arXiv subjects

Eric Z. Chen

Publications and source records attributed to Eric Z. Chen.

32 records · Page 2Linked to original sources

arXiv2022

Flow-based Visual Quality Enhancer for Super-resolution Magnetic Resonance Spectroscopic Imaging

Magnetic Resonance Spectroscopic Imaging (MRSI) is an essential tool for quantifying metabolites in the body, but the low spatial resolution limits its clinical applications. Deep learning-based super-resolution methods provided promising results for improving the spatial resolution of MRSI, but the super-resolved images are often blurry compared to the experimentally-acquired high-resolution images. Attempts have been made with the generative adversarial networks to improve the image visual quality. In this work, we consider another type of generative model, the flow-based model, of which the training is more stable and interpretable compared to the adversarial networks. Specifically, we propose a flow-based enhancer network to improve the visual quality of super-resolution MRSI. Different from previous flow-based models, our enhancer network incorporates anatomical information from additional image modalities (MRI) and uses a learnable base distribution. In addition, we impose a guide loss and a data-consistency loss to encourage the network to generate images with high visual quality while maintaining high fidelity. Experiments on a 1H-MRSI dataset acquired from 25 high-grade glioma patients indicate that our enhancer network outperforms the adversarial networks and the baseline flow-based methods. Our method also allows visual quality adjustment and uncertainty estimation.

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arXiv2022

Invertible Sharpening Network for MRI Reconstruction Enhancement

High-quality MRI reconstruction plays a critical role in clinical applications. Deep learning-based methods have achieved promising results on MRI reconstruction. However, most state-of-the-art methods were designed to optimize the evaluation metrics commonly used for natural images, such as PSNR and SSIM, whereas the visual quality is not primarily pursued. Compared to the fully-sampled images, the reconstructed images are often blurry, where high-frequency features might not be sharp enough for confident clinical diagnosis. To this end, we propose an invertible sharpening network (InvSharpNet) to improve the visual quality of MRI reconstructions. During training, unlike the traditional methods that learn to map the input data to the ground truth, InvSharpNet adapts a backward training strategy that learns a blurring transform from the ground truth (fully-sampled image) to the input data (blurry reconstruction). During inference, the learned blurring transform can be inverted to a sharpening transform leveraging the network's invertibility. The experiments on various MRI datasets demonstrate that InvSharpNet can improve reconstruction sharpness with few artifacts. The results were also evaluated by radiologists, indicating better visual quality and diagnostic confidence of our proposed method.

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arXiv2022

Pyramid Convolutional RNN for MRI Image Reconstruction

Fast and accurate MRI image reconstruction from undersampled data is crucial in clinical practice. Deep learning based reconstruction methods have shown promising advances in recent years. However, recovering fine details from undersampled data is still challenging. In this paper, we introduce a novel deep learning based method, Pyramid Convolutional RNN (PC-RNN), to reconstruct images from multiple scales. Based on the formulation of MRI reconstruction as an inverse problem, we design the PC-RNN model with three convolutional RNN (ConvRNN) modules to iteratively learn the features in multiple scales. Each ConvRNN module reconstructs images at different scales and the reconstructed images are combined by a final CNN module in a pyramid fashion. The multi-scale ConvRNN modules learn a coarse-to-fine image reconstruction. Unlike other common reconstruction methods for parallel imaging, PC-RNN does not employ coil sensitive maps for multi-coil data and directly model the multiple coils as multi-channel inputs. The coil compression technique is applied to standardize data with various coil numbers, leading to more efficient training. We evaluate our model on the fastMRI knee and brain datasets and the results show that the proposed model outperforms other methods and can recover more details. The proposed method is one of the winner solutions in the 2019 fastMRI competition.

