arXiv subjects

Jong Chul Ye

Publications and source records attributed to Jong Chul Ye.

At least 199 records · Page 11Linked to original sources

arXiv2021

Missing Cone Artifacts Removal in ODT using Unsupervised Deep Learning in Projection Domain

Optical diffraction tomography (ODT) produces three dimensional distribution of refractive index (RI) by measuring scattering fields at various angles. Although the distribution of RI index is highly informative, due to the missing cone problem stemming from the limited-angle acquisition of holograms, reconstructions have very poor resolution along axial direction compared to the horizontal imaging plane. To solve this issue, here we present a novel unsupervised deep learning framework, which learns the probability distribution of missing projection views through optimal transport driven cycleGAN. Experimental results show that missing cone artifact in ODT can be significantly resolved by the proposed method.

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arXiv2021

Federated CycleGAN for Privacy-Preserving Image-to-Image Translation

Unsupervised image-to-image translation methods such as CycleGAN learn to convert images from one domain to another using unpaired training data sets from different domains. Unfortunately, these approaches still require centrally collected unpaired records, potentially violating privacy and security issues. Although the recent federated learning (FL) allows a neural network to be trained without data exchange, the basic assumption of the FL is that all clients have their own training data from a similar domain, which is different from our image-to-image translation scenario in which each client has images from its unique domain and the goal is to learn image translation between different domains without accessing the target domain data. To address this, here we propose a novel federated CycleGAN architecture that can learn image translation in an unsupervised manner while maintaining the data privacy. Specifically, our approach arises from a novel observation that CycleGAN loss can be decomposed into the sum of client specific local objectives that can be evaluated using only their data. This local objective decomposition allows multiple clients to participate in federated CycleGAN training without sacrificing performance. Furthermore, our method employs novel switchable generator and discriminator architecture using Adaptive Instance Normalization (AdaIN) that significantly reduces the band-width requirement of the federated learning. Our experimental results on various unsupervised image translation tasks show that our federated CycleGAN provides comparable performance compared to the non-federated counterpart.

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arXiv2021

Deep learning enables reference-free isotropic super-resolution for volumetric fluorescence microscopy

Volumetric imaging by fluorescence microscopy is often limited by anisotropic spatial resolution from inferior axial resolution compared to the lateral resolution. To address this problem, here we present a deep-learning-enabled unsupervised super-resolution technique that enhances anisotropic images in volumetric fluorescence microscopy. In contrast to the existing deep learning approaches that require matched high-resolution target volume images, our method greatly reduces the effort to put into practice as the training of a network requires as little as a single 3D image stack, without a priori knowledge of the image formation process, registration of training data, or separate acquisition of target data. This is achieved based on the optimal transport driven cycle-consistent generative adversarial network that learns from an unpaired matching between high-resolution 2D images in lateral image plane and low-resolution 2D images in the other planes. Using fluorescence confocal microscopy and light-sheet microscopy, we demonstrate that the trained network not only enhances axial resolution, but also restores suppressed visual details between the imaging planes and removes imaging artifacts.

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arXiv2021

Feature Disentanglement in generating three-dimensional structure from two-dimensional slice with sliceGAN

Deep generative models are known to be able to model arbitrary probability distributions. Among these, a recent deep generative model, dubbed sliceGAN, proposed a new way of using the generative adversarial network (GAN) to capture the micro-structural characteristics of a two-dimensional (2D) slice and generate three-dimensional (3D) volumes with similar properties. While 3D micrographs are largely beneficial in simulating diverse material behavior, they are often much harder to obtain than their 2D counterparts. Hence, sliceGAN opens up many interesting directions of research by learning the representative distribution from 2D slices, and transferring the learned knowledge to generate arbitrary 3D volumes. However, one limitation of sliceGAN is that latent space steering is not possible. Hence, we combine sliceGAN with AdaIN to endow the model with the ability to disentangle the features and control the synthesis.

