新型冠状病毒肺炎(COVID-19)医学影像AI诊断研究进展

2020年3月,世界卫生组织（World Health Organization,WHO）宣布新型冠状病毒肺炎（corona virus disease 2019,COVID-19）为世界大流行病,疫情的爆发给世界各地医疗系统带来巨大压力。现有的COVID-19诊断标准是核酸检测阳性,然而核酸检测假阴性率高达17%~25.5%,为避免漏诊,需要采用基于影像学的AI诊断方法筛查大量疑似病例,扼制疾病传播。本综述将回顾疫情爆发数月以来,基于医学影像的新冠肺炎AI辅助诊断的研究成果。首先介绍CT（computed tomography）和X光片的优缺点,以及COVID-19的放射学特征,然后对数据准备、图像分割和分类识别等AI诊断的关键步骤分别进行阐述,最后介绍COVID-19的跟踪和预后（预先对疾病后续发展过程及结果的判断和估计）。本文还整理了部分公开的COVID-19相关数据集,并对数据标注不足的问题提供了弱监督学习和迁移学习等解决方案。实验验证,AI系统诊断COVID-19的敏感性达到97.4%,特异性达到92.2%,优于放射科医生的诊断结果。其中表现尤为突出的是基于语义分割网络检测COVID-19感染区域,由此可以定量分析感染率。AI系统可以辅助医生诊断和治疗COVID-19,提高放射科医生阅读X光片和CT的效率。     

An analysis model of diagnosis and treatment for COVID-19 pandemic based on medical information fusion

Exploring the complicated relationships underlying the clinical information is essential for the diagnosis and treatment of the Coronavirus Disease 2019 (COVID-19). Currently, few approaches are mature enough to show operational impact. Based on electronic medical records (EMRs) of 570 COVID-19 inpatients, we proposed an analysis model of diagnosis and treatment for COVID-19 based on the machine learning algorithms and complex networks. Introducing the medical information fusion, we constructed the heterogeneous information network to discover the complex relationships among the syndromes, symptoms, and medicines. We generated the numerical symptom (medicine) embeddings and divided them into seven communities (syndromes) using the combination of Skip-Gram model and Spectral Clustering (SC) algorithm. After analyzing the symptoms and medicine networks, we identified the key factors using six evaluation metrics of node centrality. The experimental results indicate that the proposed analysis model is capable of discovering the critical symptoms and symptom distribution for diagnosis; the key medicines and medicine combinations for treatment. Based on the latest COVID-19 clinical guidelines, this model could result in the higher accuracy results than the other representative clustering algorithms. Furthermore, the proposed model is able to provide tremendously valuable guidance and help the physicians to combat the COVID-19.     

改进卷积神经网络的COVID-19CT影像分类方法研究

针对2019年12月在中国武汉发现的新型冠状病毒,由于RT-PCR检测具有假阴性率过高且得出结果会花费大量时间等问题,研究证明计算机断层扫描(CT)已经成为了辅助诊断和治疗新型冠状病毒肺炎的重要手段之一.由于目前公开的COVID-19 CT数据集较少,提出利用条件生成对抗网络进行数据增强以获得更多样本的CT数据集,以此...     

融合频率域特征的双路网络模型诊断新冠肺炎

CT检查在新冠肺炎诊断中起着重要作用,为了能够在有限的CT胸部图像集中获得更多有关新冠肺炎的特征信息、建立更加敏感通用的诊断模型,提出了融合CT图像频域特征的双路网络模型（Dp-Net）,该模型主干部分采用ResNet网络模型,并将卷积神经网络的训练过程分为两个部分,一部分提取CT图像空间域的特征,另一部分通过傅里叶变换提取频率域上的特征,将两者训练的结果按照一定的权重进行融合,融合后再由Layer4模块进行一次特征提取。在公开的COVID-CT数据集上与ResNet、VGG等传统的CNN模型进行了比较,也与Self-Trans和LA-DNN等一些改进的CNN模型进行了比较,并对不同权重的融合方案进行了比较,实验结果表明提出的Dp-Net模型在各种评价指标上取得了更好的结果。     

COVID-19肺部CT图像多尺度编解码分割

目的 新型冠状病毒肺炎(corona virus disease 2019, COVID-19)患者肺部计算机断层扫描(computed tomography, CT)图像具有明显的病变特征,快速而准确地从患者肺部CT图像中分割出病灶部位,对COVID-19患者快速诊断和监护具有重要意义。COVID-19肺炎病灶区域复杂多变,现有方法分割精度不高,且对假阴性的关注不够,导致分割结果往往具有较高的特异度,但灵敏度却很低。方法 本文提出了一个基于深度学习的多尺度编解码网络(MED-Net(multiscale encode decode network)),该网络采用资源利用率高、计算速度快的HarDNet68(harmonic densely connected network)作为主干,它主要由5个harmonic dense block(HDB)组成,首先通过5个空洞空间卷积池化金字塔(atrous spatial pyramid pooling, ASPP)对HarDNet68的第1个卷积层和第1、3、4、5个HDB提取多尺度特征。接着在并行解码器(paralleled parti...     

