arXiv subjects

Ge Wang

Publications and source records attributed to Ge Wang.

At least 217 records · Page 12Linked to original sources

arXiv2021

Noise Entangled GAN For Low-Dose CT Simulation

We propose a Noise Entangled GAN (NE-GAN) for simulating low-dose computed tomography (CT) images from a higher dose CT image. First, we present two schemes to generate a clean CT image and a noise image from the high-dose CT image. Then, given these generated images, an NE-GAN is proposed to simulate different levels of low-dose CT images, where the level of generated noise can be continuously controlled by a noise factor. NE-GAN consists of a generator and a set of discriminators, and the number of discriminators is determined by the number of noise levels during training. Compared with the traditional methods based on the projection data that are usually unavailable in real applications, NE-GAN can directly learn from the real and/or simulated CT images and may create low-dose CT images quickly without the need of raw data or other proprietary CT scanner information. The experimental results show that the proposed method has the potential to simulate realistic low-dose CT images.

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arXiv2021

Soft Autoencoder and Its Wavelet Adaptation Interpretation

Recently, deep learning becomes the main focus of machine learning research and has greatly impacted many important fields. However, deep learning is criticized for lack of interpretability. As a successful unsupervised model in deep learning, the autoencoder embraces a wide spectrum of applications, yet it suffers from the model opaqueness as well. In this paper, we propose a new type of convolutional autoencoders, termed as Soft Autoencoder (Soft-AE), in which the activation functions of encoding layers are implemented with adaptable soft-thresholding units while decoding layers are realized with linear units. Consequently, Soft-AE can be naturally interpreted as a learned cascaded wavelet shrinkage system. Our denoising experiments demonstrate that Soft-AE not only is interpretable but also offers a competitive performance relative to its counterparts. Furthermore, we propose a generalized linear unit (GenLU) to make an autoencoder more adaptive in nonlinearly filtering images and data, such as denoising and deblurring.

cs.LG↗

arXiv2020

Clinical Micro-CT Empowered by Interior Tomography, Robotic Scanning, and Deep Learning

While micro-CT systems are instrumental in preclinical research, clinical micro-CT imaging has long been desired with cochlear implantation as a primary example. The structural details of the cochlear implant and the temporal bone require a significantly higher image resolution than that (about 0.2 mm) provided by current medical CT scanners. In this paper, we propose a clinical micro-CT (CMCT) system design integrating conventional spiral cone-beam CT, contemporary interior tomography, deep learning techniques, and technologies of micro-focus X-ray source, photon-counting detector (PCD), and robotic arms for ultrahigh resolution localized tomography of a freely-selected volume of interest (VOI) at a minimized radiation dose level. The whole system consists of a standard CT scanner for a clinical CT exam and VOI specification, and a robotic-arm based micro-CT scanner for a local scan at much higher spatial and spectral resolution as well as much reduced radiation dose. The prior information from global scan is also fully utilized for background compensation to improve interior tomography from local data for accurate and stable VOI reconstruction. Our results and analysis show that the proposed hybrid reconstruction algorithm delivers superior local reconstruction, being insensitive to the misalignment of the isocenter position and initial view angle in the data/image registration while the attenuation error caused by scale mismatch can be effectively addressed with bias correction. These findings demonstrate the feasibility of our system design. We envision that deep learning techniques can be leveraged for optimized imaging performance. With high resolution imaging, high dose efficiency and low system cost synergistically, our proposed CMCT system has great potentials in temporal bone imaging as well as various other clinical applications.

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arXiv2020

Deep Efficient End-to-end Reconstruction (DEER) Network for Few-view Breast CT Image Reconstruction

Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of small calcification (down to a few hundred microns in size) and subtle density differences. Since breast is sensitive to x-ray radiation, dose reduction of breast CT is an important topic, and for this purpose, few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for few-view breast CT image reconstruction. The major merits of our network include high dose efficiency, excellent image quality, and low model complexity. By the design, the proposed network can learn the reconstruction process with as few as O(N) parameters, where N is the side length of an image to be reconstructed, which represents orders of magnitude improvements relative to the state-of-the-art deep-learning-based reconstruction methods that map raw data to tomographic images directly. Also, validated on a cone-beam breast CT dataset prepared by Koning Corporation on a commercial scanner, our method demonstrates a competitive performance over the state-of-the-art reconstruction networks in terms of image quality. The source code of this paper is available at: https://github.com/HuidongXie/DEER.

