arXiv subjects

Enhao Gong

Publications and source records attributed to Enhao Gong.

8 recordsLinked to original sources

arXiv2026

Medical Foundation Model Features as Perceptual Loss for Brain MRI Contrast Dose Simulation

Perceptual losses are widely used in medical image synthesis because they encourage agreement in high-level structure beyond voxel-wise intensity similarity. In practice, most perceptual losses are still computed with natural-image backbones such as VGG16 or ResNet50, even when the target domain is magnetic resonance imaging (MRI). This mismatch may weaken supervision for anatomy, contrast enhancement, and acquisition variability. We test whether medical foundation model features provide a more suitable perceptual loss for brain MRI contrast dose simulation. The study has two stages. First, we compare RadImageNet, SegVol, and BrainIAC with ImageNet-pretrained VGG16 and ResNet50 as frozen feature extractors on four public medical imaging benchmarks: thyroid ultrasound, breast ultrasound, anterior cruciate ligament knee MRI, and meniscus knee MRI. RadImageNet achieves the lowest mean rank across the Stage I representation suite and is selected as $\phi^\star$. Second, we replace only the VGG16 feature extractor in an existing iterative brain MRI dose simulation framework with $\phi^\star$. The generator, reconstruction loss, adversarial loss, auxiliary losses, optimization schedule, and loss weights are kept unchanged. Standard metrics change modestly, with PSNR increasing from 41.63 to 41.74, SSIM from 0.9739 to 0.9754, RMSE decreasing from 0.1384 to 0.1369, and residual-uptake CNR from 0.0085 to 0.0082. The visual results show the main effect: RadImageNet reduces residual enhancement in marked structures, follows a more faithful dose-reduction trajectory, and remains close to the acquired 10% low-dose target. These results support domain-aligned radiology features as a practical perceptual feature space for MRI dose simulation, while leaving clinical equivalence and larger-cohort validation as future work.

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arXiv2023

One Model to Synthesize Them All: Multi-contrast Multi-scale Transformer for Missing Data Imputation

Multi-contrast magnetic resonance imaging (MRI) is widely used in clinical practice as each contrast provides complementary information. However, the availability of each imaging contrast may vary amongst patients, which poses challenges to radiologists and automated image analysis algorithms. A general approach for tackling this problem is missing data imputation, which aims to synthesize the missing contrasts from existing ones. While several convolutional neural networks (CNN) based algorithms have been proposed, they suffer from the fundamental limitations of CNN models, such as the requirement for fixed numbers of input and output channels, the inability to capture long-range dependencies, and the lack of interpretability. In this work, we formulate missing data imputation as a sequence-to-sequence learning problem and propose a multi-contrast multi-scale Transformer (MMT), which can take any subset of input contrasts and synthesize those that are missing. MMT consists of a multi-scale Transformer encoder that builds hierarchical representations of inputs combined with a multi-scale Transformer decoder that generates the outputs in a coarse-to-fine fashion. The proposed multi-contrast Swin Transformer blocks can efficiently capture intra- and inter-contrast dependencies for accurate image synthesis. Moreover, MMT is inherently interpretable as it allows us to understand the importance of each input contrast in different regions by analyzing the in-built attention maps of Transformer blocks in the decoder. Extensive experiments on two large-scale multi-contrast MRI datasets demonstrate that MMT outperforms the state-of-the-art methods quantitatively and qualitatively.

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arXiv2021

OUTCOMES: Rapid Under-sampling Optimization achieves up to 50% improvements in reconstruction accuracy for multi-contrast MRI sequences

Multi-contrast Magnetic Resonance Imaging (MRI) acquisitions from a single scan have tremendous potential to streamline exams and reduce imaging time. However, maintaining clinically feasible scan time necessitates significant undersampling, pushing the limits on compressed sensing and other low-dimensional techniques. During MRI scanning, one of the possible solutions is by using undersampling designs which can effectively improve the acquisition and achieve higher reconstruction accuracy. However, existing undersampling optimization methods are time-consuming and the limited performance prevents their clinical applications. In this paper, we proposed an improved undersampling trajectory optimization scheme to generate an optimized trajectory within seconds and apply it to subsequent multi-contrast MRI datasets on a per-subject basis, where we named it OUTCOMES. By using a data-driven method combined with improved algorithm design, GPU acceleration, and more efficient computation, the proposed method can optimize a trajectory within 5-10 seconds and achieve 30%-50% reconstruction improvement with the same acquisition cost, which makes real-time under-sampling optimization possible for clinical applications.