结构图注意力网络的新冠肺炎轻重症诊断

目的 为辅助医生快速分辨新型冠状病毒肺炎(corona virus disease 2019, COVID-19)轻、重症患者,以便对症下药减轻医疗负担,提出一种基于结构图注意力网络的轻重症诊断算法。方法 基于胸部CT图像提取的特定特征以及肺段间的位置关系构建结构图,以肺部内不同肺段为节点,以提取特征为节点属性。采用图神经网络汇聚相邻节点特征,再利用池化层获取分别代表左肺叶和右肺叶特征的图表示。使用结构注意力机制计算左、右肺叶的感染情况对结果诊断的重要性,并依据重要性融合左、右肺叶图表示以得到最终图表示,最后执行分类任务。由于数据中存在明显的类别不平衡现象,采用Focal-Loss损失函数优化模型以减轻对分类结果的影响。结果 实验将所提算法分别与传统机器学习方法和流行的图神经网络算法做性能对比。在重症诊断的准确率上,本文算法相较于传统机器学习方法和图神经网络算法分别取得14.2%～42.0%和3.6%～4.8%的提升。在AUC(area under curve)指标上,本文算法相较于上述两种算法分别取得8.9%～18.7%和3.1%～3.6%的提升。除此之外,通过消融实验发现具有结构注...     

Stacked-autoencoder-based model for COVID-19 diagnosis on CT images

With the outbreak of COVID-19, medical imaging such as computed tomography (CT) based diagnosis is proved to be an effective way to fight against the rapid spread of the virus. Therefore, it is important to study computerized models for infectious detection based on CT imaging. New deep learning-based approaches are developed for CT assisted diagnosis of COVID-19. However, most of the current studies are based on a small size dataset of COVID-19 CT images as there are less publicly available datasets for patient privacy reasons. As a result, the performance of deep learning-based detection models needs to be improved based on a small size dataset. In this paper, a stacked autoencoder detector model is proposed to greatly improve the performance of the detection models such as precision rate and recall rate. Firstly, four autoencoders are constructed as the first four layers of the whole stacked autoencoder detector model being developed to extract better features of CT images. Secondly, the four autoencoders are cascaded together and connected to the dense layer and the softmax classifier to constitute the model. Finally, a new classification loss function is constructed by superimposing reconstruction loss to enhance the detection accuracy of the model. The experiment results show that our model is performed well on a small size COVID-2019 CT image dataset. Our model achieves the average accuracy, precision, recall, and F1-score rate of 94.7%, 96.54%, 94.1%, and 94.8%, respectively. The results reflect the ability of our model in discriminating COVID-19 images which might help radiologists in the diagnosis of suspected COVID-19 patients.

     

COVID-19医学影像数据集及研究进展

由于影像学技术在新型冠状病毒肺炎（COVID-19）的诊断和评估中发挥了重要作用,COVID-19相关数据集陆续被公布,但目前针对相关文献中数据集以及研究进展的整理相对较少。为此,通过COVID-19相关的期刊论文、报告和相关开源数据集网站,对涉及到的新冠肺炎数据集及深度学习模型进行整理和分析,包括计算机断层扫描（CT）图像数据集和X射线（CXR）图像数据集。对这些数据集呈现的医学影像的特征进行分析;重点论述开源数据集,以及在相关数据集上表现较好的分类和分割模型。最后讨论了肺部影像学技术未来的发展趋势。     

Deep-CoV: An integrated deep learning model to detect COVID-19 using chest X-ray and CT images

