pt-sk/ml_research_abs huggingface dataset:
Joint Learning of 3D Lesion Segmentation and Classification for Explainable COVID-19 Diagnosis.
Authors: XiaofeiWang, LaiJiang, LiuLi, MaiXu, XinDeng, LisongDai, XiangyangXu, TianyiLi, YichenGuo, ZulinWang, Pier LuigiDragotti
Journal: IEEE transactions on medical imaging

Given the outbreak of COVID-19 pandemic and the shortage of medical resource, extensive deep learning models have been proposed for automatic COVID-19 diagnosis, based on 3D computed tomography (CT) scans. However, the existing models independently process the 3D lesion segmentation and disease classification, ignoring the inherent correlation between these two tasks. In this paper, we propose a joint deep learning model of 3D lesion segmentation and classification for diagnosing COVID-19, called DeepSC-COVID, as the first attempt in this direction. Specifically, we establish a large-scale CT database containing 1,805 3D CT scans with fine-grained lesion annotations, and reveal 4 findings about lesion difference between COVID-19 and community acquired pneumonia (CAP). Inspired by our findings, DeepSC-COVID is designed with 3 subnets: a cross-task feature subnet for feature extraction, a 3D lesion subnet for lesion segmentation, and a classification subnet for disease diagnosis. Besides, the task-aware loss is proposed for learning the task interaction across the 3D lesion and classification subnets. Different from all existing models for COVID-19 diagnosis, our model is interpretable with fine-grained 3D lesion distribution. Finally, extensive experimental results show that the joint learning framework in our model significantly improves the performance of 3D lesion segmentation and disease classification in both efficiency and efficacy.
COVID19-CT-dataset: an open-access chest CT image repository of 1000+ patients with confirmed COVID-19 diagnosis.
Authors: ShokouhShakouri, Mohammad AminBakhshali, ParvanehLayegh, BehzadKiani, FaridMasoumi, SaeedehAtaei Nakhaei, Sayyed MostafaMostafavi
Journal: BMC research notes

The ongoing Coronavirus disease 2019 (COVID-19) pandemic has drastically impacted the global health and economy. Computed tomography (CT) is the prime imaging modality for diagnosis of lung infections in COVID-19 patients. Data-driven and Artificial intelligence (AI)-powered solutions for automatic processing of CT images predominantly rely on large-scale, heterogeneous datasets. Owing to privacy and data availability issues, open-access and publicly available COVID-19 CT datasets are difficult to obtain, thus limiting the development of AI-enabled automatic diagnostic solutions. To tackle this problem, large CT image datasets encompassing diverse patterns of lung infections are in high demand.
In the present study, we provide an open-source repository containing 1000+ CT images of COVID-19 lung infections established by a team of board-certified radiologists. CT images were acquired from two main general university hospitals in Mashhad, Iran from March 2020 until January 2021. COVID-19 infections were ratified with matching tests including Reverse transcription polymerase chain reaction (RT-PCR) and accompanying clinical symptoms. All data are 16-bit grayscale images composed of 512 × 512 pixels and are stored in DICOM standard. Patient privacy is preserved by removing all patient-specific information from image headers. Subsequently, all images corresponding to each patient are compressed and stored in RAR format.
Segmenting lung lesions of COVID-19 from CT images via pyramid pooling improved Unet.
Authors: YinjinMa, PengFeng, PengHe, YongRen, XiaodongGuo, XiaoliuYu, BiaoWei
Journal: Biomedical physics & engineering express

Segmenting lesion regions of Coronavirus Disease 2019 (COVID-19) from computed tomography (CT) images is a challenge owing to COVID-19 lesions characterized by high variation, low contrast between infection lesions and around normal tissues, and blurred boundaries of infections. Moreover, a shortage of available CT dataset hinders deep learning techniques applying to tackling COVID-19. To address these issues, we propose a deep learning-based approach known as PPM-Unet to segmenting COVID-19 lesions from CT images. Our method improves an Unet by adopting pyramid pooling modules instead of the conventional skip connection and then enhances the representation of the neural network by aiding the global attention mechanism. We first pre-train PPM-Unet on COVID-19 dataset of pseudo labels containing1600 samples producing a coarse model. Then we fine-tune the coarse PPM-Unet on the standard COVID-19 dataset consisting of 100 pairs of samples to achieve a fine PPM-Unet. Qualitative and quantitative results demonstrate that our method can accurately segment COVID-19 infection regions from CT images, and achieve higher performance than other state-of-the-art segmentation models in this study. It offers a promising tool to lay a foundation for quantitatively detecting COVID-19 lesions.
The diagnostic accuracy of Artificial Intelligence-Assisted CT imaging in COVID-19 disease: A systematic review and meta-analysis.
Authors: MeisamMoezzi, KiarashShirbandi, Hassan KianiShahvandi, BabakArjmand, FakherRahim
Journal: Informatics in medicine unlocked

