Inf-Net: Automatic COVID-19 Lung Infection Segmentation From CT Images

The application of industry 4.0 technologies in pandemic management: Literature review and case study

The Covid-19 pandemic impact on people's lives has been devastating. Around the world, people have been forced to stay home, resorting to the use of digital technologies in an effort to continue their life and work as best they can. Covid-19 has thus accelerated society's digital transformation towards Industry 4.0 (the fourth industrial revolution). Using scientometric analysis, this study presents a systematic literature review of the themes within Industry 4.0. Thematic analysis reveals that the Internet of Things (IoT), Artificial Intelligence (AI), Cloud computing, Machine learning, Security, Big Data, Blockchain, Deep learning, Digitalization, and Cyber-physical system (CPS) to be the key technologies associated with Industry 4.0. Subsequently, a case study using Industry 4.0 technologies to manage the Covid-19 pandemic is discussed. In conclusion, Covid-19,is clearly shown to be an accelerant in the progression towards Industry 4.0. Moreover, the technologies of this digital transformation can be expected to be invoked in the management of future pandemics.

Full Scale Attention for Automated COVID-19 Diagnosis from CT Images

The wide spread of coronavirus pneumonia (COVID-19) has been a severe threat to global health since 2019. Apart from the nucleic acid detection, medical imaging examination is a vital diagnostic modality to confirm and treat the disease. Thus, implementing the automatic diagnosis of the COVID-19 bears particular significance. However, the limitations of data quality and size strongly hinder the clas-sification and segmentation performance and it also result in high misdiagnosis rate. To this end, we propose a novel full scale attention mechanism (FUSA) to capture more contextual dependencies of features, which enables the model easier to classify positive cases and improve the sensitivity. Specifically, FUSA parallelly extracts the information of channel domain and spatial domain, and fuses them together. The experimental study shows FUSA can significantly improve the COVID-19 automated diagnosis performance and eliminate false negative cases compared with other state-of-the-art ones.

Exploiting Shared Knowledge From Non-COVID Lesions for Annotation-Efficient COVID-19 CT Lung Infection Segmentation

The novel Coronavirus disease (COVID-19) is a highly contagious virus and has spread all over the world, posing an extremely serious threat to all countries. Automatic lung infection segmentation from computed tomography (CT) plays an important role in the quantitative analysis of COVID-19. However, the major challenge lies in the inadequacy of annotated COVID-19 datasets. Currently, there are several public non-COVID lung lesion segmentation datasets, providing the potential for generalizing useful information to the related COVID-19 segmentation task. In this paper, we propose a novel relation-driven collaborative learning model to exploit shared knowledge from non-COVID lesions for annotation-efficient COVID-19 CT lung infection segmentation. The model consists of a general encoder to capture general lung lesion features based on multiple non-COVID lesions, and a target encoder to focus on task-specific features based on COVID-19 infections. We develop a collaborative learning scheme to regularize feature-level relation consistency of given input and encourage the model to learn more general and discriminative representation of COVID-19 infections. Extensive experiments demonstrate that trained with limited COVID-19 data, exploiting shared knowledge from non-COVID lesions can further improve state-of-the-art performance with up to 3.0% in dice similarity coefficient and 4.2% in normalized surface dice. In addition, experimental results on large scale 2D dataset with CT slices show that our method significantly outperforms cutting-edge segmentation methods metrics. Our method promotes new insights into annotation-efficient deep learning and illustrates strong potential for real-world applications in the global fight against COVID-19 in the absence of sufficient high-quality annotations.

DR-MIL: deep represented multiple instance learning distinguishes COVID-19 from community-acquired pneumonia in CT images

BACKGROUND AND OBJECTIVE

Given that the novel coronavirus disease 2019 (COVID-19) has become a pandemic, a method to accurately distinguish COVID-19 from community-acquired pneumonia (CAP) is urgently needed. However, the spatial uncertainty and morphological diversity of COVID-19 lesions in the lungs, and subtle differences with respect to CAP, make differential diagnosis non-trivial.

METHODS

We propose a deep represented multiple instance learning (DR-MIL) method to fulfill this task. A 3D volumetric CT scan of one patient is treated as one bag and ten CT slices are selected as the initial instances. For each instance, deep features are extracted from the pre-trained ResNet-50 with fine-tuning and represented as one deep represented instance score (DRIS). Each bag with a DRIS for each initial instance is then input into a citation k-nearest neighbor search to generate the final prediction. A total of 141 COVID-19 and 100 CAP CT scans were used. The performance of DR-MIL is compared with other potential strategies and state-of-the-art models.

RESULTS

DR-MIL displayed an accuracy of 95% and an area under curve of 0.943, which were superior to those observed for comparable methods. COVID-19 and CAP exhibited significant differences in both the DRIS and the spatial pattern of lesions (p<0.001). As a means of content-based image retrieval, DR-MIL can identify images used as key instances, references, and citers for visual interpretation.

CONCLUSIONS

DR-MIL can effectively represent the deep characteristics of COVID-19 lesions in CT images and accurately distinguish COVID-19 from CAP in a weakly supervised manner. The resulting DRIS is a useful supplement to visual interpretation of the spatial pattern of lesions when screening for COVID-19.

CARes-UNet: Content-aware residual UNet for lesion segmentation of COVID-19 from chest CT images

PURPOSE

Coronavirus disease 2019 (COVID-19) has caused a serious global health crisis. It has been proven that the deep learning method has great potential to assist doctors in diagnosing COVID-19 by automatically segmenting the lesions in computed tomography (CT) slices. However, there are still several challenges restricting the application of these methods, including high variation in lesion characteristics and low contrast between lesion areas and healthy tissues. Moreover, the lack of high-quality labeled samples and large number of patients lead to the urgency to develop a high accuracy model, which performs well not only under supervision but also with semi-supervised methods.

METHODS

We propose a content-aware lung infection segmentation deep residual network (content-aware residual UNet (CARes-UNet)) to segment the lesion areas of COVID-19 from the chest CT slices. In our CARes-UNet, the residual connection was used in the convolutional block, which alleviated the degradation problem during the training. Then, the content-aware upsampling modules were introduced to improve the performance of the model while reducing the computation cost. Moreover, to achieve faster convergence, an advanced optimizer named Ranger was utilized to update the model's parameters during training. Finally, we employed a semi-supervised segmentation framework to deal with the problem of lacking pixel-level labeled data.

RESULTS

We evaluated our approach using three public datasets with multiple metrics and compared its performance to several models. Our method outperforms other models in multiple indicators, for instance in terms of Dice coefficient on COVID-SemiSeg Dataset, CARes-UNet got the score 0.731, and semi-CARes-UNet further boosted it to 0.776. More ablation studies were done and validated the effectiveness of each key component of our proposed model.

CONCLUSIONS

Compared with the existing neural network methods applied to the COVID-19 lesion segmentation tasks, our CARes-UNet can gain more accurate segmentation results, and semi-CARes-UNet can further improve it using semi-supervised learning methods while presenting a possible way to solve the problem of lack of high-quality annotated samples. Our CARes-UNet and semi-CARes-UNet can be used in artificial intelligence-empowered computer-aided diagnosis system to improve diagnostic accuracy in this ongoing COVID-19 pandemic.

Multilevel depth-wise context attention network with atrous mechanism for segmentation of COVID19 affected regions

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) also named COVID-19, aggressively spread all over the world in just a few months. Since then, it has multiple variants that are far more contagious than its parent. Rapid and accurate diagnosis of COVID-19 and its variants are crucial for its treatment, analysis of lungs damage and quarantine management. Deep learning-based solution for efficient and accurate diagnosis to COVID-19 and its variants using Chest X-rays, and computed tomography images could help to counter its outbreak. This work presents a novel depth-wise residual network with an atrous mechanism for accurate segmentation and lesion location of COVID-19 affected areas using volumetric CT images. The proposed framework consists of 3D depth-wise and 3D residual squeeze and excitation block in cascaded and parallel to capture uniformly multi-scale context (low-level detailed, mid-level comprehensive and high-level rich semantic features). The squeeze and excitation block adaptively recalibrates channel-wise feature responses by explicitly modeling inter-dependencies between various channels. We further have introduced an atrous mechanism with a different atrous rate as the bottom layer. Extensive experiments on benchmark CT datasets showed considerable gain (5%) for accurate segmentation and lesion location of COVID-19 affected areas.

