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.

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.

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.

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).

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

Deep clustering has achieved state-of-the-art results via joint representation learning and clustering, but still has an inferior performance for the real scene images, e.g., those in ImageNet. With such images, deep clustering methods face several challenges, including extracting discriminative features, avoiding trivial solutions, capturing semantic information, and performing on large-size image datasets. To address these problems, here we propose a self-supervised attention network for image clustering (AttentionCluster). Rather than extracting intermediate features first and then performing the traditional clustering algorithm, AttentionCluster directly outputs semantic cluster labels that are more discriminative than intermediate features and does not need further post-processing. To train the AttentionCluster in a completely unsupervised manner, we design four 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 training-friendly and memory-efficient for processing large-size images. Extensive experiments demonstrate the superiority of our proposed method in comparison with the state-of-the-art image clustering benchmarks.

Duality of Width and Depth of Neural Networks

Here, we report that the depth and the width of a neural network are dual from two perspectives. First, we employ the partially separable representation to determine the width and depth. Second, we use the De Morgan law to guide the conversion between a deep network and a wide network. Furthermore, we suggest the generalized De Morgan law to promote duality to network equivalency.

On Interpretability of Artificial Neural Networks

Deep learning has achieved great successes in many important areas to dealing with text, images, video, graphs, and so on. However, the black-box nature of deep artificial neural networks has become the primary obstacle to their public acceptance and wide popularity in critical applications such as diagnosis and therapy. Due to the huge potential of deep learning, interpreting neural networks has become one of the most critical research directions. In this paper, we systematically review recent studies in understanding the mechanism of neural networks and shed light on some future directions of interpretability research (This work is still in progress).

Deep Efficient End-to-end Reconstruction (DEER) Network for Low-dose Few-view Breast CT from Projection Data

Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of 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 low-dose few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for low-dose few-view breast CT. 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 in terms of as less as O(N) parameters, where N is the size 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 projection data to tomographic images directly. As a result, our method does not require expensive GPUs to train and run. Also, validated on a cone-beam breast CT dataset prepared by Koning Corporation on a commercial scanner, our method demonstrates competitive performance over the state-of-the-art reconstruction networks in terms of image quality.

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.