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arXiv2021

Simultaneous super-resolution and motion artifact removal in diffusion-weighted MRI using unsupervised deep learning

Diffusion-weighted MRI is nowadays performed routinely due to its prognostic ability, yet the quality of the scans are often unsatisfactory which can subsequently hamper the clinical utility. To overcome the limitations, here we propose a fully unsupervised quality enhancement scheme, which boosts the resolution and removes the motion artifact simultaneously. This process is done by first training the network using optimal transport driven cycleGAN with stochastic degradation block which learns to remove aliasing artifacts and enhance the resolution, then using the trained network in the test stage by utilizing bootstrap subsampling and aggregation for motion artifact suppression. We further show that we can control the trade-off between the amount of artifact correction and resolution by controlling the bootstrap subsampling ratio at the inference stage. To the best of our knowledge, the proposed method is the first to tackle super-resolution and motion artifact correction simultaneously in the context of MRI using unsupervised learning. We demonstrate the efficiency of our method by applying it to both quantitative evaluation using simulation study, and to in vivo diffusion-weighted MR scans, which shows that our method is superior to the current state-of-the-art methods. The proposed method is flexible in that it can be applied to various quality enhancement schemes in other types of MR scans, and also directly to the quality enhancement of apparent diffusion coefficient maps.

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arXiv2021

Continuous Conversion of CT Kernel using Switchable CycleGAN with AdaIN

X-ray computed tomography (CT) uses different filter kernels to highlight different structures. Since the raw sinogram data is usually removed after the reconstruction, in case there are additional need for other types of kernel images that were not previously generated, the patient may need to be scanned again. Accordingly, there exists increasing demand for post-hoc image domain conversion from one kernel to another without sacrificing the image quality. In this paper, we propose a novel unsupervised continuous kernel conversion method using cycle-consistent generative adversarial network (cycleGAN) with adaptive instance normalization (AdaIN). Even without paired training data, not only can our network translate the images between two different kernels, but it can also convert images along the interpolation path between the two kernel domains. We also show that the quality of generated images can be further improved if intermediate kernel domain images are available. Experimental results confirm that our method not only enables accurate kernel conversion that is comparable to supervised learning methods, but also generates intermediate kernel images in the unseen domain that are useful for hypopharyngeal cancer diagnosis.

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arXiv2021

Cycle-free CycleGAN using Invertible Generator for Unsupervised Low-Dose CT Denoising

Recently, CycleGAN was shown to provide high-performance, ultra-fast denoising for low-dose X-ray computed tomography (CT) without the need for a paired training dataset. Although this was possible thanks to cycle consistency, CycleGAN requires two generators and two discriminators to enforce cycle consistency, demanding significant GPU resources and technical skills for training. A recent proposal of tunable CycleGAN with Adaptive Instance Normalization (AdaIN) alleviates the problem in part by using a single generator. However, two discriminators and an additional AdaIN code generator are still required for training. To solve this problem, here we present a novel cycle-free Cycle-GAN architecture, which consists of a single generator and a discriminator but still guarantees cycle consistency. The main innovation comes from the observation that the use of an invertible generator automatically fulfills the cycle consistency condition and eliminates the additional discriminator in the CycleGAN formulation. To make the invertible generator more effective, our network is implemented in the wavelet residual domain. Extensive experiments using various levels of low-dose CT images confirm that our method can significantly improve denoising performance using only 10% of learnable parameters and faster training time compared to the conventional CycleGAN.