An Encoder-Decoder-Based Method for Segmentation of COVID-19 Lung Infection in CT Images

The novelty of the COVID-19 Disease and the speed of spread, created colossal chaotic, impulse all the worldwide researchers to exploit all resources and capabilities to understand and analyze characteristics of the coronavirus in terms of spread ways and virus incubation time. For that, the existing medical features such as CT-scan and X-ray images are used. For example, CT-scan images can be used for the detection of lung infection. However, the quality of these images and infection characteristics limit the effectiveness of these features. Using artificial intelligence (AI) tools and computer vision algorithms, the accuracy of detection can be more accurate and can help to overcome these issues. In this paper, we propose a multi-task deep-learning-based method for lung infection segmentation on CT-scan images. Our proposed method starts by segmenting the lung regions that may be infected. Then, segmenting the infections in these regions. In addition, to perform a multi-class segmentation the proposed model is trained using the two-stream inputs. The multi-task learning used in this paper allows us to overcome the shortage of labeled data. In addition, the multi-input stream allows the model to learn from many features that can improve the results. To evaluate the proposed method, many metrics have been used including Sorensen-Dice similarity, Sensitivity, Specificity, Precision, and MAE metrics. As a result of experiments, the proposed method can segment lung infections with high performance even with the shortage of data and labeled images. In addition, comparing with the state-of-the-art method our method achieves good performance results. For example, the proposed method reached 78..6% for Dice, 71.1% for Sensitivity metric, 99.3% for Specificity 85.6% for Precision, and 0.062 for Mean Average Error metric, which demonstrates the effectiveness of the proposed method for lung infection segmentation.

DW-UNet: Loss Balance under Local-Patch for 3D Infection Segmentation from COVID-19 CT Images

(1) Background: COVID-19 has been global epidemic. This work aims to extract 3D infection from COVID-19 CT images; (2) Methods: Firstly, COVID-19 CT images are processed with lung region extraction and data enhancement. In this strategy, gradient changes of voxels in different directions respond to geometric characteristics. Due to the complexity of tubular tissues in lung region, they are clustered to the lung parenchyma center based on their filtered possibility. Thus, infection is improved after data enhancement. Then, deep weighted UNet is established to refining 3D infection texture, and weighted loss function is introduced. It changes cost calculation of different samples, causing target samples to dominate convergence direction. Finally, the trained network effectively extracts 3D infection from CT images by adjusting driving strategy of different samples. (3) Results: Using Accuracy, Precision, Recall and Coincidence rate, 20 subjects from a private dataset and eight subjects from Kaggle Competition COVID-19 CT dataset tested this method in hold-out validation framework. This work achieved good performance both in the private dataset (99.94-00.02%, 60.42-11.25%, 70.79-09.35% and 63.15-08.35%) and public dataset (99.73-00.12%, 77.02-06.06%, 41.23-08.61% and 52.50-08.18%). We also applied some extra indicators to test data augmentation and different models. The statistical tests have verified the significant difference of different models. (4) Conclusions: This study provides a COVID-19 infection segmentation technology, which provides an important prerequisite for the quantitative analysis of COVID-19 CT images.

Outbreak COVID-19 in Medical Image Processing Using Deep Learning: A State-of-the-Art Review

From the month of December-19, the outbreak of Coronavirus (COVID-19) triggered several deaths and overstated every aspect of individual health. COVID-19 has been designated as a pandemic by World Health Organization. The circumstances placed serious trouble on every country worldwide, particularly with health arrangements and time-consuming responses. The increase in the positive cases of COVID-19 globally spread every day. The quantity of accessible diagnosing kits is restricted because of complications in detecting the existence of the illness. Fast and correct diagnosis of COVID-19 is a timely requirement for the prevention and controlling of the pandemic through suitable isolation and medicinal treatment. The significance of the present work is to discuss the outline of the deep learning techniques with medical imaging such as outburst prediction, virus transmitted indications, detection and treatment aspects, vaccine availability with remedy research. Abundant image resources of medical imaging as X-rays, Computed Tomography Scans, Magnetic Resonance imaging, formulate deep learning high-quality methods to fight against the pandemic COVID-19. The review presents a comprehensive idea of deep learning and its related applications in healthcare received over the past decade. At the last, some issues and confrontations to control the health crisis and outbreaks have been introduced. The progress in technology has contributed to developing individual's lives. The problems faced by the radiologists during medical imaging techniques and deep learning approaches for diagnosing the COVID-19 infections have been also discussed.

Optimized-Unet: Novel Algorithm for Parapapillary Atrophy Segmentation

In recent years, an increasing number of people have myopia in China, especially the younger generation. Common myopia may develop into high myopia. High myopia causes visual impairment and blindness. Parapapillary atrophy (PPA) is a typical retinal pathology related to high myopia, which is also a basic clue for diagnosing high myopia. Therefore, accurate segmentation of the PPA is essential for high myopia diagnosis and treatment. In this study, we propose an optimized Unet (OT-Unet) to solve this important task. OT-Unet uses one of the pre-trained models: Visual Geometry Group (VGG), ResNet, and Res2Net, as a backbone and is combined with edge attention, parallel partial decoder, and reverse attention modules to improve the segmentation accuracy. In general, using the pre-trained models can improve the accuracy with fewer samples. The edge attention module extracts contour information, the parallel partial decoder module combines the multi-scale features, and the reverse attention module integrates high- and low-level features. We also propose an augmented loss function to increase the weight of complex pixels to enable the network to segment more complex lesion areas. Based on a dataset containing 360 images (Including 26 pictures provided by PALM), the proposed OT-Unet achieves a high AUC (Area Under Curve) of 0.9235, indicating a significant improvement over the original Unet (0.7917).

AIoT Used for COVID-19 Pandemic Prevention and Control

The pandemic of COVID-19 is continuing to wreak havoc in 2021, with at least 170 million victims around the world. Healthcare systems are overwhelmed by the large-scale virus infection. Luckily, Internet of Things (IoT) is one of the most effective paradigms in the intelligent world, in which the technology of artificial intelligence (AI), like cloud computing and big data analysis, is playing a vital role in preventing the spread of the pandemic of COVID-19. AI and 5G technologies are advancing by leaps and bounds, further strengthening the intelligence and connectivity of IoT applications, and conventional IoT has been gradually upgraded to be more powerful AI + IoT (AIoT). For example, in terms of remote screening and diagnosis of COVID-19 patients, AI technology based on machine learning and deep learning has recently upgraded medical equipment significantly and has reshaped the workflow with minimal contact with patients, so medical specialists can make clinical decisions more efficiently, providing the best protection not only to patients but also to specialists themselves. This paper reviews the latest progress made in combating COVID-19 with both IoT and AI and also provides comprehensive details on how to combat the pandemic of COVID-19 as well as the technologies that may be applied in the future.

Domain-Adaptive Artificial Intelligence-Based Model for Personalized Diagnosis of Trivial Lesions Related to COVID-19 in Chest Computed Tomography Scans

BACKGROUND

Early and accurate detection of COVID-19-related findings (such as well-aerated regions, ground-glass opacity, crazy paving and linear opacities, and consolidation in lung computed tomography (CT) scan) is crucial for preventive measures and treatment. However, the visual assessment of lung CT scans is a time-consuming process particularly in case of trivial lesions and requires medical specialists.

METHOD

A recent breakthrough in deep learning methods has boosted the diagnostic capability of computer-aided diagnosis (CAD) systems and further aided health professionals in making effective diagnostic decisions. In this study, we propose a domain-adaptive CAD framework, namely the dilated aggregation-based lightweight network (DAL-Net), for effective recognition of trivial COVID-19 lesions in CT scans. Our network design achieves a fast execution speed (inference time is 43 ms on a single image) with optimal memory consumption (almost 9 MB). To evaluate the performances of the proposed and state-of-the-art models, we considered two publicly accessible datasets, namely COVID-19-CT-Seg (comprising a total of 3520 images of 20 different patients) and MosMed (including a total of 2049 images of 50 different patients).

RESULTS

Our method exhibits average area under the curve (AUC) up to 98.84%, 98.47%, and 95.51% for COVID-19-CT-Seg, MosMed, and cross-dataset, respectively, and outperforms various state-of-the-art methods.