The COVID-19 virus has fatal effect on lung function and due to its rapidity the early detection is necessary at the moment. The radiographic images have already been used by the researchers for the early diagnosis of COVID-19. Though several existing research exhibited very good performance with either x-ray or computer tomography (CT) images, to the best of our knowledge no such work has reported the assembled performance of both x-ray and CT images. Thus increase in accuracy with higher scalability is the main concern of the recent research. In this article, an integrated deep learning model has been developed for detection of COVID-19 at an early stage using both chest x-ray and CT images. The lack of publicly available data about COVID-19 disease motivates the authors to combine three benchmark datasets into a single dataset of large size. The proposed model has applied various transfer learning techniques for feature extraction and to find out the best suite. Finally the capsule network is used to categorize the sub-dataset into COVID positive and normal patients. The experimental results show that, the best performance exhibits by the ResNet50 with capsule network as an extractor-classifier pair with the combined dataset, which is composed of 575 numbers of x-ray images and 930 numbers of CT images. The proposed model achieves accuracy of 98.2% and 97.8% with x-ray and CT images, respectively, and an average of 98%.     

AI aiding in diagnosing,tracking recovery of COVID-19 using deep learning on Chest CT scans

Coronavirus (COVID-19) has spread throughout the world, causing mayhem from January 2020 to this day. Owing to its rapidly spreading existence and high death count, the WHO has classified it as a pandemic. Biomedical engineers, virologists, epidemiologists, and people from other medical fields are working to help contain this epidemic as soon as possible. The virus incubates for five days in the human body and then begins displaying symptoms, in some cases, as late as 27 days. In some instances, CT scan based diagnosis has been found to have better sensitivity than RT-PCR, which is currently the gold standard for COVID-19 diagnosis. Lung conditions relevant to COVID-19 in CT scans are ground-glass opacity (GGO), consolidation, and pleural effusion. In this paper, two segmentation tasks are performed to predict lung spaces (segregated from ribcage and flesh in Chest CT) and COVID-19 anomalies from chest CT scans. A 2D deep learning architecture with U-Net as its backbone is proposed to solve both the segmentation tasks. It is observed that change in hyperparameters such as number of filters in down and up sampling layers, addition of attention gates, addition of spatial pyramid pooling as basic block and maintaining the homogeneity of 32 filters after each down-sampling block resulted in a good performance. The proposed approach is assessed using publically available datasets from GitHub and Kaggle. Model performance is evaluated in terms of F1-Score, Mean intersection over union (Mean IoU). It is noted that the proposed approach results in 97.31% of F1-Score and 84.6% of Mean IoU. The experimental results illustrate that the proposed approach using U-Net architecture as backbone with the changes in hyperparameters shows better results in comparison to existing U-Net architecture and attention U-net architecture. The study also recommends how this methodology can be integrated into the workflow of healthcare systems to help control the spread of COVID-19.

     

多区域融合注意力网络模型下的核性白内障分类

目的 核性白内障是主要致盲和导致视觉损害的眼科疾病,早期干预和白内障手术可以有效改善患者的视力和生活质量。眼前节光学相干断层成像图像(anterior segment optical coherence tomography, AS-OCT)能够非接触、客观和快速地获取白内障混浊信息。临床研究已经发现在AS-OCT图像中核性白内障严重程度与核性区域像素特征,如均值存在强相关性和高可重复性。但目前基于AS-OCT图像的自动核性白内障分类工作较少且分类结果还有较大提升空间。为此,本文提出一种新颖的多区域融合注意力网络(multi-region fusion attention network, MRA-Net)对AS-OCT图像中的核性白内障严重程度进行精准分类。方法 在提出的多区域融合注意力模型中,本文设计了一个多区域融合注意力模块(multi-region fusion attention, MRA),对不同核性区域特征表示进行融合来增强分类结果;另外,本文验证了以人和眼为单位的AS-OCT图像数据集拆分方式对核性白内障分类结果的影响。结果 在一个自建的AS-OCT图像数据集上结果表明...     

超级计算支撑的新冠肺炎CT影像综合分析辅助系统应用

目的 新冠肺炎（COVID-19）已经成为全球大流行疾病,在全球范围数百万人确诊。基于计算机断层扫描（computed tomography,CT）数据的影像学分析是临床诊断的重要手段。为了实现快速高效高精度地检测,提出了一种超级计算支撑的新冠肺炎CT影像综合分析辅助系统构建方法。方法 系统整个处理流程依次包括输入处理模块、预处理模块、影像学分析子系统和人工智能（artifiaial intelligence,AI）分析子系统4部分。其中影像学分析子系统通过分析肺实变、磨玻璃影和铺路石等影像学典型特征检测是否有肺炎和典型新冠肺炎特征,给出肺炎影像分析结论;AI分析子系统通过构建深度学习模型来区分普通病毒肺炎与新冠肺炎,增加肺炎的筛查甄别能力。结果 系统发布以来,持续稳定地为国内外超过三十家医院与一百多家科研机构提供了新冠肺炎辅助诊断服务和科研支撑,为抗击疫情提供重要支撑。结论 本文提出的超级计算支撑的新冠肺炎CT影像综合分析辅助系统构建方法,取得了应用效果,是一种有效实现快速部署服务、对突发疫情提供高效支撑的服务方式。     