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arXiv2021

Vision Transformer using Low-level Chest X-ray Feature Corpus for COVID-19 Diagnosis and Severity Quantification

Developing a robust algorithm to diagnose and quantify the severity of COVID-19 using Chest X-ray (CXR) requires a large number of well-curated COVID-19 datasets, which is difficult to collect under the global COVID-19 pandemic. On the other hand, CXR data with other findings are abundant. This situation is ideally suited for the Vision Transformer (ViT) architecture, where a lot of unlabeled data can be used through structural modeling by the self-attention mechanism. However, the use of existing ViT is not optimal, since feature embedding through direct patch flattening or ResNet backbone in the standard ViT is not intended for CXR. To address this problem, here we propose a novel Vision Transformer that utilizes low-level CXR feature corpus obtained from a backbone network that extracts common CXR findings. Specifically, the backbone network is first trained with large public datasets to detect common abnormal findings such as consolidation, opacity, edema, etc. Then, the embedded features from the backbone network are used as corpora for a Transformer model for the diagnosis and the severity quantification of COVID-19. We evaluate our model on various external test datasets from totally different institutions to evaluate the generalization capability. The experimental results confirm that our model can achieve the state-of-the-art performance in both diagnosis and severity quantification tasks with superior generalization capability, which are sine qua non of widespread deployment.

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arXiv2021

PyNET-CA: Enhanced PyNET with Channel Attention for End-to-End Mobile Image Signal Processing

Reconstructing RGB image from RAW data obtained with a mobile device is related to a number of image signal processing (ISP) tasks, such as demosaicing, denoising, etc. Deep neural networks have shown promising results over hand-crafted ISP algorithms on solving these tasks separately, or even replacing the whole reconstruction process with one model. Here, we propose PyNET-CA, an end-to-end mobile ISP deep learning algorithm for RAW to RGB reconstruction. The model enhances PyNET, a recently proposed state-of-the-art model for mobile ISP, and improve its performance with channel attention and subpixel reconstruction module. We demonstrate the performance of the proposed method with comparative experiments and results from the AIM 2020 learned smartphone ISP challenge. The source code of our implementation is available at https://github.com/egyptdj/skyb-aim2020-public

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arXiv2021

Vision Transformer for COVID-19 CXR Diagnosis using Chest X-ray Feature Corpus

Under the global COVID-19 crisis, developing robust diagnosis algorithm for COVID-19 using CXR is hampered by the lack of the well-curated COVID-19 data set, although CXR data with other disease are abundant. This situation is suitable for vision transformer architecture that can exploit the abundant unlabeled data using pre-training. However, the direct use of existing vision transformer that uses the corpus generated by the ResNet is not optimal for correct feature embedding. To mitigate this problem, we propose a novel vision Transformer by using the low-level CXR feature corpus that are obtained to extract the abnormal CXR features. Specifically, the backbone network is trained using large public datasets to obtain the abnormal features in routine diagnosis such as consolidation, glass-grass opacity (GGO), etc. Then, the embedded features from the backbone network are used as corpus for vision transformer training. We examine our model on various external test datasets acquired from totally different institutions to assess the generalization ability. Our experiments demonstrate that our method achieved the state-of-art performance and has better generalization capability, which are crucial for a widespread deployment.

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arXiv2021

Severity Quantification and Lesion Localization of COVID-19 on CXR using Vision Transformer

Under the global pandemic of COVID-19, building an automated framework that quantifies the severity of COVID-19 and localizes the relevant lesion on chest X-ray images has become increasingly important. Although pixel-level lesion severity labels, e.g. lesion segmentation, can be the most excellent target to build a robust model, collecting enough data with such labels is difficult due to time and labor-intensive annotation tasks. Instead, array-based severity labeling that assigns integer scores on six subdivisions of lungs can be an alternative choice enabling the quick labeling. Several groups proposed deep learning algorithms that quantify the severity of COVID-19 using the array-based COVID-19 labels and localize the lesions with explainability maps. To further improve the accuracy and interpretability, here we propose a novel Vision Transformer tailored for both quantification of the severity and clinically applicable localization of the COVID-19 related lesions. Our model is trained in a weakly-supervised manner to generate the full probability maps from weak array-based labels. Furthermore, a novel progressive self-training method enables us to build a model with a small labeled dataset. The quantitative and qualitative analysis on the external testset demonstrates that our method shows comparable performance with radiologists for both tasks with stability in a real-world application.