Artificial intelligence (AI) systems have become critical in support of decision-making. This systematic review summarizes all the data currently available on the AI-assisted CT-Scan prediction accuracy for COVID-19. The ISI Web of Science, Cochrane Library, PubMed, Scopus, CINAHL, Science Direct, PROSPERO, and EMBASE were systematically searched. We used the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool to assess all included studies' quality and potential bias. A hierarchical receiver-operating characteristic summary (HSROC) curve and a summary receiver operating characteristic (SROC) curve have been implemented. The area under the curve (AUC) was computed to determine the diagnostic accuracy. Finally, 36 studies (a total of 39,246 image data) were selected for inclusion into the final meta-analysis. The pooled sensitivity for AI was 0.90 (95% CI, 0.90-0.91), specificity was 0.91 (95% CI, 0.90-0.92) and the AUC was 0.96 (95% CI, 0.91-0.98). For deep learning (DL) method, the pooled sensitivity was 0.90 (95% CI, 0.90-0.91), specificity was 0.88 (95% CI, 0.87-0.88) and the AUC was 0.96 (95% CI, 0.93-0.97). In case of machine learning (ML), the pooled sensitivity was 0.90 (95% CI, 0.90-0.91), specificity was 0.95 (95% CI, 0.94-0.95) and the AUC was 0.97 (95% CI, 0.96-0.99). AI in COVID-19 patients is useful in identifying symptoms of lung involvement. More prospective real-time trials are required to confirm AI's role for high and quick COVID-19 diagnosis due to the possible selection bias and retrospective existence of currently available studies.
COVID-19 diagnosis from CT scans and chest X-ray images using low-cost Raspberry Pi.
Authors: Khalid MHosny, Mohamed MDarwish, KenliLi, AhmadSalah
Journal: PloS one

The diagnosis of COVID-19 is of vital demand. Several studies have been conducted to decide whether the chest X-ray and computed tomography (CT) scans of patients indicate COVID-19. While these efforts resulted in successful classification systems, the design of a portable and cost-effective COVID-19 diagnosis system has not been addressed yet. The memory requirements of the current state-of-the-art COVID-19 diagnosis systems are not suitable for embedded systems due to the required large memory size of these systems (e.g., hundreds of megabytes). Thus, the current work is motivated to design a similar system with minimal memory requirements. In this paper, we propose a diagnosis system using a Raspberry Pi Linux embedded system. First, local features are extracted using local binary pattern (LBP) algorithm. Second, the global features are extracted from the chest X-ray or CT scans using multi-channel fractional-order Legendre-Fourier moments (MFrLFMs). Finally, the most significant features (local and global) are selected. The proposed system steps are integrated to fit the low computational and memory capacities of the embedded system. The proposed method has the smallest computational and memory resources,less than the state-of-the-art methods by two to three orders of magnitude, among existing state-of-the-art deep learning (DL)-based methods.
Classification of COVID-19 chest X-Ray and CT images using a type of dynamic CNN modification method.
Authors: GuangyuJia, Hak-KeungLam, YujiaXu
Journal: Computers in biology and medicine

Understanding and classifying Chest X-Ray (CXR) and computerised tomography (CT) images are of great significance for COVID-19 diagnosis. The existing research on the classification for COVID-19 cases faces the challenges of data imbalance, insufficient generalisability, the lack of comparative study, etc. To address these problems, this paper proposes a type of modified MobileNet to classify COVID-19 CXR images and a modified ResNet architecture for CT image classification. In particular, a modification method of convolutional neural networks (CNN) is designed to solve the gradient vanishing problem and improve the classification performance through dynamically combining features in different layers of a CNN. The modified MobileNet is applied to the classification of COVID-19, Tuberculosis, viral pneumonia (with the exception of COVID-19), bacterial pneumonia and normal controls using CXR images. Also, the proposed modified ResNet is used for the classification of COVID-19, non-COVID-19 infections and normal controls using CT images. The results show that the proposed methods achieve 99.6% test accuracy on the five-category CXR image dataset and 99.3% test accuracy on the CT image dataset. Six advanced CNN architectures and two specific COVID-19 detection models, i.e., COVID-Net and COVIDNet-CT are used in comparative studies. Two benchmark datasets and a CXR image dataset which combines eight different CXR image sources are employed to evaluate the performance of the above models. The results show that the proposed methods outperform the comparative models in classification accuracy, sensitivity, and precision, which demonstrate their potential in computer-aided diagnosis for healthcare applications.
On the role of artificial intelligence in medical imaging of COVID-19.
Authors: JannisBorn, DavidBeymer, DeeptaRajan, AdamCoy, Vandana VMukherjee, MatteoManica, PrasanthPrasanna, DeddehBallah, MichalGuindy, DorithShaham, Pallav LShah, EmmanouilKarteris, Jan LRobertus, MariaGabrani, MichalRosen-Zvi
Journal: Patterns (New York, N.Y.)