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arXiv2020

Integrative Analysis for COVID-19 Patient Outcome Prediction

While image analysis of chest computed tomography (CT) for COVID-19 diagnosis has been intensively studied, little work has been performed for image-based patient outcome prediction. Management of high-risk patients with early intervention is a key to lower the fatality rate of COVID-19 pneumonia, as a majority of patients recover naturally. Therefore, an accurate prediction of disease progression with baseline imaging at the time of the initial presentation can help in patient management. In lieu of only size and volume information of pulmonary abnormalities and features through deep learning based image segmentation, here we combine radiomics of lung opacities and non-imaging features from demographic data, vital signs, and laboratory findings to predict need for intensive care unit (ICU) admission. To our knowledge, this is the first study that uses holistic information of a patient including both imaging and non-imaging data for outcome prediction. The proposed methods were thoroughly evaluated on datasets separately collected from three hospitals, one in the United States, one in Iran, and another in Italy, with a total 295 patients with reverse transcription polymerase chain reaction (RT-PCR) assay positive COVID-19 pneumonia. Our experimental results demonstrate that adding non-imaging features can significantly improve the performance of prediction to achieve AUC up to 0.884 and sensitivity as high as 96.1%, which can be valuable to provide clinical decision support in managing COVID-19 patients. Our methods may also be applied to other lung diseases including but not limited to community acquired pneumonia. The source code of our work is available at https://github.com/DIAL-RPI/COVID19-ICUPrediction.

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arXiv2020

Parameter-Transferred Wasserstein Generative Adversarial Network (PT-WGAN) for Low-Dose PET Image Denoising

Due to the widespread use of positron emission tomography (PET) in clinical practice, the potential risk of PET-associated radiation dose to patients needs to be minimized. However, with the reduction in the radiation dose, the resultant images may suffer from noise and artifacts that compromise diagnostic performance. In this paper, we propose a parameter-transferred Wasserstein generative adversarial network (PT-WGAN) for low-dose PET image denoising. The contributions of this paper are twofold: i) a PT-WGAN framework is designed to denoise low-dose PET images without compromising structural details, and ii) a task-specific initialization based on transfer learning is developed to train PT-WGAN using trainable parameters transferred from a pretrained model, which significantly improves the training efficiency of PT-WGAN. The experimental results on clinical data show that the proposed network can suppress image noise more effectively while preserving better image fidelity than recently published state-of-the-art methods. We make our code available at https://github.com/90n9-yu/PT-WGAN.

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arXiv2020

Low-dimensional Manifold Constrained Disentanglement Network for Metal Artifact Reduction

Deep neural network based methods have achieved promising results for CT metal artifact reduction (MAR), most of which use many synthesized paired images for training. As synthesized metal artifacts in CT images may not accurately reflect the clinical counterparts, an artifact disentanglement network (ADN) was proposed with unpaired clinical images directly, producing promising results on clinical datasets. However, without sufficient supervision, it is difficult for ADN to recover structural details of artifact-affected CT images based on adversarial losses only. To overcome these problems, here we propose a low-dimensional manifold (LDM) constrained disentanglement network (DN), leveraging the image characteristics that the patch manifold is generally low-dimensional. Specifically, we design an LDM-DN learning algorithm to empower the disentanglement network through optimizing the synergistic network loss functions while constraining the recovered images to be on a low-dimensional patch manifold. Moreover, learning from both paired and unpaired data, an efficient hybrid optimization scheme is proposed to further improve the MAR performance on clinical datasets. Extensive experiments demonstrate that the proposed LDM-DN approach can consistently improve the MAR performance in paired and/or unpaired learning settings, outperforming competing methods on synthesized and clinical datasets.

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arXiv2020

X-ray Photon-Counting Data Correction through Deep Learning

X-ray photon-counting detectors (PCDs) are drawing an increasing attention in recent years due to their low noise and energy discrimination capabilities. The energy/spectral dimension associated with PCDs potentially brings great benefits such as for material decomposition, beam hardening and metal artifact reduction, as well as low-dose CT imaging. However, X-ray PCDs are currently limited by several technical issues, particularly charge splitting (including charge sharing and K-shell fluorescence re-absorption or escaping) and pulse pile-up effects which distort the energy spectrum and compromise the data quality. Correction of raw PCD measurements with hardware improvement and analytic modeling is rather expensive and complicated. Hence, here we proposed a deep neural network based PCD data correction approach which directly maps imperfect data to the ideal data in the supervised learning mode. In this work, we first establish a complete simulation model incorporating the charge splitting and pulse pile-up effects. The simulated PCD data and the ground truth counterparts are then fed to a specially designed deep adversarial network for PCD data correction. Next, the trained network is used to correct separately generated PCD data. The test results demonstrate that the trained network successfully recovers the ideal spectrum from the distorted measurement within $\pm6\%$ relative error. Significant data and image fidelity improvements are clearly observed in both projection and reconstruction domains.