CONCLUSIONS

These results demonstrate that deep learning-based models are an effective tool for building a robust CAD solution based on CT data in response to present disaster of COVID-19.

Fusion of intelligent learning for COVID-19: A state-of-the-art review and analysis on real medical data

The unprecedented surge of a novel coronavirus in the month of December 2019, named as COVID-19 by the World Health organization has caused a serious impact on the health and socioeconomic activities of the public all over the world. Since its origin, the number of infected and deceased cases has been growing exponentially in almost all the affected countries of the world. The rapid spread of the novel coronavirus across the world results in the scarcity of medical resources and overburdened hospitals. As a result, the researchers and technocrats are continuously working across the world for the inculcation of efficient strategies which may assist the government and healthcare system in controlling and managing the spread of the COVID-19 pandemic. Therefore, this study provides an extensive review of the ongoing strategies such as diagnosis, prediction, drug and vaccine development and preventive measures used in combating the COVID-19 along with technologies used and limitations. Moreover, this review also provides a comparative analysis of the distinct type of data, emerging technologies, approaches used in diagnosis and prediction of COVID-19, statistics of contact tracing apps, vaccine production platforms used in the COVID-19 pandemic. Finally, the study highlights some challenges and pitfalls observed in the systematic review which may assist the researchers to develop more efficient strategies used in controlling and managing the spread of COVID-19.

C+EffxNet: A novel hybrid approach for COVID-19 diagnosis on CT images based on CBAM and EfficientNet

COVID-19, one of the biggest diseases of our age, continues to spread rapidly around the world. Studies continue rapidly for the diagnosis and treatment of this disease. It is of great importance that individuals who are infected with this virus be isolated from the rest of the society so that the disease does not spread further. In addition to the tests performed in the detection process of the patients, X-ray and computed tomography are also used. In this study, a new hybrid model that can diagnose COVID-19 from computed tomography images created using EfficientNet, one of the current deep learning models, with a model consisting of attention blocks is proposed. In the first step of this new model, channel attention, spatial attention, and residual blocks are used to extract the most important features from the images. The extracted features are combined in accordance with the hyper-column technique. The combined features are given as input to the EfficientNet models in the second step of the model. The deep features obtained from this proposed hybrid model were classified with the Support Vector Machine classifier after feature selection. Principal Components Analysis was used for feature selection. The approach can accurately predict COVID-19 with a 99% accuracy rate. The first four versions of EfficientNet are used in the approach. In addition, Bayesian optimization was used in the hyper parameter estimation of the Support Vector Machine classifier. Comparative performance analysis of the approach with other approaches in the field is given.

Label-Free Segmentation of COVID-19 Lesions in Lung CT

Scarcity of annotated images hampers the building of automated solution for reliable COVID-19 diagnosis and evaluation from CT. To alleviate the burden of data annotation, we herein present a label-free approach for segmenting COVID-19 lesions in CT via voxel-level anomaly modeling that mines out the relevant knowledge from normal CT lung scans. Our modeling is inspired by the observation that the parts of tracheae and vessels, which lay in the high-intensity range where lesions belong to, exhibit strong patterns. To facilitate the learning of such patterns at a voxel level, we synthesize 'lesions' using a set of simple operations and insert the synthesized 'lesions' into normal CT lung scans to form training pairs, from which we learn a normalcy-recognizing network (NormNet) that recognizes normal tissues and separate them from possible COVID-19 lesions. Our experiments on three different public datasets validate the effectiveness of NormNet, which conspicuously outperforms a variety of unsupervised anomaly detection (UAD) methods.

DEANet: Dual Encoder with Attention Network for Semantic Segmentation of Remote Sensing Imagery

Remote sensing has now been widely used in various fields, and the research on the automatic land-cover segmentation methods of remote sensing imagery is significant to the development of remote sensing technology. Deep learning methods, which are developing rapidly in the field of semantic segmentation, have been widely applied to remote sensing imagery segmentation. In this work, a novel deep learning network—Dual Encoder with Attention Network (DEANet) is proposed. In this network, a dual-branch encoder structure, whose first branch is used to generate a rough guidance feature map as area attention to help re-encode feature maps in the next branch, is proposed to improve the encoding ability of the network, and an improved pyramid partial decoder (PPD) based on the parallel partial decoder is put forward to make fuller use of the features form the encoder along with the receptive filed block (RFB). In addition, an edge attention module using the transfer learning method is introduced to explicitly advance the segmentation performance in edge areas. Except for structure, a loss function composed with the weighted Cross Entropy (CE) loss and weighted Union subtract Intersection (UsI) loss is designed for training, where UsI loss represents a new region-based aware loss which replaces the IoU loss to adapt to multi-classification tasks. Furthermore, a detailed training strategy for the network is introduced as well. Extensive experiments on three public datasets verify the effectiveness of each proposed module in our framework and demonstrate that our method achieves more excellent performance over some state-of-the-art methods.

A Histogram-Based Low-Complexity Approach for the Effective Detection of COVID-19 Disease from CT and X-ray Images

The global COVID-19 pandemic certainly has posed one of the more difficult challenges for researchers in the current century. The development of an automatic diagnostic tool, able to detect the disease in its early stage, could undoubtedly offer a great advantage to the battle against the pandemic. In this regard, most of the research efforts have been focused on the application of Deep Learning (DL) techniques to chest images, including traditional chest X-rays (CXRs) and Computed Tomography (CT) scans. Although these approaches have demonstrated their effectiveness in detecting the COVID-19 disease, they are of huge computational complexity and require large datasets for training. In addition, there may not exist a large amount of COVID-19 CXRs and CT scans available to researchers. To this end, in this paper, we propose an approach based on the evaluation of the histogram from a common class of images that is considered as the target. A suitable inter-histogram distance measures how this target histogram is far from the histogram evaluated on a test image: if this distance is greater than a threshold, the test image is labeled as anomaly, i.e., the scan belongs to a patient affected by COVID-19 disease. Extensive experimental results and comparisons with some benchmark state-of-the-art methods support the effectiveness of the developed approach, as well as demonstrate that, at least when the images of the considered datasets are homogeneous enough (i.e., a few outliers are present), it is not really needed to resort to complex-to-implement DL techniques, in order to attain an effective detection of the COVID-19 disease. Despite the simplicity of the proposed approach, all the considered metrics (i.e., accuracy, precision, recall, and F-measure) attain a value of 1.0 under the selected datasets, a result comparable to the corresponding state-of-the-art DNN approaches, but with a remarkable computational simplicity.

Per-COVID-19: A Benchmark Dataset for COVID-19 Percentage Estimation from CT-Scans

COVID-19 infection recognition is a very important step in the fight against the COVID-19 pandemic. In fact, many methods have been used to recognize COVID-19 infection including Reverse Transcription Polymerase Chain Reaction (RT-PCR), X-ray scan, and Computed Tomography scan (CT- scan). In addition to the recognition of the COVID-19 infection, CT scans can provide more important information about the evolution of this disease and its severity. With the extensive number of COVID-19 infections, estimating the COVID-19 percentage can help the intensive care to free up the resuscitation beds for the critical cases and follow other protocol for less severity cases. In this paper, we introduce COVID-19 percentage estimation dataset from CT-scans, where the labeling process was accomplished by two expert radiologists. Moreover, we evaluate the performance of three Convolutional Neural Network (CNN) architectures: ResneXt-50, Densenet-161, and Inception-v3. For the three CNN architectures, we use two loss functions: MSE and Dynamic Huber. In addition, two pretrained scenarios are investigated (ImageNet pretrained models and pretrained models using X-ray data). The evaluated approaches achieved promising results on the estimation of COVID-19 infection. Inception-v3 using Dynamic Huber loss function and pretrained models using X-ray data achieved the best performance for slice-level results: 0.9365, 5.10, and 9.25 for Pearson Correlation coefficient (PC), Mean Absolute Error (MAE), and Root Mean Square Error (RMSE), respectively. On the other hand, the same approach achieved 0.9603, 4.01, and 6.79 for PCsubj, MAEsubj, and RMSEsubj, respectively, for subject-level results. These results prove that using CNN architectures can provide accurate and fast solution to estimate the COVID-19 infection percentage for monitoring the evolution of the patient state.

