arXiv subjects

Feng Shi

Publications and source records attributed to Feng Shi.

At least 91 records · Page 5Linked to original sources

arXiv2020

Review of Artificial Intelligence Techniques in Imaging Data Acquisition, Segmentation and Diagnosis for COVID-19

(This paper was submitted as an invited paper to IEEE Reviews in Biomedical Engineering on April 6, 2020.) The pandemic of coronavirus disease 2019 (COVID-19) is spreading all over the world. Medical imaging such as X-ray and computed tomography (CT) plays an essential role in the global fight against COVID-19, whereas the recently emerging artificial intelligence (AI) technologies further strengthen the power of the imaging tools and help medical specialists. We hereby review the rapid responses in the community of medical imaging (empowered by AI) toward COVID-19. For example, AI-empowered image acquisition can significantly help automate the scanning procedure and also reshape the workflow with minimal contact to patients, providing the best protection to the imaging technicians. Also, AI can improve work efficiency by accurate delination of infections in X-ray and CT images, facilitating subsequent quantification. Moreover, the computer-aided platforms help radiologists make clinical decisions, i.e., for disease diagnosis, tracking, and prognosis. In this review paper, we thus cover the entire pipeline of medical imaging and analysis techniques involved with COVID-19, including image acquisition, segmentation, diagnosis, and follow-up. We particularly focus on the integration of AI with X-ray and CT, both of which are widely used in the frontline hospitals, in order to depict the latest progress of medical imaging and radiology fighting against COVID-19.

eess.IV↗

arXiv2020

Severity Assessment of Coronavirus Disease 2019 (COVID-19) Using Quantitative Features from Chest CT Images

Background: Chest computed tomography (CT) is recognized as an important tool for COVID-19 severity assessment. As the number of affected patients increase rapidly, manual severity assessment becomes a labor-intensive task, and may lead to delayed treatment. Purpose: Using machine learning method to realize automatic severity assessment (non-severe or severe) of COVID-19 based on chest CT images, and to explore the severity-related features from the resulting assessment model. Materials and Method: Chest CT images of 176 patients (age 45.3$\pm$16.5 years, 96 male and 80 female) with confirmed COVID-19 are used, from which 63 quantitative features, e.g., the infection volume/ratio of the whole lung and the volume of ground-glass opacity (GGO) regions, are calculated. A random forest (RF) model is trained to assess the severity (non-severe or severe) based on quantitative features. Importance of each quantitative feature, which reflects the correlation to the severity of COVID-19, is calculated from the RF model. Results: Using three-fold cross validation, the RF model shows promising results, i.e., 0.933 of true positive rate, 0.745 of true negative rate, 0.875 of accuracy, and 0.91 of area under receiver operating characteristic curve (AUC). The resulting importance of quantitative features shows that the volume and its ratio (with respect to the whole lung volume) of ground glass opacity (GGO) regions are highly related to the severity of COVID-19, and the quantitative features calculated from the right lung are more related to the severity assessment than those of the left lung. Conclusion: The RF based model can achieve automatic severity assessment (non-severe or severe) of COVID-19 infection, and the performance is promising. Several quantitative features, which have the potential to reflect the severity of COVID-19, were revealed.

eess.IV↗

arXiv2020

Large-Scale Screening of COVID-19 from Community Acquired Pneumonia using Infection Size-Aware Classification

The worldwide spread of coronavirus disease (COVID-19) has become a threatening risk for global public health. It is of great importance to rapidly and accurately screen patients with COVID-19 from community acquired pneumonia (CAP). In this study, a total of 1658 patients with COVID-19 and 1027 patients of CAP underwent thin-section CT. All images were preprocessed to obtain the segmentations of both infections and lung fields, which were used to extract location-specific features. An infection Size Aware Random Forest method (iSARF) was proposed, in which subjects were automated categorized into groups with different ranges of infected lesion sizes, followed by random forests in each group for classification. Experimental results show that the proposed method yielded sensitivity of 0.907, specificity of 0.833, and accuracy of 0.879 under five-fold cross-validation. Large performance margins against comparison methods were achieved especially for the cases with infection size in the medium range, from 0.01% to 10%. The further inclusion of Radiomics features show slightly improvement. It is anticipated that our proposed framework could assist clinical decision making.