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arXiv2020

Cine Cardiac MRI Motion Artifact Reduction Using a Recurrent Neural Network

Cine cardiac magnetic resonance imaging (MRI) is widely used for diagnosis of cardiac diseases thanks to its ability to present cardiovascular features in excellent contrast. As compared to computed tomography (CT), MRI, however, requires a long scan time, which inevitably induces motion artifacts and causes patients' discomfort. Thus, there has been a strong clinical motivation to develop techniques to reduce both the scan time and motion artifacts. Given its successful applications in other medical imaging tasks such as MRI super-resolution and CT metal artifact reduction, deep learning is a promising approach for cardiac MRI motion artifact reduction. In this paper, we propose a recurrent neural network to simultaneously extract both spatial and temporal features from under-sampled, motion-blurred cine cardiac images for improved image quality. The experimental results demonstrate substantially improved image quality on two clinical test datasets. Also, our method enables data-driven frame interpolation at an enhanced temporal resolution. Compared with existing methods, our deep learning approach gives a superior performance in terms of structural similarity (SSIM) and peak signal-to-noise ratio (PSNR).

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arXiv2020

X-ray Monochromatic Imaging from Single-spectrum CT via Machine Learning

In clinical CT system, the x-ray tube emits polychromatic x-rays, and the x-ray detectors operate in the current-integrating mode. This physical process is accurately described by an energy-dependent non-linear integral equation. However, the non-linear model is not invertible with a computationally efficient solution, and is often approximated as a linear integral model in the form of the Radon transform. Such approximation basically ignores energy-dependent information and would generate beam hardening artifacts. Dual-energy CT (DECT) scans one object using two different x-ray energy spectra for the acquisition of two spectrally distinct projection datasets to improve imaging performance. Thus, DECT can reconstruct energy and material-selective images, realizing monochromatic imaging and material decomposition. Nevertheless, DECT would increase radiation dose, system complexity, and equipment cost relative to single-spectrum CT. In this paper, a machine-learning-based CT reconstruction method is proposed to perform monochromatic image reconstruction using a single-spectrum CT scanner. Specifically, a residual neural network (ResNet) model is adapted to map a CT image to a monochromatic counterpart at a pre-specified energy level. This ResNet is trained on clinical dual-energy data, showing an excellent convergence to a minimal loss. The trained network produces high-quality monochromatic images on testing data, with a relative error of less than 0.2%. This work has great potential in clinical DECT applications such as tissue characterization, beam hardening correction and proton therapy planning.

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arXiv2020

GATCluster: Self-Supervised Gaussian-Attention Network for Image Clustering

We propose a self-supervised Gaussian ATtention network for image Clustering (GATCluster). Rather than extracting intermediate features first and then performing the traditional clustering algorithm, GATCluster directly outputs semantic cluster labels without further post-processing. Theoretically, we give a Label Feature Theorem to guarantee the learned features are one-hot encoded vectors, and the trivial solutions are avoided. To train the GATCluster in a completely unsupervised manner, we design four self-learning tasks with the constraints of transformation invariance, separability maximization, entropy analysis, and attention mapping. Specifically, the transformation invariance and separability maximization tasks learn the relationships between sample pairs. The entropy analysis task aims to avoid trivial solutions. To capture the object-oriented semantics, we design a self-supervised attention mechanism that includes a parameterized attention module and a soft-attention loss. All the guiding signals for clustering are self-generated during the training process. Moreover, we develop a two-step learning algorithm that is memory-efficient for clustering large-size images. Extensive experiments demonstrate the superiority of our proposed method in comparison with the state-of-the-art image clustering benchmarks. Our code has been made publicly available at https://github.com/niuchuangnn/GATCluster.

cs.CV↗

arXiv2019

Shape and Margin-Aware Lung Nodule Classification in Low-dose CT Images via Soft Activation Mapping