COVID-19: A Comprehensive Review of Learning Models

Coronavirus disease is communicable and inhibits the infected person's immune system. It belongs to the Coronaviridae family and has affected 213 nations and territories so far. Many kinds of studies are being carried out to filter advice and provide oversight to monitor this outbreak. A comparative and brief review was carried out in this paper on research concerning the early identification of symptoms, estimation of the end of the pandemic, and examination of user-generated conversations. Chest X-ray images, abdominal computed tomography scan, tweets shared on social media are several of the datasets used by researchers. Using machine learning and deep learning methods such as K-means clustering, Random Forest, Convolutional Neural Network, Long Short-Term Memory, Auto-Encoder, and Regression approaches, the above-mentioned datasets are processed. The studies on COVID-19 with machine learning and deep learning models with their results and limitations are outlined in this article. The challenges with open future research directions are discussed at the end.

A weakly supervised learning method based on attention fusion for Covid-19 segmentation in CT images

Since the end of 2019, the COVID-19, which has swept across the world, has caused serious impacts on public health and economy. Although Reverse Transcription-Polymerase Chain Reaction (RT-PCR) is the gold standard for clinical diagnosis, it is very time-consuming and labor-intensive. At the same time, more and more people have doubted the sensitivity of RT-PCR. Therefore, Computed Tomography (CT) images are used as a substitute for RT-PCR. Powered by the research of the field of artificial intelligence, deep learning, which is a branch of machine learning, has made a great success on medical image segmentation. However, general full supervision methods require pixel-level point-by-point annotations, which is very costly. In this paper, we put forward an image segmentation method based on weakly supervised learning for CT images of COVID-19, which can effectively segment the lung infection area and doesn’t require pixel-level labels. Our method is contrasted with another four weakly supervised learning methods in recent years, and the results have been significantly improved.

Automatic deep learning system for COVID-19 infection quantification in chest CT

The paper proposes an automatic deep learning system for COVID-19 infection areas segmentation in chest CT scans. CT imaging proved its ability to detect the COVID-19 disease even for asymptotic patients, which make it a trustworthy alternative for PCR. Coronavirus disease spread globally and PCR screening is the adopted diagnostic testing method for COVID-19 detection. However, PCR is criticized due its low sensitivity ratios, also, it is time-consuming and manual complicated process. The proposed framework includes different steps; it starts to prepare the region of interest by segmenting the lung organ, which then undergoes edge enhancing diffusion filtering (EED) to improve the infection areas contrast and intensity homogeneity. The proposed FCN is implemented using U-net architecture with modified residual block to include concatenation skip connection. The block improves the learning of gradient values by forwarding the infection area features through the network. The proposed system is evaluated using different measures and achieved dice overlapping score of 0.961 and 0.780 for lung and infection areas segmentation, respectively. The proposed system is trained and tested using many 2D CT slices extracted from diverse datasets from different sources, which demonstrate the system generalization and effectiveness. The use of more datasets from different sources helps to enhance the system accuracy and generalization, which can be accomplished based on the data availability in in the future.

Unsupervised domain adaptation based COVID-19 CT infection segmentation network

Automatic segmentation of infection areas in computed tomography (CT) images has proven to be an effective diagnostic approach for COVID-19. However, due to the limited number of pixel-level annotated medical images, accurate segmentation remains a major challenge. In this paper, we propose an unsupervised domain adaptation based segmentation network to improve the segmentation performance of the infection areas in COVID-19 CT images. In particular, we propose to utilize the synthetic data and limited unlabeled real COVID-19 CT images to jointly train the segmentation network. Furthermore, we develop a novel domain adaptation module, which is used to align the two domains and effectively improve the segmentation network's generalization capability to the real domain. Besides, we propose an unsupervised adversarial training scheme, which encourages the segmentation network to learn the domain-invariant feature, so that the robust feature can be used for segmentation. Experimental results demonstrate that our method can achieve state-of-the-art segmentation performance on COVID-19 CT images.

A multi-class COVID-19 segmentation network with pyramid attention and edge loss in CT images

At the end of 2019, a novel coronavirus COVID-19 broke out. Due to its high contagiousness, more than 74 million people have been infected worldwide. Automatic segmentation of the COVID-19 lesion area in CT images is an effective auxiliary medical technology which can quantitatively diagnose and judge the severity of the disease. In this paper, a multi-class COVID-19 CT image segmentation network is proposed, which includes a pyramid attention module to extract multi-scale contextual attention information, and a residual convolution module to improve the discriminative ability of the network. A wavelet edge loss function is also proposed to extract edge features of the lesion area to improve the segmentation accuracy. For the experiment, a dataset of 4369 CT slices is constructed, including three symptoms: ground glass opacities, interstitial infiltrates, and lung consolidation. The dice similarity coefficients of three symptoms of the model achieve 0.7704, 0.7900, 0.8241 respectively. The performance of the proposed network on public dataset COVID-SemiSeg is also evaluated. The results demonstrate that this model outperforms other state-of-the-art methods and can be a powerful tool to assist in the diagnosis of positive infection cases, and promote the development of intelligent technology in the medical field.

CovTANet: A Hybrid Tri-Level Attention-Based Network for Lesion Segmentation, Diagnosis, and Severity Prediction of COVID-19 Chest CT Scans

Rapid and precise diagnosis of COVID-19 is one of the major challenges faced by the global community to control the spread of this overgrowing pandemic. In this article, a hybrid neural network is proposed, named CovTANet, to provide an end-to-end clinical diagnostic tool for early diagnosis, lesion segmentation, and severity prediction of COVID-19 utilizing chest computer tomography (CT) scans. A multiphase optimization strategy is introduced for solving the challenges of complicated diagnosis at a very early stage of infection, where an efficient lesion segmentation network is optimized initially, which is later integrated into a joint optimization framework for the diagnosis and severity prediction tasks providing feature enhancement of the infected regions. Moreover, for overcoming the challenges with diffused, blurred, and varying shaped edges of COVID lesions with novel and diverse characteristics, a novel segmentation network is introduced, namely tri-level attention-based segmentation network. This network has significantly reduced semantic gaps in subsequent encoding-decoding stages, with immense parallelization of multiscale features for faster convergence providing considerable performance improvement over traditional networks. Furthermore, a novel tri-level attention mechanism has been introduced, which is repeatedly utilized over the network, combining channel, spatial, and pixel attention schemes for faster and efficient generalization of contextual information embedded in the feature map through feature recalibration and enhancement operations. Outstanding performances have been achieved in all three tasks through extensive experimentation on a large publicly available dataset containing 1110 chest CT-volumes, which signifies the effectiveness of the proposed scheme at the current stage of the pandemic.

COVID-19 Imaging-based AI Research - A Literature Review

BACKGROUND

The new coronavirus disease 2019 (COVID-19) is spreading rapidly around the world. Artificial intelligence (AI) assisted identification and detection of diseases is an ef-fective method of medical diagnosis.

OBJECTIVES

To present recent advances in AI-assisted diagnosis of COVID-19, we introduce major aspects of AI in the process of diagnosing COVID-19.

METHODS

In this paper, we firstly cover the latest collection and processing methods of da-tasets of COVID-19. The processing methods mainly include building public datasets, transfer learning, unsupervised learning and weakly supervised learning, semi-supervised learning methods and so on. Secondly, we introduce the algorithm application and evaluation metrics of AI in medical imaging segmentation and automatic screening. Then, we introduce the quantifi-cation and severity assessment of infection in COVID-19 patients based on image segmenta-tion and automatic screening. Finally, we analyze and point out the current AI-assisted diagno-sis of COVID-19 problems, which may provide useful clues for future work.

CONCLUSION

AI is critical for COVID-19 diagnosis. Combining chest imaging with AI can not only save time and effort, but also provide more accurate and efficient medical diagnosis results.

An Effective Deep Neural Network for Lung Lesions Segmentation From COVID-19 CT Images

Automatic segmentation of lung lesions from COVID-19 computed tomography (CT) images can help to establish a quantitative model for diagnosis and treatment. For this reason, this article provides a new segmentation method to meet the needs of CT images processing under COVID-19 epidemic. The main steps are as follows: First, the proposed region of interest extraction implements patch mechanism strategy to satisfy the applicability of 3-D network and remove irrelevant background. Second, 3-D network is established to extract spatial features, where 3-D attention model promotes network to enhance target area. Then, to improve the convergence of network, a combination loss function is introduced to lead gradient optimization and training direction. Finally, data augmentation and conditional random field are applied to realize data resampling and binary segmentation. This method was assessed with some comparative experiment. By comparison, the proposed method reached the highest performance. Therefore, it has potential clinical applications.