eess.IV↗

arXiv2020

MRI Super-Resolution with GAN and 3D Multi-Level DenseNet: Smaller, Faster, and Better

High-resolution (HR) magnetic resonance imaging (MRI) provides detailed anatomical information that is critical for diagnosis in the clinical application. However, HR MRI typically comes at the cost of long scan time, small spatial coverage, and low signal-to-noise ratio (SNR). Recent studies showed that with a deep convolutional neural network (CNN), HR generic images could be recovered from low-resolution (LR) inputs via single image super-resolution (SISR) approaches. Additionally, previous works have shown that a deep 3D CNN can generate high-quality SR MRIs by using learned image priors. However, 3D CNN with deep structures, have a large number of parameters and are computationally expensive. In this paper, we propose a novel 3D CNN architecture, namely a multi-level densely connected super-resolution network (mDCSRN), which is light-weight, fast and accurate. We also show that with the generative adversarial network (GAN)-guided training, the mDCSRN-GAN provides appealing sharp SR images with rich texture details that are highly comparable with the referenced HR images. Our results from experiments on a large public dataset with 1,113 subjects showed that this new architecture outperformed other popular deep learning methods in recovering 4x resolution-downgraded images in both quality and speed.

cs.CV↗

arXiv2020

Runtime Performances of Randomized Search Heuristics for the Dynamic Weighted Vertex Cover Problem

Randomized search heuristics such as evolutionary algorithms are frequently applied to dynamic combinatorial optimization problems. Within this paper, we present a dynamic model of the classic Weighted Vertex Cover problem and analyze the runtime performances of the well-studied algorithms Randomized Local Search and (1+1) EA adapted to it, to contribute to the theoretical understanding of evolutionary computing for problems with dynamic changes. In our investigations, we use an edge-based representation based on the dual form of the Linear Programming formulation for the problem and study the expected runtime that the adapted algorithms require to maintain a 2-approximate solution when the given weighted graph is modified by an edge-editing or weight-editing operation. Considering the weights on the vertices may be exponentially large with respect to the size of the graph, the step size adaption strategy is incorporated, with or without the 1/5-th rule that is employed to control the increasing/decreasing rate of the step size. Our results show that three of the four algorithms presented in the paper can recompute 2-approximate solutions for the studied dynamic changes in polynomial expected runtime, but the (1+1) EA with 1/5-th Rule requires pseudo-polynomial expected runtime.

cs.NE↗

arXiv2020

Science and Technology Advance through Surprise

Breakthrough discoveries and inventions involve unexpected combinations of contents including problems, methods, and natural entities, and also diverse contexts such as journals, subfields, and conferences. Drawing on data from tens of millions of research papers, patents, and researchers, we construct models that predict next year's content and context combinations with an AUC of 95% based on embeddings constructed from high-dimensional stochastic block models, where the improbability of new combinations itself predicts up to 50% of the likelihood that they will gain outsized citations and major awards. Most of these breakthroughs occur when problems in one field are unexpectedly solved by researchers from a distant other. These findings demonstrate the critical role of surprise in advance, and enable evaluation of scientific institutions ranging from education and peer review to awards in supporting it.

cs.DL↗

arXiv2020

Community Detection for Hypergraph Networks via Regularized Tensor Power Iteration

To date, social network analysis has been largely focused on pairwise interactions. The study of higher-order interactions, via a hypergraph network, brings in new insights. We study community detection in a hypergraph network. A popular approach is to project the hypergraph to a graph and then apply community detection methods for graph networks, but we show that this approach may cause unwanted information loss. We propose a new method for community detection that operates directly on the hypergraph. At the heart of our method is a regularized higher-order orthogonal iteration (reg-HOOI) algorithm that computes an approximate low-rank decomposition of the network adjacency tensor. Compared with existing tensor decomposition methods such as HOSVD and vanilla HOOI, reg-HOOI yields better performance, especially when the hypergraph is sparse. Given the output of tensor decomposition, we then generalize the community detection method SCORE (Jin, 2015) from graph networks to hypergraph networks. We call our new method Tensor-SCORE. In theory, we introduce a degree-corrected block model for hypergraphs (hDCBM), and show that Tensor-SCORE yields consistent community detection for a wide range of network sparsity and degree heterogeneity. As a byproduct, we derive the rates of convergence on estimating the principal subspace by reg-HOOI, with different initializations, including the two new initialization methods we propose, a diagonal-removed HOSVD and a randomized graph projection. We apply our method to several real hypergraph networks which yields encouraging results. It suggests that exploring higher-order interactions provides additional information not seen in graph representations.