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arXiv2019

Joint multi-contrast Variational Network reconstruction (jVN) with application to rapid 2D and 3D imaging

Purpose: To improve the image quality of highly accelerated multi-channel MRI data by learning a joint variational network that reconstructs multiple clinical contrasts jointly. Methods: Data from our multi-contrast acquisition was embedded into the variational network architecture where shared anatomical information is exchanged by mixing the input contrasts. Complementary k-space sampling across imaging contrasts and Bunch-Phase/Wave-Encoding were used for data acquisition to improve the reconstruction at high accelerations. At 3T, our joint variational network approach across T1w, T2w and T2-FLAIR-weighted brain scans was tested for retrospective under-sampling at R=6 (2D) and R=4x4 (3D) acceleration. Prospective acceleration was also performed for 3D data where the combined acquisition time for whole brain coverage at 1 mm isotropic resolution across three contrasts was less than three minutes. Results: Across all test datasets, our joint multi-contrast network better preserved fine anatomical details with reduced image-blurring when compared to the corresponding single-contrast reconstructions. Improvement in image quality was also obtained through complementary k-space sampling and Bunch-Phase/Wave-Encoding where the synergistic combination yielded the overall best performance as evidenced by exemplarily slices and quantitative error metrics. Conclusion: By leveraging shared anatomical structures across the jointly reconstructed scans, our joint multi-contrast approach learnt more efficient regularizers which helped to retain natural image appearance and avoid over-smoothing. When synergistically combined with advanced encoding techniques, the performance was further improved, enabling up to R=16-fold acceleration with good image quality. This should help pave the way to very rapid high-resolution brain exams.

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arXiv2018

Quantitative Susceptibility Mapping using Deep Neural Network: QSMnet

Deep neural networks have demonstrated promising potential for the field of medical image reconstruction. In this work, an MRI reconstruction algorithm, which is referred to as quantitative susceptibility mapping (QSM), has been developed using a deep neural network in order to perform dipole deconvolution, which restores magnetic susceptibility source from an MRI field map. Previous approaches of QSM require multiple orientation data (e.g. Calculation of Susceptibility through Multiple Orientation Sampling or COSMOS) or regularization terms (e.g. Truncated K-space Division or TKD; Morphology Enabled Dipole Inversion or MEDI) to solve the ill-conditioned deconvolution problem. Unfortunately, they either require long multiple orientation scans or suffer from artifacts. To overcome these shortcomings, a deep neural network, QSMnet, is constructed to generate a high quality susceptibility map from single orientation data. The network has a modified U-net structure and is trained using gold-standard COSMOS QSM maps. 25 datasets from 5 subjects (5 orientation each) were applied for patch-wise training after doubling the data using augmentation. Two additional datasets of 5 orientation data were used for validation and test (one dataset each). The QSMnet maps of the test dataset were compared with those from TKD and MEDI for image quality and consistency in multiple head orientations. Quantitative and qualitative image quality comparisons demonstrate that the QSMnet results have superior image quality to those of TKD or MEDI and have comparable image quality to those of COSMOS. Additionally, QSMnet maps reveal substantially better consistency across the multiple orientations than those from TKD or MEDI. As a preliminary application, the network was tested for two patients. The QSMnet maps showed similar lesion contrasts with those from MEDI, demonstrating potential for future applications.