COVID-19 Lesion Segmentation Using Lung CT Scan Images: Comparative Study Based on Active Contour Models

Pneumonia is a lung infection that threatens all age groups. In this paper, we use CT scans to investigate the effectiveness of active contour models (ACMs) for segmentation of pneumonia caused by the Coronavirus disease (COVID-19) as one of the successful methods for image segmentation. A comparison has been made between the performances of the state-of-the-art methods performed based on a database of lung CT scan images. This review helps the reader to identify starting points for research in the field of active contour models on COVID-19, which is a high priority for researchers and practitioners. Finally, the experimental results indicate that active contour methods achieve promising results when there are not enough images to use deep learning-based methods as one of the powerful tools for image segmentation.

Automatic detection of COVID-19 using pruned GLCM-Based texture features and LDCRF classification

Recently, automatic computer-aided detection (CAD) of COVID-19 using radiological images has received a great deal of attention from many researchers and medical practitioners, and consequently several CAD frameworks and methods have been presented in the literature to assist the radiologist physicians in performing diagnostic COVID-19 tests quickly, reliably and accurately. This paper presents an innovative framework for the automatic detection of COVID-19 from chest X-ray (CXR) images, in which a rich and effective representation of lung tissue patterns is generated from the gray level co-occurrence matrix (GLCM) based textural features. The input CXR image is first preprocessed by spatial filtering along with median filtering and contrast limited adaptive histogram equalization to improve the CXR image's poor quality and reduce image noise. Automatic thresholding by the optimized formula of Otsu's method is applied to find a proper threshold value to best segment lung regions of interest (ROIs) out from CXR images. Then, a concise set of GLCM-based texture features is extracted to accurately represent the segmented lung ROIs of each CXR image. Finally, the normalized features are fed into a trained discriminative latent-dynamic conditional random fields (LDCRFs) model for fine-grained classification to divide the cases into two categories: COVID-19 and non-COVID-19. The presented method has been experimentally tested and validated on a relatively large dataset of frontal CXR images, achieving an average accuracy, precision, recall, and F1-score of 95.88%, 96.17%, 94.45%, and 95.79%, respectively, which compare favorably with and occasionally exceed those previously reported in similar studies in the literature.

Accurate detection of COVID-19 using deep features based on X-Ray images and feature selection methods

COVID-19 is a severe epidemic affecting the whole world. This epidemic, which has a high mortality rate, affects the health systems and the economies of countries significantly. Therefore, ending the epidemic is one of the most important priorities of all states. For this, automatic diagnosis and detection systems are very important to control the epidemic. In addition to the recommendation of the “reverse transcription-polymerase chain reaction (RT-PCR)” test, additional diagnosis and detection systems are required. Hence, based on the fact that the COVID-19 virus attacks the lungs, automatic diagnosis and detection systems developed using X-ray and CT images come to the fore. In this study, a high-performance detection system was implemented with three different CNN (ResNet50, ResNet101, InceptionResNetV2) models and X-ray images of three different classes (COVID-19, Normal, Pneumonia). The particle swarm optimization (PSO) algorithm and ant colony algorithm (ACO) was applied among the feature selection methods, and their performances were compared. The results were obtained using support vector machines (SVM) and a k-nearest neighbor (k-NN) classifier using the 10-fold cross-validation method. The highest overall accuracy performance was 99.83% with the SVM algorithm without feature selection. The highest performance was achieved after the feature selection process with the SVM + PSO method as 99.86%. As a result, higher performance with less computational load has been achieved by realizing the feature selection. Based on the high results obtained, it is thought that this study will benefit radiologists as a decision support system.

A Comprehensive Survey of COVID-19 Detection Using Medical Images

The outbreak of the Coronavirus disease 2019 (COVID-19) caused the death of a large number of people and declared as a pandemic by the World Health Organization. Millions of people are infected by this virus and are still getting infected every day. As the cost and required time of conventional Reverse Transcription Polymerase Chain Reaction (RT-PCR) tests to detect COVID-19 is uneconomical and excessive, researchers are trying to use medical images such as X-ray and Computed Tomography (CT) images to detect this disease with the help of Artificial Intelligence (AI)-based systems, to assist in automating the scanning procedure. In this paper, we reviewed some of these newly emerging AI-based models that can detect COVID-19 from X-ray or CT of lung images. We collected information about available research resources and inspected a total of 80 papers till June 20, 2020. We explored and analyzed data sets, preprocessing techniques, segmentation methods, feature extraction, classification, and experimental results which can be helpful for finding future research directions in the domain of automatic diagnosis of COVID-19 disease using AI-based frameworks. It is also reflected that there is a scarcity of annotated medical images/data sets of COVID-19 affected people, which requires enhancing, segmentation in preprocessing, and domain adaptation in transfer learning for a model, producing an optimal result in model performance. This survey can be the starting point for a novice/beginner level researcher to work on COVID-19 classification.

X-Ray Equipped with Artificial Intelligence: Changing the COVID-19 Diagnostic Paradigm during the Pandemic

PURPOSE

Due to the excessive use of raw materials in diagnostic tools and equipment during the COVID-19 pandemic, there is a dire need for cheaper and more effective methods in the healthcare system. With the development of artificial intelligence (AI) methods in medical sciences as low-cost and safer diagnostic methods, researchers have turned their attention to the use of imaging tools with AI that have fewer complications for patients and reduce the consumption of healthcare resources. Despite its limitations, X-ray is suggested as the first-line diagnostic modality for detecting and screening COVID-19 cases.

METHOD

This systematic review assessed the current state of AI applications and the performance of algorithms in X-ray image analysis. The search strategy yielded 322 results from four databases and google scholar, 60 of which met the inclusion criteria. The performance statistics included the area under the receiver operating characteristics (AUC) curve, accuracy, sensitivity, and specificity.

RESULT

The average sensitivity and specificity of CXR equipped with AI algorithms for COVID-19 diagnosis were >96% (83%-100%) and 92% (80%-100%), respectively. For common X-ray methods in COVID-19 detection, these values were 0.56 (95% CI 0.51-0.60) and 0.60 (95% CI 0.54-0.65), respectively. AI has substantially improved the diagnostic performance of X-rays in COVID-19.

CONCLUSION

X-rays equipped with AI can serve as a tool to screen the cases requiring CT scans. The use of this tool does not waste time or impose extra costs, has minimal complications, and can thus decrease or remove unnecessary CT slices and other healthcare resources.

iCOVID: interpretable deep learning framework for early recovery-time prediction of COVID-19 patients

Most prior studies focused on developing models for the severity or mortality prediction of COVID-19 patients. However, effective models for recovery-time prediction are still lacking. Here, we present a deep learning solution named iCOVID that can successfully predict the recovery-time of COVID-19 patients based on predefined treatment schemes and heterogeneous multimodal patient information collected within 48 hours after admission. Meanwhile, an interpretable mechanism termed FSR is integrated into iCOVID to reveal the features greatly affecting the prediction of each patient. Data from a total of 3008 patients were collected from three hospitals in Wuhan, China, for large-scale verification. The experiments demonstrate that iCOVID can achieve a time-dependent concordance index of 74.9% (95% CI: 73.6-76.3%) and an average day error of 4.4 days (95% CI: 4.2-4.6 days). Our study reveals that treatment schemes, age, symptoms, comorbidities, and biomarkers are highly related to recovery-time predictions.

Domain adaptation based self-correction model for COVID-19 infection segmentation in CT images

The capability of generalization to unseen domains is crucial for deep learning models when considering real-world scenarios. However, current available medical image datasets, such as those for COVID-19 CT images, have large variations of infections and domain shift problems. To address this issue, we propose a prior knowledge driven domain adaptation and a dual-domain enhanced self-correction learning scheme. Based on the novel learning scheme, a domain adaptation based self-correction model (DASC-Net) is proposed for COVID-19 infection segmentation on CT images. DASC-Net consists of a novel attention and feature domain enhanced domain adaptation model (AFD-DA) to solve the domain shifts and a self-correction learning process to refine segmentation results. The innovations in AFD-DA include an image-level activation feature extractor with attention to lung abnormalities and a multi-level discrimination module for hierarchical feature domain alignment. The proposed self-correction learning process adaptively aggregates the learned model and corresponding pseudo labels for the propagation of aligned source and target domain information to alleviate the overfitting to noises caused by pseudo labels. Extensive experiments over three publicly available COVID-19 CT datasets demonstrate that DASC-Net consistently outperforms state-of-the-art segmentation, domain shift, and coronavirus infection segmentation methods. Ablation analysis further shows the effectiveness of the major components in our model. The DASC-Net enriches the theory of domain adaptation and self-correction learning in medical imaging and can be generalized to multi-site COVID-19 infection segmentation on CT images for clinical deployment.