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arXiv2021

Multi-scale Neural ODEs for 3D Medical Image Registration

Image registration plays an important role in medical image analysis. Conventional optimization based methods provide an accurate estimation due to the iterative process at the cost of expensive computation. Deep learning methods such as learn-to-map are much faster but either iterative or coarse-to-fine approach is required to improve accuracy for handling large motions. In this work, we proposed to learn a registration optimizer via a multi-scale neural ODE model. The inference consists of iterative gradient updates similar to a conventional gradient descent optimizer but in a much faster way, because the neural ODE learns from the training data to adapt the gradient efficiently at each iteration. Furthermore, we proposed to learn a modal-independent similarity metric to address image appearance variations across different image contrasts. We performed evaluations through extensive experiments in the context of multi-contrast 3D MR images from both public and private data sources and demonstrate the superior performance of our proposed methods.

cs.CV↗

arXiv2021

Cardiac Functional Analysis with Cine MRI via Deep Learning Reconstruction

Retrospectively gated cine (retro-cine) MRI is the clinical standard for cardiac functional analysis. Deep learning (DL) based methods have been proposed for the reconstruction of highly undersampled MRI data and show superior image quality and magnitude faster reconstruction time than CS-based methods. Nevertheless, it remains unclear whether DL reconstruction is suitable for cardiac function analysis. To address this question, in this study we evaluate and compare the cardiac functional values (EDV, ESV and EF for LV and RV, respectively) obtained from highly accelerated MRI acquisition using DL based reconstruction algorithm (DL-cine) with values from CS-cine and conventional retro-cine. To the best of our knowledge, this is the first work to evaluate the cine MRI with deep learning reconstruction for cardiac function analysis and compare it with other conventional methods. The cardiac functional values obtained from cine MRI with deep learning reconstruction are consistent with values from clinical standard retro-cine MRI.

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arXiv2021

Accelerating 3D MULTIPLEX MRI Reconstruction with Deep Learning

Multi-contrast MRI images provide complementary contrast information about the characteristics of anatomical structures and are commonly used in clinical practice. Recently, a multi-flip-angle (FA) and multi-echo GRE method (MULTIPLEX MRI) has been developed to simultaneously acquire multiple parametric images with just one single scan. However, it poses two challenges for MULTIPLEX to be used in the 3D high-resolution setting: a relatively long scan time and the huge amount of 3D multi-contrast data for reconstruction. Currently, no DL based method has been proposed for 3D MULTIPLEX data reconstruction. We propose a deep learning framework for undersampled 3D MRI data reconstruction and apply it to MULTIPLEX MRI. The proposed deep learning method shows good performance in image quality and reconstruction time.

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arXiv2020

MRI Image Reconstruction via Learning Optimization Using Neural ODEs

We propose to formulate MRI image reconstruction as an optimization problem and model the optimization trajectory as a dynamic process using ordinary differential equations (ODEs). We model the dynamics in ODE with a neural network and solve the desired ODE with the off-the-shelf (fixed) solver to obtain reconstructed images. We extend this model and incorporate the knowledge of off-the-shelf ODE solvers into the network design (learned solvers). We investigate several models based on three ODE solvers and compare models with fixed solvers and learned solvers. Our models achieve better reconstruction results and are more parameter efficient than other popular methods such as UNet and cascaded CNN. We introduce a new way of tackling the MRI reconstruction problem by modeling the continuous optimization dynamics using neural ODEs.

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arXiv2020

Measure Anatomical Thickness from Cardiac MRI with Deep Neural Networks

Accurate estimation of shape thickness from medical images is crucial in clinical applications. For example, the thickness of myocardium is one of the key to cardiac disease diagnosis. While mathematical models are available to obtain accurate dense thickness estimation, they suffer from heavy computational overhead due to iterative solvers. To this end, we propose novel methods for dense thickness estimation, including a fast solver that estimates thickness from binary annular shapes and an end-to-end network that estimates thickness directly from raw cardiac images.We test the proposed models on three cardiac datasets and one synthetic dataset, achieving impressive results and generalizability on all. Thickness estimation is performed without iterative solvers or manual correction, which is 100 times faster than the mathematical model. We also analyze thickness patterns on different cardiac pathologies with a standard clinical model and the results demonstrate the potential clinical value of our method for thickness based cardiac disease diagnosis.

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arXiv2020

Real-Time Cardiac Cine MRI with Residual Convolutional Recurrent Neural Network

Real-time cardiac cine MRI does not require ECG gating in the data acquisition and is more useful for patients who can not hold their breaths or have abnormal heart rhythms. However, to achieve fast image acquisition, real-time cine commonly acquires highly undersampled data, which imposes a significant challenge for MRI image reconstruction. We propose a residual convolutional RNN for real-time cardiac cine reconstruction. To the best of our knowledge, this is the first work applying deep learning approach to Cartesian real-time cardiac cine reconstruction. Based on the evaluation from radiologists, our deep learning model shows superior performance than compressed sensing.