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arXiv2017

200x Low-dose PET Reconstruction using Deep Learning

Positron emission tomography (PET) is widely used in various clinical applications, including cancer diagnosis, heart disease and neuro disorders. The use of radioactive tracer in PET imaging raises concerns due to the risk of radiation exposure. To minimize this potential risk in PET imaging, efforts have been made to reduce the amount of radio-tracer usage. However, lowing dose results in low Signal-to-Noise-Ratio (SNR) and loss of information, both of which will heavily affect clinical diagnosis. Besides, the ill-conditioning of low-dose PET image reconstruction makes it a difficult problem for iterative reconstruction algorithms. Previous methods proposed are typically complicated and slow, yet still cannot yield satisfactory results at significantly low dose. Here, we propose a deep learning method to resolve this issue with an encoder-decoder residual deep network with concatenate skip connections. Experiments shows the proposed method can reconstruct low-dose PET image to a standard-dose quality with only two-hundredth dose. Different cost functions for training model are explored. Multi-slice input strategy is introduced to provide the network with more structural information and make it more robust to noise. Evaluation on ultra-low-dose clinical data shows that the proposed method can achieve better result than the state-of-the-art methods and reconstruct images with comparable quality using only 0.5% of the original regular dose.

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arXiv2017

Deep Generative Adversarial Networks for Compressed Sensing Automates MRI

Magnetic resonance image (MRI) reconstruction is a severely ill-posed linear inverse task demanding time and resource intensive computations that can substantially trade off {\it accuracy} for {\it speed} in real-time imaging. In addition, state-of-the-art compressed sensing (CS) analytics are not cognizant of the image {\it diagnostic quality}. To cope with these challenges we put forth a novel CS framework that permeates benefits from generative adversarial networks (GAN) to train a (low-dimensional) manifold of diagnostic-quality MR images from historical patients. Leveraging a mixture of least-squares (LS) GANs and pixel-wise $\ell_1$ cost, a deep residual network with skip connections is trained as the generator that learns to remove the {\it aliasing} artifacts by projecting onto the manifold. LSGAN learns the texture details, while $\ell_1$ controls the high-frequency noise. A multilayer convolutional neural network is then jointly trained based on diagnostic quality images to discriminate the projection quality. The test phase performs feed-forward propagation over the generator network that demands a very low computational overhead. Extensive evaluations are performed on a large contrast-enhanced MR dataset of pediatric patients. In particular, images rated based on expert radiologists corroborate that GANCS retrieves high contrast images with detailed texture relative to conventional CS, and pixel-wise schemes. In addition, it offers reconstruction under a few milliseconds, two orders of magnitude faster than state-of-the-art CS-MRI schemes.

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arXiv2017

DSD: Dense-Sparse-Dense Training for Deep Neural Networks

Modern deep neural networks have a large number of parameters, making them very hard to train. We propose DSD, a dense-sparse-dense training flow, for regularizing deep neural networks and achieving better optimization performance. In the first D (Dense) step, we train a dense network to learn connection weights and importance. In the S (Sparse) step, we regularize the network by pruning the unimportant connections with small weights and retraining the network given the sparsity constraint. In the final D (re-Dense) step, we increase the model capacity by removing the sparsity constraint, re-initialize the pruned parameters from zero and retrain the whole dense network. Experiments show that DSD training can improve the performance for a wide range of CNNs, RNNs and LSTMs on the tasks of image classification, caption generation and speech recognition. On ImageNet, DSD improved the Top1 accuracy of GoogLeNet by 1.1%, VGG-16 by 4.3%, ResNet-18 by 1.2% and ResNet-50 by 1.1%, respectively. On the WSJ'93 dataset, DSD improved DeepSpeech and DeepSpeech2 WER by 2.0% and 1.1%. On the Flickr-8K dataset, DSD improved the NeuralTalk BLEU score by over 1.7. DSD is easy to use in practice: at training time, DSD incurs only one extra hyper-parameter: the sparsity ratio in the S step. At testing time, DSD doesn't change the network architecture or incur any inference overhead. The consistent and significant performance gain of DSD experiments shows the inadequacy of the current training methods for finding the best local optimum, while DSD effectively achieves superior optimization performance for finding a better solution. DSD models are available to download at https://songhan.github.io/DSD.

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