Precise Segmentation of COVID-19 Infected Lung from CT Images Based on Adaptive First-Order Appearance Model with Morphological/Anatomical Constraints

A new segmentation technique is introduced for delineating the lung region in 3D computed tomography (CT) images. To accurately model the distribution of Hounsfield scale values within both chest and lung regions, a new probabilistic model is developed that depends on a linear combination of Gaussian (LCG). Moreover, we modified the conventional expectation-maximization (EM) algorithm to be run in a sequential way to estimate both the dominant Gaussian components (one for the lung region and one for the chest region) and the subdominant Gaussian components, which are used to refine the final estimated joint density. To estimate the marginal density from the mixed density, a modified k-means clustering approach is employed to classify the Gaussian subdominant components to determine which components belong properly to a lung and which components belong to a chest. The initial segmentation, based on the LCG-model, is then refined by the imposition of 3D morphological constraints based on a 3D Markov-Gibbs random field (MGRF) with analytically estimated potentials. The proposed approach was tested on CT data from 32 coronavirus disease 2019 (COVID-19) patients. Segmentation quality was quantitatively evaluated using four metrics: Dice similarity coefficient (DSC), overlap coefficient, 95th-percentile bidirectional Hausdorff distance (BHD), and absolute lung volume difference (ALVD), and it achieved 95.67±1.83%, 91.76±3.29%, 4.86±5.01, and 2.93±2.39, respectively. The reported results showed the capability of the proposed approach to accurately segment healthy lung tissues in addition to pathological lung tissues caused by COVID-19, outperforming four current, state-of-the-art deep learning-based lung segmentation approaches.

Self-Ensembling Co-Training Framework for Semi-Supervised COVID-19 CT Segmentation

The coronavirus disease 2019 (COVID-19) has become a severe worldwide health emergency and is spreading at a rapid rate. Segmentation of COVID lesions from computed tomography (CT) scans is of great importance for supervising disease progression and further clinical treatment. As labeling COVID-19 CT scans is labor-intensive and time-consuming, it is essential to develop a segmentation method based on limited labeled data to conduct this task. In this paper, we propose a self-ensembled co-training framework, which is trained by limited labeled data and large-scale unlabeled data, to automatically extract COVID lesions from CT scans. Specifically, to enrich the diversity of unsupervised information, we build a co-training framework consisting of two collaborative models, in which the two models teach each other during training by using their respective predicted pseudo-labels of unlabeled data. Moreover, to alleviate the adverse impacts of noisy pseudo-labels for each model, we propose a self-ensembling strategy to perform consistency regularization for the up-to-date predictions of unlabeled data, in which the predictions of unlabeled data are gradually ensembled via moving average at the end of every training epoch. We evaluate our framework on a COVID-19 dataset containing 103 CT scans. Experimental results show that our proposed method achieves better performance in the case of only 4 labeled CT scans compared to the state-of-the-art semi-supervised segmentation networks.

Diagnostic accuracy of sagittal TSE-T2W, variable flip angle 3D TSE-T2W and high-resolution 3D heavily T2W sequences for the stenosis of two localizations: the cerebral aqueduct and the superior medullary velum

OBJECTIVES

This study aimed to investigate the accuracy of conventional sagittal turbo spin echo T2-weighted (Sag TSE-T2W), variable flip angle 3D TSE (VFA-3D-TSE) and high-resolution 3D heavily T2W (HR-3D-HT2W) sequences in the diagnosis of primary aqueductal stenosis (PAS) and superior medullary velum stenosis (SMV-S), and the effect of stenosis localization on diagnosis.

METHODS

Seventy-seven patients were included in the study. The diagnosis accuracy of the HR-3D-HT2W, Sag TSE-T2W and VFA-3D-TSE sequences, was classified into three grades by two experienced neuroradiologists: grade 0 (the sequence has no diagnostic ability), grade 1 (the sequence diagnoses stenosis but does not show focal stenosis itself or membrane formation), and grade 2 (the sequence makes a definitive diagnosis of stenosis and shows focal stenosis itself or membrane formation). Stenosis localizations were divided into three as Cerebral Aquaduct (CA), superior medullary velum (SMV) and SMV+CA. In the statistical analysis, the grades of the sequences were compared without making a differentiation based on localization. Then, the effect of localization on diagnosis was determined by comparing the grades for individual localizations.

RESULTS

In the sequence comparison, grade 0 was not detected in the VFA-3D-TSE and HR-3D-HT2W sequences, and these sequences diagnosed all cases. On the other hand, 25.4% of grade 0 was detected with the Sag TSE-T2W sequence (P<0.05). Grade 1 was detected by VFA-3D-TSE in 23% of the cases, while grade 1 (12.5%) was detected by HRH-3D-T2W in only one case, and the difference was statistically significant (P<0.05). When the sequences were examined according to localizations, the rate of grade 0 in the Sag TSE-T2W sequence was statistically significantly higher for the SMV localization (33.3%) compared to CA (66.7%) and SMV+CA (0%) (P<0.05). Localization had no effect on diagnosis using the other sequences.

CONCLUSION

In our study, we found that the VFA-3D-TSE and HR-3D-HT2W sequences were successful in the diagnosis of PAS and SMV-S contrary to the Sag TSE-T2W sequence.

Customized Efficient Neural Network for COVID-19 Infected Region Identification in CT Images

BACKGROUND

In the field of biomedical imaging, radiomics is a promising approach that aims to provide quantitative features from images. It is highly dependent on accurate identification and delineation of the volume of interest to avoid mistakes in the implementation of the texture-based prediction model. In this context, we present a customized deep learning approach aimed at addressing the real-time, and fully automated identification and segmentation of COVID-19 infected regions in computed tomography images.

METHODS

In a previous study, we adopted ENET, originally used for image segmentation tasks in self-driving cars, for whole parenchyma segmentation in patients with idiopathic pulmonary fibrosis which has several similarities to COVID-19 disease. To automatically identify and segment COVID-19 infected areas, a customized ENET, namely C-ENET, was implemented and its performance compared to the original ENET and some state-of-the-art deep learning architectures.

RESULTS

The experimental results demonstrate the effectiveness of our approach. Considering the performance obtained in terms of similarity of the result of the segmentation to the gold standard (dice similarity coefficient ~75%), our proposed methodology can be used for the identification and delineation of COVID-19 infected areas without any supervision of a radiologist, in order to obtain a volume of interest independent from the user.

CONCLUSIONS

We demonstrated that the proposed customized deep learning model can be applied to rapidly identify, and segment COVID-19 infected regions to subsequently extract useful information for assessing disease severity through radiomics analyses.

RCoNet: Deformable Mutual Information Maximization and High-Order Uncertainty-Aware Learning for Robust COVID-19 Detection

The novel 2019 Coronavirus (COVID-19) infection has spread worldwide and is currently a major healthcare challenge around the world. Chest computed tomography (CT) and X-ray images have been well recognized to be two effective techniques for clinical COVID-19 disease diagnoses. Due to faster imaging time and considerably lower cost than CT, detecting COVID-19 in chest X-ray (CXR) images is preferred for efficient diagnosis, assessment, and treatment. However, considering the similarity between COVID-19 and pneumonia, CXR samples with deep features distributed near category boundaries are easily misclassified by the hyperplanes learned from limited training data. Moreover, most existing approaches for COVID-19 detection focus on the accuracy of prediction and overlook uncertainty estimation, which is particularly important when dealing with noisy datasets. To alleviate these concerns, we propose a novel deep network named RCoNet ^k_s for robust COVID-19 detection which employs Deformable Mutual Information Maximization (DeIM), Mixed High-order Moment Feature (MHMF), and Multiexpert Uncertainty-aware Learning (MUL). With DeIM, the mutual information (MI) between input data and the corresponding latent representations can be well estimated and maximized to capture compact and disentangled representational characteristics. Meanwhile, MHMF can fully explore the benefits of using high-order statistics and extract discriminative features of complex distributions in medical imaging. Finally, MUL creates multiple parallel dropout networks for each CXR image to evaluate uncertainty and thus prevent performance degradation caused by the noise in the data. The experimental results show that RCoNet ^k_s achieves the state-of-the-art performance on an open-source COVIDx dataset of 15 134 original CXR images across several metrics. Crucially, our method is shown to be more effective than existing methods with the presence of noise in the data.