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arXiv2020

CycleQSM: Unsupervised QSM Deep Learning using Physics-Informed CycleGAN

Quantitative susceptibility mapping (QSM) is a useful magnetic resonance imaging (MRI) technique which provides spatial distribution of magnetic susceptibility values of tissues. QSMs can be obtained by deconvolving the dipole kernel from phase images, but the spectral nulls in the dipole kernel make the inversion ill-posed. In recent times, deep learning approaches have shown a comparable QSM reconstruction performance as the classic approaches, despite the fast reconstruction time. Most of the existing deep learning methods are, however, based on supervised learning, so matched pairs of input phase images and the ground-truth maps are needed. Moreover, it was reported that the supervised learning often leads to underestimated QSM values. To address this, here we propose a novel unsupervised QSM deep learning method using physics-informed cycleGAN, which is derived from optimal transport perspective. In contrast to the conventional cycleGAN, our novel cycleGAN has only one generator and one discriminator thanks to the known dipole kernel. Experimental results confirm that the proposed method provides more accurate QSM maps compared to the existing deep learning approaches, and provide competitive performance to the best classical approaches despite the ultra-fast reconstruction.

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arXiv2020

DeepPhaseCut: Deep Relaxation in Phase for Unsupervised Fourier Phase Retrieval

Fourier phase retrieval is a classical problem of restoring a signal only from the measured magnitude of its Fourier transform. Although Fienup-type algorithms, which use prior knowledge in both spatial and Fourier domains, have been widely used in practice, they can often stall in local minima. Modern methods such as PhaseLift and PhaseCut may offer performance guarantees with the help of convex relaxation. However, these algorithms are usually computationally intensive for practical use. To address this problem, we propose a novel, unsupervised, feed-forward neural network for Fourier phase retrieval which enables immediate high quality reconstruction. Unlike the existing deep learning approaches that use a neural network as a regularization term or an end-to-end blackbox model for supervised training, our algorithm is a feed-forward neural network implementation of PhaseCut algorithm in an unsupervised learning framework. Specifically, our network is composed of two generators: one for the phase estimation using PhaseCut loss, followed by another generator for image reconstruction, all of which are trained simultaneously using a cycleGAN framework without matched data. The link to the classical Fienup-type algorithms and the recent symmetry-breaking learning approach is also revealed. Extensive experiments demonstrate that the proposed method outperforms all existing approaches in Fourier phase retrieval problems.

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arXiv2020

Unsupervised MR Motion Artifact Deep Learning using Outlier-Rejecting Bootstrap Aggregation

Recently, deep learning approaches for MR motion artifact correction have been extensively studied. Although these approaches have shown high performance and reduced computational complexity compared to classical methods, most of them require supervised training using paired artifact-free and artifact-corrupted images, which may prohibit its use in many important clinical applications. For example, transient severe motion (TSM) due to acute transient dyspnea in Gd-EOB-DTPA-enhanced MR is difficult to control and model for paired data generation. To address this issue, here we propose a novel unsupervised deep learning scheme through outlier-rejecting bootstrap subsampling and aggregation. This is inspired by the observation that motions usually cause sparse k-space outliers in the phase encoding direction, so k-space subsampling along the phase encoding direction can remove some outliers and the aggregation step can further improve the results from the reconstruction network. Our method does not require any paired data because the training step only requires artifact-free images. Furthermore, to address the smoothing from potential bias to the artifact-free images, the network is trained in an unsupervised manner using optimal transport driven cycleGAN. We verify that our method can be applied for artifact correction from simulated motion as well as real motion from TSM successfully, outperforming existing state-of-the-art deep learning methods.