A number of studies on lung nodule classification lack clinical/biological interpretations of the features extracted by convolutional neural network (CNN). The methods like class activation mapping (CAM) and gradient-based CAM (Grad-CAM) are tailored for interpreting localization and classification tasks while they ignored fine-grained features. Therefore, CAM and Grad-CAM cannot provide optimal interpretation for lung nodule categorization task in low-dose CT images, in that fine-grained pathological clues like discrete and irregular shape and margins of nodules are capable of enhancing sensitivity and specificity of nodule classification with regards to CNN. In this paper, we first develop a soft activation mapping (SAM) to enable fine-grained lung nodule shape \& margin (LNSM) feature analysis with a CNN so that it can access rich discrete features. Secondly, by combining high-level convolutional features with SAM, we further propose a high-level feature enhancement scheme (HESAM) to localize LNSM features. Experiments on the LIDC-IDRI dataset indicate that 1) SAM captures more fine-grained and discrete attention regions than existing methods, 2) HESAM localizes more accurately on LNSM features and obtains the state-of-the-art predictive performance, reducing the false positive rate, and 3) we design and conduct a visually matching experiment which incorporates radiologists study to increase the confidence level of applying our method to clinical diagnosis.

cs.CV↗

arXiv2019

Knowledge-based Analysis for Mortality Prediction from CT Images

Recent studies have highlighted the high correlation between cardiovascular diseases (CVD) and lung cancer, and both are associated with significant morbidity and mortality. Low-Dose CT (LCDT) scans have led to significant improvements in the accuracy of lung cancer diagnosis and thus the reduction of cancer deaths. However, the high correlation between lung cancer and CVD has not been well explored for mortality prediction. This paper introduces a knowledge-based analytical method using deep convolutional neural network (CNN) for all-cause mortality prediction. The underlying approach combines structural image features extracted from CNNs, based on LDCT volume in different scale, and clinical knowledge obtained from quantitative measurements, to comprehensively predict the mortality risk of lung cancer screening subjects. The introduced method is referred to here as the Knowledge-based Analysis of Mortality Prediction Network, or KAMP-Net. It constitutes a collaborative framework that utilizes both imaging features and anatomical information, instead of completely relying on automatic feature extraction. Our work demonstrates the feasibility of incorporating quantitative clinical measurements to assist CNNs in all-cause mortality prediction from chest LDCT images. The results of this study confirm that radiologist defined features are an important complement to CNNs to achieve a more comprehensive feature extraction. Thus, the proposed KAMP-Net has shown to achieve a superior performance when compared to other methods. Our code is available at https://github.com/DIAL-RPI/KAMP-Net.

cs.CV↗

arXiv2019

Deep Encoder-decoder Adversarial Reconstruction (DEAR) Network for 3D CT from Few-view Data

X-ray computed tomography (CT) is widely used in clinical practice. The involved ionizing X-ray radiation, however, could increase cancer risk. Hence, the reduction of the radiation dose has been an important topic in recent years. Few-view CT image reconstruction is one of the main ways to minimize radiation dose and potentially allow a stationary CT architecture. In this paper, we propose a deep encoder-decoder adversarial reconstruction (DEAR) network for 3D CT image reconstruction from few-view data. Since the artifacts caused by few-view reconstruction appear in 3D instead of 2D geometry, a 3D deep network has a great potential for improving the image quality in a data-driven fashion. More specifically, our proposed DEAR-3D network aims at reconstructing 3D volume directly from clinical 3D spiral cone-beam image data. DEAR is validated on a publicly available abdominal CT dataset prepared and authorized by Mayo Clinic. Compared with other 2D deep-learning methods, the proposed DEAR-3D network can utilize 3D information to produce promising reconstruction results.

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arXiv2019

Quadratic Autoencoder (Q-AE) for Low-dose CT Denoising

Inspired by complexity and diversity of biological neurons, our group proposed quadratic neurons by replacing the inner product in current artificial neurons with a quadratic operation on input data, thereby enhancing the capability of an individual neuron. Along this direction, we are motivated to evaluate the power of quadratic neurons in popular network architectures, simulating human-like learning in the form of quadratic-neuron-based deep learning. Our prior theoretical studies have shown important merits of quadratic neurons and networks in representation, efficiency, and interpretability. In this paper, we use quadratic neurons to construct an encoder-decoder structure, referred as the quadratic autoencoder, and apply it to low-dose CT denoising. The experimental results on the Mayo low-dose CT dataset demonstrate the utility of quadratic autoencoder in terms of image denoising and model efficiency. To our best knowledge, this is the first time that the deep learning approach is implemented with a new type of neurons and demonstrates a significant potential in the medical imaging field.

cs.LG↗

arXiv2019

Deep learning for accelerating Monte Carlo radiation transport simulation in intensity-modulated radiation therapy