D2A U-Net: Automatic segmentation of COVID-19 CT slices based on dual attention and hybrid dilated convolution

Coronavirus Disease 2019 (COVID-19) has become one of the most urgent public health events worldwide due to its high infectivity and mortality. Computed tomography (CT) is a significant screening tool for COVID-19 infection, and automatic segmentation of lung infection in COVID-19 CT images can assist diagnosis and health care of patients. However, accurate and automatic segmentation of COVID-19 lung infections is faced with a few challenges, including blurred edges of infection and relatively low sensitivity. To address the issues above, a novel dilated dual attention U-Net based on the dual attention strategy and hybrid dilated convolutions, namely D2A U-Net, is proposed for COVID-19 lesion segmentation in CT slices. In our D2A U-Net, the dual attention strategy composed of two attention modules is utilized to refine feature maps and reduce the semantic gap between different levels of feature maps. Moreover, the hybrid dilated convolutions are introduced to the model decoder to achieve larger receptive fields, which refines the decoding process. The proposed method is evaluated on an open-source dataset and achieves a Dice score of 0.7298 and recall score of 0.7071, which outperforms the popular cutting-edge methods in the semantic segmentation. The proposed network is expected to be a potential AI-based approach used for the diagnosis and prognosis of COVID-19 patients.

Multi-level semantic adaptation for few-shot segmentation on cardiac image sequences

Obtaining manual labels is time-consuming and labor-intensive on cardiac image sequences. Few-shot segmentation can utilize limited labels to learn new tasks. However, it suffers from two challenges: spatial-temporal distribution bias and long-term information bias. These challenges derive from the impact of the time dimension on cardiac image sequences, resulting in serious over-adaptation. In this paper, we propose the multi-level semantic adaptation (MSA) for few-shot segmentation on cardiac image sequences. The MSA addresses the two biases by exploring the domain adaptation and the weight adaptation on the semantic features in multiple levels, including sequence-level, frame-level, and pixel-level. First, the MSA proposes the dual-level feature adjustment for domain adaptation in spatial and temporal directions. This adjustment explicitly aligns the frame-level feature and the sequence-level feature to improve the model adaptation on diverse modalities. Second, the MSA explores the hierarchical attention metric for weight adaptation in the frame-level feature and the pixel-level feature. This metric focuses on the similar frame and the target region to promote the model discrimination on the border features. The extensive experiments demonstrate that our MSA is effective in few-shot segmentation on cardiac image sequences with three modalities, i.e. MR, CT, and Echo (e.g. the average Dice is 0.9243), as well as superior to the ten state-of-the-art methods.

Attention-RefNet: Interactive Attention Refinement Network for Infected Area Segmentation of COVID-19

COVID-19 pneumonia is a disease that causes an existential health crisis in many people by directly affecting and damaging lung cells. The segmentation of infected areas from computed tomography (CT) images can be used to assist and provide useful information for COVID-19 diagnosis. Although several deep learning-based segmentation methods have been proposed for COVID-19 segmentation and have achieved state-of-the-art results, the segmentation accuracy is still not high enough (approximately 85%) due to the variations of COVID-19 infected areas (such as shape and size variations) and the similarities between COVID-19 and non-COVID-infected areas. To improve the segmentation accuracy of COVID-19 infected areas, we propose an interactive attention refinement network (Attention RefNet). The interactive attention refinement network can be connected with any segmentation network and trained with the segmentation network in an end-to-end fashion. We propose a skip connection attention module to improve the important features in both segmentation and refinement networks and a seed point module to enhance the important seeds (positions) for interactive refinement. The effectiveness of the proposed method was demonstrated on public datasets (COVID-19CTSeg and MICCAI) and our private multicenter dataset. The segmentation accuracy was improved to more than 90%. We also confirmed the generalizability of the proposed network on our multicenter dataset. The proposed method can still achieve high segmentation accuracy.

A deep-learning-based framework for severity assessment of COVID-19 with CT images

Millions of positive COVID-19 patients are suffering from the pandemic around the world, a critical step in the management and treatment is severity assessment, which is quite challenging with the limited medical resources. Currently, several artificial intelligence systems have been developed for the severity assessment. However, imprecise severity assessment and insufficient data are still obstacles. To address these issues, we proposed a novel deep-learning-based framework for the fine-grained severity assessment using 3D CT scans, by jointly performing lung segmentation and lesion segmentation. The main innovations in the proposed framework include: 1) decomposing 3D CT scan into multi-view slices for reducing the complexity of 3D model, 2) integrating prior knowledge (dual-Siamese channels and clinical metadata) into our model for improving the model performance. We evaluated the proposed method on 1301 CT scans of 449 COVID-19 cases collected by us, our method achieved an accuracy of 86.7% for four-way classification, with the sensitivities of 92%, 78%, 95%, 89% for four stages. Moreover, ablation study demonstrated the effectiveness of the major components in our model. This indicates that our method may contribute a potential solution to severity assessment of COVID-19 patients using CT images and clinical metadata.

Robust chest CT image segmentation of COVID-19 lung infection based on limited data

BACKGROUND

The coronavirus disease 2019 (COVID-19) affects billions of lives around the world and has a significant impact on public healthcare. For quantitative assessment and disease monitoring medical imaging like computed tomography offers great potential as alternative to RT-PCR methods. For this reason, automated image segmentation is highly desired as clinical decision support. However, publicly available COVID-19 imaging data is limited which leads to overfitting of traditional approaches.

METHODS

To address this problem, we propose an innovative automated segmentation pipeline for COVID-19 infected regions, which is able to handle small datasets by utilization as variant databases. Our method focuses on on-the-fly generation of unique and random image patches for training by performing several preprocessing methods and exploiting extensive data augmentation. For further reduction of the overfitting risk, we implemented a standard 3D U-Net architecture instead of new or computational complex neural network architectures.

RESULTS

Through a k-fold cross-validation on 20 CT scans as training and validation of COVID-19, we were able to develop a highly accurate as well as robust segmentation model for lungs and COVID-19 infected regions without overfitting on limited data. We performed an in-detail analysis and discussion on the robustness of our pipeline through a sensitivity analysis based on the cross-validation and impact on model generalizability of applied preprocessing techniques. Our method achieved Dice similarity coefficients for COVID-19 infection between predicted and annotated segmentation from radiologists of 0.804 on validation and 0.661 on a separate testing set consisting of 100 patients.

CONCLUSIONS

We demonstrated that the proposed method outperforms related approaches, advances the state-of-the-art for COVID-19 segmentation and improves robust medical image analysis based on limited data.

Self-supervised deep learning model for COVID-19 lung CT image segmentation highlighting putative causal relationship among age, underlying disease and COVID-19

Background

Coronavirus disease 2019 (COVID-19) is very contagious. Cases appear faster than the available Polymerase Chain Reaction test kits in many countries. Recently, lung computerized tomography (CT) has been used as an auxiliary COVID-19 testing approach. Automatic analysis of the lung CT images is needed to increase the diagnostic efficiency and release the human participant. Deep learning is successful in automatically solving computer vision problems. Thus, it can be introduced to the automatic and rapid COVID-19 CT diagnosis. Many advanced deep learning-based computer vison techniques were developed to increase the model performance but have not been introduced to medical image analysis.

Methods

In this study, we propose a self-supervised two-stage deep learning model to segment COVID-19 lesions (ground-glass opacity and consolidation) from chest CT images to support rapid COVID-19 diagnosis. The proposed deep learning model integrates several advanced computer vision techniques such as generative adversarial image inpainting, focal loss, and lookahead optimizer. Two real-life datasets were used to evaluate the model’s performance compared to the previous related works. To explore the clinical and biological mechanism of the predicted lesion segments, we extract some engineered features from the predicted lung lesions. We evaluate their mediation effects on the relationship of age with COVID-19 severity, as well as the relationship of underlying diseases with COVID-19 severity using statistic mediation analysis.