stat.ME↗

arXiv2019

DS-GCNs: Connectome Classification Using Dynamic Spectral Graph Convolution Networks with Assistant Task Training

Functional Connectivity (FC) matrices measure the regional interactions in the brain and have been widely used in neurological brain disease classification. However, a FC matrix is neither a natural image which contains shape and texture information, nor a vector of independent features, which renders the extracting of efficient features from matrices as a challenging problem. A brain network, also named as connectome, could forma a graph structure naturally, the nodes of which are brain regions and the edges are interregional connectivity. Thus, in this study, we proposed novel graph convolutional networks (GCNs) to extract efficient disease-related features from FC matrices. Considering the time-dependent nature of brain activity, we computed dynamic FC matrices with sliding-windows and implemented a graph convolution based LSTM (long short term memory) layer to process dynamic graphs. Moreover, the demographics of patients were also used to guide the classification. However, unlike in conventional methods where personal information, i.e., gender and age were added as extra inputs, we argue that this kind of approach may not actually improve the classification performance, for such personal information given in dataset was usually balanced distributed. In this paper, we proposed to utilize the demographic information as extra outputs and to share parameters among three networks predicting subject status, gender and age, which serve as assistant tasks. We tested the performance of the proposed architecture in ADNI II dataset to classify Alzheimer's disease patients from normal controls. The classification accuracy, sensitivity and specificity reach 0.90, 0.92 and 0.89 on ADNI II dataset.

physics.med-ph↗

arXiv2019

Infer Implicit Contexts in Real-time Online-to-Offline Recommendation

Understanding users' context is essential for successful recommendations, especially for Online-to-Offline (O2O) recommendation, such as Yelp, Groupon, and Koubei. Different from traditional recommendation where individual preference is mostly static, O2O recommendation should be dynamic to capture variation of users' purposes across time and location. However, precisely inferring users' real-time contexts information, especially those implicit ones, is extremely difficult, and it is a central challenge for O2O recommendation. In this paper, we propose a new approach, called Mixture Attentional Constrained Denoise AutoEncoder (MACDAE), to infer implicit contexts and consequently, to improve the quality of real-time O2O recommendation. In MACDAE, we first leverage the interaction among users, items, and explicit contexts to infer users' implicit contexts, then combine the learned implicit-context representation into an end-to-end model to make the recommendation. MACDAE works quite well in the real system. We conducted both offline and online evaluations of the proposed approach. Experiments on several real-world datasets (Yelp, Dianping, and Koubei) show our approach could achieve significant improvements over state-of-the-arts. Furthermore, online A/B test suggests a 2.9% increase for click-through rate and 5.6% improvement for conversion rate in real-world traffic. Our model has been deployed in the product of "Guess You Like" recommendation in Koubei.

cs.IR↗

arXiv2019

Social Clustering in Epidemic Spread on Coevolving Networks

Even though transitivity is a central structural feature of social networks, its influence on epidemic spread on coevolving networks has remained relatively unexplored. Here we introduce and study an adaptive SIS epidemic model wherein the infection and network coevolve with non-trivial probability to close triangles during edge rewiring, leading to substantial reinforcement of network transitivity. This new model provides a unique opportunity to study the role of transitivity in altering the SIS dynamics on a coevolving network. Using numerical simulations and Approximate Master Equations (AME), we identify and examine a rich set of dynamical features in the new model. In many cases, the AME including transitivity reinforcement provides accurate predictions of stationary-state disease prevalences and network degree distributions. Furthermore, for some parameter settings, the AME accurately trace the temporal evolution of the system. We show that higher transitivity reinforcement in the model leads to lower levels of infective individuals in the population, when closing a triangle is the dominant rewiring mechanism. These methods and results may be useful in developing ideas and modeling strategies for controlling SIS type epidemics.