Cancer is a primary cause of morbidity and mortality worldwide. The radiotherapy plays a more and more important role in cancer treatment. In the radiotherapy, the dose distribution maps in patient need to be calculated and evaluated for the purpose of killing tumor and protecting healthy tissue. Monte Carlo (MC) radiation transport calculation is able to account for all aspects of radiological physics within 3D heterogeneous media such as the human body and generate the dose distribution maps accurately. However, an MC calculation for doses in radiotherapy usually takes a great mass of time to achieve acceptable statistical uncertainty, impeding the MC methods from wider clinic applications. Here we introduce a convolutional neural network (CNN), termed as Monte Carlo Denoising Net (MCDNet), to achieve the acceleration of the MC dose calculations in radiotherapy, which is trained to directly predict the high-photon (noise-free) dose maps from the low-photon (noise-much) dose maps. Thirty patients with postoperative rectal cancer who accepted intensity-modulated radiation therapy (IMRT) were enrolled in this study. 3D Gamma Index Passing Rate (GIPR) is used to evaluate the performance of predicted dose maps. The experimental results demonstrate that the MCDNet can improve the GIPR of dose maps of 1x107 photons over that of 1x108 photons, yielding over 10x speed-up in terms of photon numbers used in the MC simulations of IMRT. It is of great potential to investigate the performance of this method on the other tumor sites and treatment modalities.

physics.med-ph↗

arXiv2019

A Method of Rapid Quantification of Patient-Specific Organ Dose for CT Using Coupled Deep-Learning based Multi-Organ Segmentation and GPU-accelerated Monte Carlo Dose Computing

Purpose: This paper describes a new method to apply deep-learning algorithms for automatic segmentation of radiosensitive organs from 3D tomographic CT images before computing organ doses using a GPU-based Monte Carlo code. Methods: A deep convolutional neural network (CNN) for organ segmentation is trained to automatically delineate radiosensitive organs from CT. With a GPU-based Monte Carlo dose engine (ARCHER) to derive CT dose of a phantom made from a subject's CT scan, we are then able to compute the patient-specific CT dose for each of the segmented organs. The developed tool is validated by using Relative Dose Error (RDE) against the organ doses calculated by ARCHER with manual segmentation performed by radiologists. The dose computation results are also compared against organ doses from population-average phantoms to demonstrate the improvement achieved by using the developed tool. In this study, two datasets were used: The Lung CT Segmentation Challenge 2017 (LCTSC) dataset, which contains 60 thoracic CT scan patients each with 5 segmented organs, and the Pancreas-CT (PCT) dataset, which contains 43 abdominal CT scan patients each with 8 segmented organs. Five-fold cross-validation of the new method is performed on both datasets. Results: Comparing with the traditional organ dose evaluation method that based on population-average phantom, our proposed method achieved the smaller RDE range on all organs with -4.3%~1.5% vs -31.5%~33.9% (lung), -7.0%~2.3% vs -15.2%~125.1% (heart), -18.8%~40.2% vs -10.3%~124.1% (esophagus) in the LCTSC dataset and -5.6%~1.6% vs -20.3%~57.4% (spleen), -4.5%~4.6% vs -19.5%~61.0% (pancreas), -2.3%~4.4% vs -37.8%~75.8% (left kidney), -14.9%~5.4% vs -39.9% ~14.6% (gall bladder), -0.9%~1.6% vs -30.1%~72.5% (liver), and -23.0%~11.1% vs -52.5%~-1.3% (stomach) in the PCT dataset.

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arXiv2019

Deep-learning-based Breast CT for Radiation Dose Reduction

Cone-beam breast computed tomography (CT) provides true 3D breast images with isotropic resolution and high-contrast information, detecting calcifications as small as a few hundred microns and revealing subtle tissue differences. However, breast is highly sensitive to x-ray radiation. It is critically important for healthcare to reduce radiation dose. Few-view cone-beam CT only uses a fraction of x-ray projection data acquired by standard cone-beam breast CT, enabling significant reduction of the radiation dose. However, insufficient sampling data would cause severe streak artifacts in CT images reconstructed using conventional methods. In this study, we propose a deep-learning-based method to establish a residual neural network model for the image reconstruction, which is applied for few-view breast CT to produce high quality breast CT images. We respectively evaluate the deep-learning-based image reconstruction using one third and one quarter of x-ray projection views of the standard cone-beam breast CT. Based on clinical breast imaging dataset, we perform a supervised learning to train the neural network from few-view CT images to corresponding full-view CT images. Experimental results show that the deep learning-based image reconstruction method allows few-view breast CT to achieve a radiation dose <6 mGy per cone-beam CT scan, which is a threshold set by FDA for mammographic screening.

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