Results

The best overall F1 score is observed in the proposed self-supervised two-stage segmentation model (0.63) compared to the two related baseline models (0.55, 0.49). We also identified several CT image phenotypes that mediate the potential causal relationship between underlying diseases with COVID-19 severity as well as the potential causal relationship between age with COVID-19 severity.

Conclusions

This work contributes a promising COVID-19 lung CT image segmentation model and provides predicted lesion segments with potential clinical interpretability. The model could automatically segment the COVID-19 lesions from the raw CT images with higher accuracy than related works. The features of these lesions are associated with COVID-19 severity through mediating the known causal of the COVID-19 severity (age and underlying diseases).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02992-2.

MSDS-UNet: A multi-scale deeply supervised 3D U-Net for automatic segmentation of lung tumor in CT

Lung cancer is one of the most common and deadly malignant cancers. Accurate lung tumor segmentation from CT is therefore very important for correct diagnosis and treatment planning. The automated lung tumor segmentation is challenging due to the high variance in appearance and shape of the targeting tumors. To overcome the challenge, we present an effective 3D U-Net equipped with ResNet architecture and a two-pathway deep supervision mechanism to increase the network's capacity for learning richer representations of lung tumors from global and local perspectives. Extensive experiments on two real medical datasets: the lung CT dataset from Liaoning Cancer Hospital in China with 220 cases and the public dataset of TCIA with 422 cases. Our experiments demonstrate that our model achieves an average dice score (0.675), sensitivity (0.731) and F1-score (0.682) on the dataset from Liaoning Cancer Hospital, and an average dice score (0.691), sensitivity (0.746) and F1-score (0.724) on the TCIA dataset, respectively. The results demonstrate that the proposed 3D MSDS-UNet outperforms the state-of-the-art segmentation models for segmenting all scales of tumors, especially for small tumors. Moreover, we evaluated our proposed MSDS-UNet on another challenging volumetric medical image segmentation task: COVID-19 lung infection segmentation, which shows consistent improvement in the segmentation performance.

A Hybrid Method of Covid-19 Patient Detection from Modified CT-Scan/Chest-X-Ray Images Combining Deep Convolutional Neural Network And Two- Dimensional Empirical Mode Decomposition

The outbreak of the SARS-CoV-2/Covid-19 virus in 2019-2020 has made the world look for fast and accurate detection methods of the disease. The most commonly used tools for detecting Covid patients are Chest-X-ray or Chest-CT-scans of the patient. However, sometimes it's hard for the physicians to diagnose the SARS-CoV-2 infection from the raw image. Moreover, sometimes, deep-learning-based techniques, using raw images, fail to detect the infection. Hence, this paper represents a hybrid method employing both traditional signal processing and deep learning technique for quick detection of SARS-CoV-2 patients based on the CT-scan and Chest-X-ray images of a patient. Unlike the other AI-based methods, here, a CT-scan/Chest-X-ray image is decomposed by two-dimensional Empirical Mode Decomposition (2DEMD), and it generates different orders of Intrinsic Mode Functions (IMFs). Next, The decomposed IMF signals are fed into a deep Convolutional Neural Network (CNN) for feature extraction and classification of Covid patients and Non-Covid patients. The proposed method is validated on three publicly available SARS-CoV-2 data sets using two deep CNN architectures. In all the databases, the modified CT-scan/Chest-X-ray image provides a better result than the raw image in terms of classification accuracy of two fundamental CNNs. This paper represents a new viewpoint of extracting preprocessed features from the raw image using 2DEMD.

AI-Empowered Computational Examination of Chest Imaging for COVID-19 Treatment: A Review

Since the first case of coronavirus disease 2019 (COVID-19) was discovered in December 2019, COVID-19 swiftly spread over the world. By the end of March 2021, more than 136 million patients have been infected. Since the second and third waves of the COVID-19 outbreak are in full swing, investigating effective and timely solutions for patients' check-ups and treatment is important. Although the SARS-CoV-2 virus-specific reverse transcription polymerase chain reaction test is recommended for the diagnosis of COVID-19, the test results are prone to be false negative in the early course of COVID-19 infection. To enhance the screening efficiency and accessibility, chest images captured via X-ray or computed tomography (CT) provide valuable information when evaluating patients with suspected COVID-19 infection. With advanced artificial intelligence (AI) techniques, AI-driven models training with lung scans emerge as quick diagnostic and screening tools for detecting COVID-19 infection in patients. In this article, we provide a comprehensive review of state-of-the-art AI-empowered methods for computational examination of COVID-19 patients with lung scans. In this regard, we searched for papers and preprints on bioRxiv, medRxiv, and arXiv published for the period from January 1, 2020, to March 31, 2021, using the keywords of COVID, lung scans, and AI. After the quality screening, 96 studies are included in this review. The reviewed studies were grouped into three categories based on their target application scenarios: automatic detection of coronavirus disease, infection segmentation, and severity assessment and prognosis prediction. The latest AI solutions to process and analyze chest images for COVID-19 treatment and their advantages and limitations are presented. In addition to reviewing the rapidly developing techniques, we also summarize publicly accessible lung scan image sets. The article ends with discussions of the challenges in current research and potential directions in designing effective computational solutions to fight against the COVID-19 pandemic in the future.

AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGING

Objectives

Ground-glass opacity (GGO) - a hazy, gray appearing density on computed tomography (CT) of lungs - is one of the hallmark features of SARS-CoV-2 in COVID-19 patients. This AI-driven study is focused on segmentation, morphology, and distribution patterns of GGOs.

Method

We use an AI-driven unsupervised machine learning approach called PointNet++ to detect and quantify GGOs in CT scans of COVID-19 patients and to assess the severity of the disease. We have conducted our study on the "MosMedData", which contains CT lung scans of 1110 patients with or without COVID-19 infections. We quantify the morphologies of GGOs using Minkowski tensors and compute the abnormality score of individual regions of segmented lung and GGOs.

Results

PointNet++ detects GGOs with the highest evaluation accuracy (98%), average class accuracy (95%), and intersection over union (92%) using only a fraction of 3D data. On average, the shapes of GGOs in the COVID-19 datasets deviate from sphericity by 15% and anisotropies in GGOs are dominated by dipole and hexapole components. These anisotropies may help to quantitatively delineate GGOs of COVID-19 from other lung diseases.

Conclusion

The PointNet++ and the Minkowski tensor based morphological approach together with abnormality analysis will provide radiologists and clinicians with a valuable set of tools when interpreting CT lung scans of COVID-19 patients. Implementation would be particularly useful in countries severely devastated by COVID-19 such as India, where the number of cases has outstripped available resources creating delays or even breakdowns in patient care. This AI-driven approach synthesizes both the unique GGO distribution pattern and severity of the disease to allow for more efficient diagnosis, triaging and conservation of limited resources.

Key Points

Our approach to GGO analysis has four distinguishing features:We combine an unsupervised computer vision approach with convex hull and convex points algorithms to segment and preserve the actual structure of the lung.To the best of our knowledge, we are the first group to use PointNet++ architecture for 3D visualization, segmentation, classification, and pattern analysis of GGOs.We make abnormality predictions using a deep network and Cox proportional hazards model using lung CT images of COVID-19 patients.We quantify the shapes and sizes of GGOs using Minkowski tensors to understand the morphological variations of GGOs within the COVID-19 cohort.

COVID-19 lesion detection and segmentation-A deep learning method

PURPOSE

In this paper, we utilized deep learning methods to screen the positive COVID-19 cases in chest CT. Our primary goal is to supply rapid and precise assistance for disease surveillance on the medical imaging aspect.

MATERIALS AND METHODS

Basing on deep learning, we combined semantic segmentation and object detection methods to study the lesion performance of COVID-19. We put forward a novel end-to-end model which takes advantage of the Spatio-temporal features. Furthermore, a segmentation model attached with a fully connected CRF was designed for a more effective ROI input.

RESULTS

Our method showed a better performance across different metrics against the comparison models. Moreover, our strategy highlighted strong robustness for the processed augmented testing samples.

CONCLUSION

The comprehensive fusion of Spatio-temporal correlations can exploit more valuable features for locating target regions, and this mechanism is friendly to detect tiny lesions. Although it remains in discrete form, the feature extracting in temporal dimension improves the precision of final prediction.