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arXiv2020

Anatomy-Aware Cardiac Motion Estimation

Cardiac motion estimation is critical to the assessment of cardiac function. Myocardium feature tracking (FT) can directly estimate cardiac motion from cine MRI, which requires no special scanning procedure. However, current deep learning-based FT methods may result in unrealistic myocardium shapes since the learning is solely guided by image intensities without considering anatomy. On the other hand, motion estimation through learning is challenging because ground-truth motion fields are almost impossible to obtain. In this study, we propose a novel Anatomy-Aware Tracker (AATracker) for cardiac motion estimation that preserves anatomy by weak supervision. A convolutional variational autoencoder (VAE) is trained to encapsulate realistic myocardium shapes. A baseline dense motion tracker is trained to approximate the motion fields and then refined to estimate anatomy-aware motion fields under the weak supervision from the VAE. We evaluate the proposed method on long-axis cardiac cine MRI, which has more complex myocardium appearances and motions than short-axis. Compared with other methods, AATracker significantly improves the tracking performance and provides visually more realistic tracking results, demonstrating the effectiveness of the proposed weakly-supervision scheme in cardiac motion estimation.

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arXiv2019

What evidence does deep learning model use to classify Skin Lesions?

Melanoma is a type of skin cancer with the most rapidly increasing incidence. Early detection of melanoma using dermoscopy images significantly increases patients' survival rate. However, accurately classifying skin lesions by eye, especially in the early stage of melanoma, is extremely challenging for the dermatologists. Hence, the discovery of reliable biomarkers will be meaningful for melanoma diagnosis. Recent years, the value of deep learning empowered computer-assisted diagnose has been shown in biomedical imaging based decision making. However, much research focuses on improving disease detection accuracy but not exploring the evidence of pathology. In this paper, we propose a method to interpret the deep learning classification findings. Firstly, we propose an accurate neural network architecture to classify skin lesions. Secondly, we utilize a prediction difference analysis method that examines each patch on the image through patch-wised corrupting to detect the biomarkers. Lastly, we validate that our biomarker findings are corresponding to the patterns in the literature. The findings can be significant and useful to guide clinical diagnosis.

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arXiv2009

New Construction of A Family of Quasi-Twisted Two-Weight Codes

Based on cyclic and consta-cyclic simplex codes, a new explicit construction of a family of two-weight codes is presented. These two-weight codes obtained are in the form of 2-generator quasi-cyclic, or quasi-twisted structure. Based on this construction, new optimal binary quasi-cyclic [195, 8, 96], [210, 8, 104] and [240, 8, 120] codes, and good QC ternary [208, 6, 135] and [221, 6, 144] codes are thus obtained. It is also shown that many codes among the family meet the Griesmer bound and thereful are optimal.

cs.IT↗

arXiv2009

Constructions of Quasi-Twisted Two-Weight Codes

A code is said to be two-weight if the non-zero codewords have only two different a weight w1 and w2. Two-weight codes are closely related to strongly regular graphs. In this paper. It is shown that a consta-cyclic code of composite length can be put in the quasi-twisted form. Based on this transformation, a new construction method of quasi-twisted (QT) two-weight codes is presented. A large amount of QT two-weight codes are found, and some new codes are also constructed.

cs.IT↗

arXiv2008

New Construction of 2-Generator Quasi-Twisted Codes

Quasi-twisted (QT) codes are a generalization of quasi-cyclic (QC) codes. Based on consta-cyclic simplex codes, a new explicit construction of a family of 2-generator quasi-twisted (QT) two-weight codes is presented. It is also shown that many codes in the family meet the Griesmer bound and therefore are length-optimal. New distance-optimal binary QC [195, 8, 96], [210, 8, 104] and [240, 8, 120] codes, and good ternary QC [208, 6, 135] and [221, 6, 144] codes are also obtained by the construction.

cs.IT↗