physics.soc-ph↗

arXiv2019

The Next Generation of Cosmological Measurements with Type Ia Supernovae

While Type Ia Supernovae (SNe Ia) are one of the most mature cosmological probes, the next era promises to be extremely exciting in the number of different ways SNe Ia are used to measure various cosmological parameters. Here we review the experiments in the 2020s that will yield orders of magnitudes more SNe Ia, and the new understandings and capabilities to constrain systematic uncertainties at a level to match these statistics. We then discuss five different cosmological probes with SNe Ia: the conventional Hubble diagram for measuring dark energy properties, the distance ladder for measuring the Hubble constant, peculiar velocities and weak lensing for measuring sigma8 and strong-lens measurements of H0 and other cosmological parameters. For each of these probes, we discuss the experiments that will provide the best measurements and also the SN Ia-related systematics that affect each one.

astro-ph.CO↗

arXiv2018

Explanatory Graphs for CNNs

This paper introduces a graphical model, namely an explanatory graph, which reveals the knowledge hierarchy hidden inside conv-layers of a pre-trained CNN. Each filter in a conv-layer of a CNN for object classification usually represents a mixture of object parts. We develop a simple yet effective method to disentangle object-part pattern components from each filter. We construct an explanatory graph to organize the mined part patterns, where a node represents a part pattern, and each edge encodes co-activation relationships and spatial relationships between patterns. More crucially, given a pre-trained CNN, the explanatory graph is learned without a need of annotating object parts. Experiments show that each graph node consistently represented the same object part through different images, which boosted the transferability of CNN features. We transferred part patterns in the explanatory graph to the task of part localization, and our method significantly outperformed other approaches.

cs.CV↗

arXiv2018

Leveraging local network communities to predict academic performance

For more than 20 years, social network analysis of student collaboration networks has focused on a student's centrality to predict academic performance. And even though a growing amount of sociological literature has supported that academic success is contagious, identifying central students in the network alone does not capture how peer interactions facilitate the spread of academic success throughout the network. Consequently, we propose novel predictors that treat academic success as a contagion by identifying a student's learning community, consisting of the peers that are most likely to influence a student's performance in a course. We evaluate the importance of these learning communities by predicting academic outcomes in an introductory college statistics course with 103 students. In particular, we observe that by including these learning community predictors, the resulting model is 68 times more likely to be the correct model than the current state-of-the-art centrality network models in the literature.

cs.SI↗

arXiv2018

Sparse Winograd Convolutional neural networks on small-scale systolic arrays

The reconfigurability, energy-efficiency, and massive parallelism on FPGAs make them one of the best choices for implementing efficient deep learning accelerators. However, state-of-art implementations seldom consider the balance between high throughput of computation power and the ability of the memory subsystem to support it. In this paper, we implement an accelerator on FPGA by combining the sparse Winograd convolution, clusters of small-scale systolic arrays, and a tailored memory layout design. We also provide an analytical model analysis for the general Winograd convolution algorithm as a design reference. Experimental results on VGG16 show that it achieves very high computational resource utilization, 20x ~ 30x energy efficiency, and more than 5x speedup compared with the dense implementation.

cs.DC↗

arXiv2018

Mapping the Real Space Distributions of Galaxies in SDSS DR7: II. Measuring the growth rate, clustering amplitude of matter and biases of galaxies at redshift $0.1$