基于深度学习的新型冠状病毒肺炎诊断研究综述

新型冠状病毒肺炎(COVID-19)具有高传染性和高致病性,严重威胁人民群众的生命安全和身体健康,快速准确地检测和诊断COVID-19对于疫情控制至关重要.目前COVID-19检测诊断方法主要包括核酸检测和基于医学影像的人工诊断,但是核酸检测耗时较长并且需要专用的测试盒,而基于医学影像的人工诊断过于依赖专业知识,分析耗...     

CT图像肺及肺病变区域分割方法综述

计算机断层扫描(computed tomography, CT)技术能为新冠肺炎(corona virus disease 2019,COVID-19)和肺癌等肺部疾病的诊断与治疗提供更全面的信息,但是由于肺部疾病的类型多样且复杂,使得对肺CT图像进行高质量的肺病变区域分割成为计算机辅助诊断的重难点问题。为了对肺CT图像的肺及肺病变区域分割方法的现状进行全面研究,本文综述了近年国内外发表的相关文献：对基于区域和活动轮廓的肺CT图像传统分割方法的优缺点进行比较与总结,传统的肺CT图像分割方法因其实现原理简单且分割速度快等优点,早期使用较多,但其存在分割精度不高的缺点,目前仍有不少基于传统方法的改进策略;重点分析了基于卷积神经网络(convolutional neural network, CNN)、全卷积网络(fully convolutional network, FCN)、U-Net和生成对抗网络(generative adversarial network, GAN)的肺CT图像分割网络结构改进模型的研究进展,基于深度学习的分割方法具有分割精度高、迁移学习能力强和鲁棒性高等优点,特...     

改进U-Net的新冠肺炎图像分割方法

新型冠状病毒肺炎（COVID-19）大流行疾病正在全球范围内蔓延。计算机断层扫描（CT）影像技术,在抗击全球 COVID-19 的斗争中起着至关重要的作用,诊断新冠肺炎时,如果能够从CT图像中自动准确分割出新冠肺炎病灶区域,将有助于医生进行更准确和快速的诊断。针对新冠肺炎病灶分割问题,提出基于U-Net改进模型的自动分割方法。在编码器中运用了在 ImageNet 上预训练好的 EfficientNet-B0网络,对有效信息进行特征提取。在解码器中将传统的上采样操作换成DUpsampling结构,以此来充分获取病灶边缘的细节特征信息,最后通过模型快照的集成提高分割的精度。在公开数据集上的实验结果表明,所提算法的准确率、召回率和Dice系数分别为84.24%、80.43%和85.12%,与其他的语义分割算法相比,该方法能有效分割新冠肺炎病灶区域,具有良好的分割性能。     

改进Faster R-CNN模型的CT图磨玻璃密度影目标检测

目的 针对Faster R-CNN （faster region convolutional neural network）模型在肺部计算机断层扫描（computed tomography，CT）图磨玻璃密度影目标检测中小尺寸目标无法有效检测与模型检测速度慢等问题，对Faster R-CNN模型特征提取网络与区域候选网络（region proposal network，RPN）提出了改进方法。方法 使用特征金字塔网络替换Faster R-CNN的特征提取网络，生成特征金字塔；使用基于位置映射的RPN产生锚框，并计算每个锚框的中心到真实物体中心的远近程度（用参数“中心度”表示），对RPN判定为前景的锚框进一步修正位置作为候选区域（region proposal），并将RPN预测的前景/背景分类置信度与中心度结合作为候选区域的排序依据，候选区域经过非极大抑制筛选出感兴趣区域（region of interest，RoI）。将RoI对应的特征区域送入分类回归网络得到检测结果。结果 实验结果表明，在新冠肺炎患者肺部CT图数据集上，本文改进的模型相比于Faster R-CNN模型，召回率（recall）增加了7%，平均精度均值（mean average precision，mAP）增加了3.9%，传输率（frames per second，FPS）由5帧/s提升至9帧/s。特征金字塔网络的引入明显提升了模型的召回率与mAP指标，基于位置映射的RPN显著提升了模型的检测速度。与其他最新改进的目标检测模型相比，本文改进的模型保持了双阶段目标检测模型的高精度，并拉近了与单阶段目标检测模型在检测速度指标上的距离。结论 本文改进的模型能够有效检测到患者肺部CT图的磨玻璃密度影目标区域，对小尺寸目标同样适用，可以快速有效地为医生提供辅助诊断。     