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arXiv2020

AIM 2020 Challenge on Learned Image Signal Processing Pipeline

This paper reviews the second AIM learned ISP challenge and provides the description of the proposed solutions and results. The participating teams were solving a real-world RAW-to-RGB mapping problem, where to goal was to map the original low-quality RAW images captured by the Huawei P20 device to the same photos obtained with the Canon 5D DSLR camera. The considered task embraced a number of complex computer vision subtasks, such as image demosaicing, denoising, white balancing, color and contrast correction, demoireing, etc. The target metric used in this challenge combined fidelity scores (PSNR and SSIM) with solutions' perceptual results measured in a user study. The proposed solutions significantly improved the baseline results, defining the state-of-the-art for practical image signal processing pipeline modeling.

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arXiv2020

DeepRegularizer: Rapid Resolution Enhancement of Tomographic Imaging using Deep Learning

Optical diffraction tomography measures the three-dimensional refractive index map of a specimen and visualizes biochemical phenomena at the nanoscale in a non-destructive manner. One major drawback of optical diffraction tomography is poor axial resolution due to limited access to the three-dimensional optical transfer function. This missing cone problem has been addressed through regularization algorithms that use a priori information, such as non-negativity and sample smoothness. However, the iterative nature of these algorithms and their parameter dependency make real-time visualization impossible. In this article, we propose and experimentally demonstrate a deep neural network, which we term DeepRegularizer, that rapidly improves the resolution of a three-dimensional refractive index map. Trained with pairs of datasets (a raw refractive index tomogram and a resolution-enhanced refractive index tomogram via the iterative total variation algorithm), the three-dimensional U-net-based convolutional neural network learns a transformation between the two tomogram domains. The feasibility and generalizability of our network are demonstrated using bacterial cells and a human leukaemic cell line, and by validating the model across different samples. DeepRegularizer offers more than an order of magnitude faster regularization performance compared to the conventional iterative method. We envision that the proposed data-driven approach can bypass the high time complexity of various image reconstructions in other imaging modalities.

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arXiv2020

Switchable Deep Beamformer

Recent proposals of deep beamformers using deep neural networks have attracted significant attention as computational efficient alternatives to adaptive and compressive beamformers. Moreover, deep beamformers are versatile in that image post-processing algorithms can be combined with the beamforming. Unfortunately, in the current technology, a separate beamformer should be trained and stored for each application, demanding significant scanner resources. To address this problem, here we propose a {\em switchable} deep beamformer that can produce various types of output such as DAS, speckle removal, deconvolution, etc., using a single network with a simple switch. In particular, the switch is implemented through Adaptive Instance Normalization (AdaIN) layers, so that various output can be generated by merely changing the AdaIN code. Experimental results using B-mode focused ultrasound confirm the flexibility and efficacy of the proposed methods for various applications.

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arXiv2020

Optimal Transport driven CycleGAN for Unsupervised Learning in Inverse Problems

To improve the performance of classical generative adversarial network (GAN), Wasserstein generative adversarial networks (W-GAN) was developed as a Kantorovich dual formulation of the optimal transport (OT) problem using Wasserstein-1 distance. However, it was not clear how cycleGAN-type generative models can be derived from the optimal transport theory. Here we show that a novel cycleGAN architecture can be derived as a Kantorovich dual OT formulation if a penalized least square (PLS) cost with deep learning-based inverse path penalty is used as a transportation cost. One of the most important advantages of this formulation is that depending on the knowledge of the forward problem, distinct variations of cycleGAN architecture can be derived: for example, one with two pairs of generators and discriminators, and the other with only a single pair of generator and discriminator. Even for the two generator cases, we show that the structural knowledge of the forward operator can lead to a simpler generator architecture which significantly simplifies the neural network training. The new cycleGAN formulation, what we call the OT-cycleGAN, have been applied for various biomedical imaging problems, such as accelerated magnetic resonance imaging (MRI), super-resolution microscopy, and low-dose x-ray computed tomography (CT). Experimental results confirm the efficacy and flexibility of the theory.

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