an attention module to increase the expressivity of the underlying neural network. Our method can be implemented in both k-space domain and image domain that can be trained in an end-to-end manner. Experimental results show that the proposed schemes significantly improve reconstruction performance with negligible complexity increases.

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arXiv2020

Adaptive and Compressive Beamforming Using Deep Learning for Medical Ultrasound

In ultrasound (US) imaging, various types of adaptive beamforming techniques have been investigated to improve the resolution and contrast-to-noise ratio of the delay and sum (DAS) beamformers. Unfortunately, the performance of these adaptive beamforming approaches degrade when the underlying model is not sufficiently accurate and the number of channels decreases. To address this problem, here we propose a deep learning-based beamformer to generate significantly improved images over widely varying measurement conditions and channel subsampling patterns. In particular, our deep neural network is designed to directly process full or sub-sampled radio-frequency (RF) data acquired at various subsampling rates and detector configurations so that it can generate high quality ultrasound images using a single beamformer. The origin of such input-dependent adaptivity is also theoretically analyzed. Experimental results using B-mode focused ultrasound confirm the efficacy of the proposed methods.

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arXiv2020

Unsupervised Denoising for Satellite Imagery using Wavelet Subband CycleGAN

Multi-spectral satellite imaging sensors acquire various spectral band images such as red (R), green (G), blue (B), near-infrared (N), etc. Thanks to the unique spectroscopic property of each spectral band with respective to the objects on the ground, multi-spectral satellite imagery can be used for various geological survey applications. Unfortunately, image artifacts from imaging sensor noises often affect the quality of scenes and have negative impacts on the applications of satellite imagery. Recently, deep learning approaches have been extensively explored for the removal of noises in satellite imagery. Most deep learning denoising methods, however, follow a supervised learning scheme, which requires matched noisy image and clean image pairs that are difficult to collect in real situations. In this paper, we propose a novel unsupervised multispectral denoising method for satellite imagery using wavelet subband cycle-consistent adversarial network (WavCycleGAN). The proposed method is based on unsupervised learning scheme using adversarial loss and cycle-consistency loss to overcome the lack of paired data. Moreover, in contrast to the standard image domain cycleGAN, we introduce a wavelet subband domain learning scheme for effective denoising without sacrificing high frequency components such as edges and detail information. Experimental results for the removal of vertical stripe and wave noises in satellite imaging sensors demonstrate that the proposed method effectively removes noises and preserves important high frequency features of satellite images.

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arXiv2019

Structured Low-Rank Algorithms: Theory, MR Applications, and Links to Machine Learning

In this survey, we provide a detailed review of recent advances in the recovery of continuous domain multidimensional signals from their few non-uniform (multichannel) measurements using structured low-rank matrix completion formulation. This framework is centered on the fundamental duality between the compactness (e.g., sparsity) of the continuous signal and the rank of a structured matrix, whose entries are functions of the signal. This property enables the reformulation of the signal recovery as a low-rank structured matrix completion, which comes with performance guarantees. We will also review fast algorithms that are comparable in complexity to current compressed sensing methods, which enables the application of the framework to large-scale magnetic resonance (MR) recovery problems. The remarkable flexibility of the formulation can be used to exploit signal properties that are difficult to capture by current sparse and low-rank optimization strategies. We demonstrate the utility of the framework in a wide range of MR imaging (MRI) applications, including highly accelerated imaging, calibration-free acquisition, MR artifact correction, and ungated dynamic MRI.

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arXiv2019

Mumford-Shah Loss Functional for Image Segmentation with Deep Learning

Recent state-of-the-art image segmentation algorithms are mostly based on deep neural networks, thanks to their high performance and fast computation time. However, these methods are usually trained in a supervised manner, which requires large number of high quality ground-truth segmentation masks. On the other hand, classical image segmentation approaches such as level-set methods are formulated in a self-supervised manner by minimizing energy functions such as Mumford-Shah functional, so they are still useful to help generation of segmentation masks without labels. Unfortunately, these algorithms are usually computationally expensive and often have limitation in semantic segmentation. In this paper, we propose a novel loss function based on Mumford-Shah functional that can be used in deep-learning based image segmentation without or with small labeled data. This loss function is based on the observation that the softmax layer of deep neural networks has striking similarity to the characteristic function in the Mumford-Shah functional. We show that the new loss function enables semi-supervised and unsupervised segmentation. In addition, our loss function can be also used as a regularized function to enhance supervised semantic segmentation algorithms. Experimental results on multiple datasets demonstrate the effectiveness of the proposed method.

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