Speech-based solution to Parkinson’s disease management

Parkinson’s disease (PD) is a neurological disorder marked by decreased dopamine levels in the brain. Persons suffering from PD, exhibits vocal symptoms such as dysphonia and dysarthria. Speech impairments in PD are grouped together and called as hypokinetic dysarthria. Traditional PD management is based on a patient’s clinical history and through physical examination as there are currently no known biomarkers for its diagnosis. Automatic analysis techniques aid clinicians in diagnosis and monitoring patients using speech and provide frequent, cost effective and objective assessment. This paper presents pilot experiment to detect presence of dysarthria in speech and detect level of severity based on deep learning approach. Automated feature extraction and classification using convolutional neural network shows 77.48% accuracy on test samples of TORGO database with five fold validation. Using transfer learning, system performance is further analyzed for gender specific performance as well as in detection of severity of disease.

     

COVID-19 classification by CCSHNet with deep fusion using transfer learning and discriminant correlation analysis

Aim: COVID-19 is a disease caused by a new strain of coronavirus. Up to 18th October 2020, worldwide there have been 39.6 million confirmed cases resulting in more than 1.1 million deaths. To improve diagnosis, we aimed to design and develop a novel advanced AI system for COVID-19 classification based on chest CT (CCT) images.Methods: Our dataset from local hospitals consisted of 284 COVID-19 images, 281 community-acquired pneumonia images, 293 secondary pulmonary tuberculosis images; and 306 healthy control images. We first used pretrained models (PTMs) to learn features, and proposed a novel (L, 2) transfer feature learning algorithm to extract features, with a hyperparameter of number of layers to be removed (NLR, symbolized as L). Second, we proposed a selection algorithm of pretrained network for fusion to determine the best two models characterized by PTM and NLR. Third, deep CCT fusion by discriminant correlation analysis was proposed to help fuse the two features from the two models. Micro-averaged (MA) F1 score was used as the measuring indicator. The final determined model was named CCSHNet.Results: On the test set, CCSHNet achieved sensitivities of four classes of 95.61%, 96.25%, 98.30%, and 97.86%, respectively. The precision values of four classes were 97.32%, 96.42%, 96.99%, and 97.38%, respectively. The F1 scores of four classes were 96.46%, 96.33%, 97.64%, and 97.62%, respectively. The MA F1 score was 97.04%. In addition, CCSHNet outperformed 12 state-of-the-art COVID-19 detection methods.Conclusions: CCSHNet is effective in detecting COVID-19 and other lung infectious diseases using first-line clinical imaging and can therefore assist radiologists in making accurate diagnoses based on CCTs.     

Corona-Nidaan: lightweight deep convolutional neural network for chest X-Ray based COVID-19 infection detection

The coronavirus COVID-19 pandemic is today’s major public health crisis, we have faced since the Second World War. The pandemic is spreading around the globe like a wave, and according to the World Health Organization’s recent report, the number of confirmed cases and deaths are rising rapidly. COVID-19 pandemic has created severe social, economic, and political crises, which in turn will leave long-lasting scars. One of the countermeasures against controlling coronavirus outbreak is specific, accurate, reliable, and rapid detection technique to identify infected patients. The availability and affordability of RT-PCR kits remains a major bottleneck in many countries, while handling COVID-19 outbreak effectively. Recent findings indicate that chest radiography anomalies can characterize patients with COVID-19 infection. In this study, Corona-Nidaan, a lightweight deep convolutional neural network (DCNN), is proposed to detect COVID-19, Pneumonia, and Normal cases from chest X-ray image analysis; without any human intervention. We introduce a simple minority class oversampling method for dealing with imbalanced dataset problem. The impact of transfer learning with pre-trained CNNs on chest X-ray based COVID-19 infection detection is also investigated. Experimental analysis shows that Corona-Nidaan model outperforms prior works and other pre-trained CNN based models. The model achieved 95% accuracy for three-class classification with 94% precision and recall for COVID-19 cases. While studying the performance of various pre-trained models, it is also found that VGG19 outperforms other pre-trained CNN models by achieving 93% accuracy with 87% recall and 93% precision for COVID-19 infection detection. The model is evaluated by screening the COVID-19 infected Indian Patient chest X-ray dataset with good accuracy.