We extend the real-space mapping method developed in Shi et at. (2016) so that it can be applied to flux-limited galaxy samples. We use an ensemble of mock catalogs to demonstrate the reliability of this extension, showing that it allows for an accurate recovery of the real-space correlation functions and galaxy biases. We also demonstrate that, using an iterative method applied to intermediate-scale clustering data, we can obtain an unbiased estimate of the growth rate of structure $fσ_8$, which is related to the clustering amplitude of matter, to an accuracy of $\sim 10\%$. Applying this method to the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7), we construct a real-space galaxy catalog spanning the redshift range $0.01 \leq z \leq 0.2$, which contains 584,473 galaxies in the north Galactic cap (NGC). Using this data, we infer $\fss$ at a median redshift $z=0.1$, which is consistent with the WMAP9 cosmology at the $1σ$ level. By combining this measurement with the real-space clustering of galaxies and with galaxy-galaxy weak lensing measurements for the same sets of galaxies, we are able to break the degeneracy between $f$, $σ_8$, and $b$. From the SDSS DR7 data alone, we obtain the following cosmological constraints at redshift $z=0.1$: $f=$$0.464^{+0.040}_{-0.040}$, $σ_8=0.769^{+0.121}_{-0.089}$, and $b=1.910^{+0.234}_{-0.268}$, $1.449^{+0.194}_{-0.196}$, $1.301^{+0.170}_{-0.177}$, and $1.196^{+0.159}_{-0.161}~$ for galaxies within different absolute magnitude bins $^{0.1}{\rm M}_r-5\log h=[-23,0, -22.0], [-22,0, -21.0], [-21.0, -20.0]$ and $[-20.0, -19.0]$, respectively.

astro-ph.CO↗

arXiv2018

Efficient and Accurate MRI Super-Resolution using a Generative Adversarial Network and 3D Multi-Level Densely Connected Network

High-resolution (HR) magnetic resonance images (MRI) provide detailed anatomical information important for clinical application and quantitative image analysis. However, HR MRI conventionally comes at the cost of longer scan time, smaller spatial coverage, and lower signal-to-noise ratio (SNR). Recent studies have shown that single image super-resolution (SISR), a technique to recover HR details from one single low-resolution (LR) input image, could provide high-quality image details with the help of advanced deep convolutional neural networks (CNN). However, deep neural networks consume memory heavily and run slowly, especially in 3D settings. In this paper, we propose a novel 3D neural network design, namely a multi-level densely connected super-resolution network (mDCSRN) with generative adversarial network (GAN)-guided training. The mDCSRN quickly trains and inferences and the GAN promotes realistic output hardly distinguishable from original HR images. Our results from experiments on a dataset with 1,113 subjects show that our new architecture beats other popular deep learning methods in recovering 4x resolution-downgraded im-ages and runs 6x faster.

cs.CV↗

arXiv2018

ELUCID V. Lighting dark matter halos with galaxies

In a recent study, using the distribution of galaxies in the north galactic pole of SDSS DR7 region enclosed in a 500$\mpch$ box, we carried out our ELUCID simulation (Wang et al. 2016, ELUCID III). Here we {\it light} the dark matter halos and subhalos in the reconstructed region in the simulation with galaxies in the SDSS observations using a novel {\it neighborhood} abundance matching method. Before we make use of thus established galaxy-subhalo connections in the ELUCID simulation to evaluate galaxy formation models, we set out to explore the reliability of such a link. For this purpose, we focus on the following a few aspects of galaxies: (1) the central-subhalo luminosity and mass relations; (2) the satellite fraction of galaxies; (3) the conditional luminosity function (CLF) and conditional stellar mass function (CSMF) of galaxies; and (4) the cross correlation functions between galaxies and the dark matter particles, most of which are measured separately for all, red and blue galaxy populations. We find that our neighborhood abundance matching method accurately reproduces the central-subhalo relations, satellite fraction, the CLFs and CSMFs and the biases of galaxies. These features ensure that thus established galaxy-subhalo connections will be very useful in constraining galaxy formation processes. And we provide some suggestions on the three levels of using the galaxy-subhalo pairs for galaxy formation constraints. The galaxy-subhalo links and the subhalo merger trees in the SDSS DR7 region extracted from our ELUCID simulation are available upon request.

astro-ph.GA↗

arXiv2018

Calcium Removal From Cardiac CT Images Using Deep Convolutional Neural Network

Coronary calcium causes beam hardening and blooming artifacts on cardiac computed tomography angiography (CTA) images, which lead to overestimation of lumen stenosis and reduction of diagnostic specificity. To properly remove coronary calcification and restore arterial lumen precisely, we propose a machine learning-based method with a multi-step inpainting process. We developed a new network configuration, Dense-Unet, to achieve optimal performance with low computational cost. Results after the calcium removal process were validated by comparing with gold-standard X-ray angiography. Our results demonstrated that removing coronary calcification from images with the proposed approach was feasible, and may potentially improve the diagnostic accuracy of CTA.

cs.CV↗