Although a plethora of research articles on AI methods on COVID-19 medical imaging are published, their clinical value remains unclear. We conducted the largest systematic review of the literature addressing the utility of AI in imaging for COVID-19 patient care. By keyword searches on PubMed and preprint servers throughout 2020, we identified 463 manuscripts and performed a systematic meta-analysis to assess their technical merit and clinical relevance. Our analysis evidences a significant disparity between clinical and AI communities, in the focus on both imaging modalities (AI experts neglected CT and ultrasound, favoring X-ray) and performed tasks (71.9% of AI papers centered on diagnosis). The vast majority of manuscripts were found to be deficient regarding potential use in clinical practice, but 2.7% (n = 12) publications were assigned a high maturity level and are summarized in greater detail. We provide an itemized discussion of the challenges in developing clinically relevant AI solutions with recommendations and remedies.
Clinical Factors and Quantitative CT Parameters Associated With ICU Admission in Patients of COVID-19 Pneumonia: A Multicenter Study.
Authors: ChengxiYan, YingChang, HuanYu, JingxuXu, ChencuiHuang, MingleiYang, YiqiaoWang, DiWang, TianYu, ShuqinWei, ZhenyuLi, FeifeiGong, MingqingKou, WenjingGou, QiliZhao, PenghuiSun, XiuqinJia, ZhaoyangFan, JialiXu, SijieLi, QiYang
Journal: Frontiers in public health

The clinical spectrum of COVID-19 pneumonia is varied. Thus, it is important to identify risk factors at an early stage for predicting deterioration that require transferring the patients to ICU. A retrospective multicenter study was conducted on COVID-19 patients admitted to designated hospitals in China from Jan 17, 2020, to Feb 17, 2020. Clinical presentation, laboratory data, and quantitative CT parameters were also collected. The result showed that increasing risks of ICU admission were associated with age > 60 years (odds ratio [OR], 12.72; 95% confidence interval [CI], 2.42-24.61;
Computed Tomography Image Processing Analysis in COVID-19 Patient Follow-Up Assessment.
Authors: SantiagoTello-Mijares, LuisaWoo
Journal: Journal of healthcare engineering

The rapid worldwide spread of the COVID-19 pandemic has infected patients around the world in a short space of time. Chest computed tomography (CT) images of patients who are infected with COVID-19 can offer early diagnosis and efficient forecast monitoring at a low cost. The diagnosis of COVID-19 on CT in an automated way can speed up many tasks and the application of medical treatments. This can help complement reverse transcription-polymerase chain reaction (RT-PCR) diagnosis. The aim of this work is to develop a system that automatically identifies ground-glass opacity (GGO) and pulmonary infiltrates (PIs) on CT images from patients with COVID-19. The purpose is to assess the disease progression during the patient's follow-up assessment and evaluation. We propose an efficient methodology that incorporates oversegmentation mean shift followed by superpixel-SLIC (simple linear iterative clustering) algorithm on CT images with COVID-19 for pulmonary parenchyma segmentation. To identify the pulmonary parenchyma, we described each superpixel cluster according to its position, grey intensity, second-order texture, and spatial-context-saliency features to classify by a tree random forest (TRF). Second, by applying the watershed segmentation to the mean-shift clusters, only pulmonary parenchyma segmentation-identified zones showed GGO and PI based on the description of each watershed cluster of its position, grey intensity, gradient entropy, second-order texture, Euclidean position to the border region of the PI zone, and global saliency features, after using TRF. Our classification results for pulmonary parenchyma identification on CT images with COVID-19 had a precision of over 92% and recall of over 92% on twofold cross validation. For GGO, the PI identification showed 96% precision and 96% recall on twofold cross validation.
Prediction of COVID-19 with Computed Tomography Images using Hybrid Learning Techniques.
Authors: VaralakshmiPerumal, VasumathiNarayanan, Sakthi Jaya SundarRajasekar
Journal: Disease markers

Reverse Transcription Polymerase Chain Reaction (RT-PCR) used for diagnosing COVID-19 has been found to give low detection rate during early stages of infection. Radiological analysis of CT images has given higher prediction rate when compared to RT-PCR technique. In this paper, hybrid learning models are used to classify COVID-19 CT images, Community-Acquired Pneumonia (CAP) CT images, and normal CT images with high specificity and sensitivity. The proposed system in this paper has been compared with various machine learning classifiers and other deep learning classifiers for better data analysis. The outcome of this study is also compared with other studies which were carried out recently on COVID-19 classification for further analysis. The proposed model has been found to outperform with an accuracy of 96.69%, sensitivity of 96%, and specificity of 98%.
Pneumonia Detection Using an Improved Algorithm Based on Faster R-CNN.
Authors: ShangjieYao, YaowuChen, XiangTian, RongxinJiang
Journal: Computational and mathematical methods in medicine

Pneumonia remains a threat to human health; the coronavirus disease 2019 (COVID-19) that began at the end of 2019 had a major impact on the world. It is still raging in many countries and has caused great losses to people's lives and property. In this paper, we present a method based on DeepConv-DilatedNet of identifying and localizing pneumonia in chest X-ray (CXR) images. Two-stage detector Faster R-CNN is adopted as the structure of a network. Feature Pyramid Network (FPN) is integrated into the residual neural network of a dilated bottleneck so that the deep features are expanded to preserve the deep feature and position information of the object. In the case of DeepConv-DilatedNet, the deconvolution network is used to restore high-level feature maps into its original size, and the target information is further retained. On the other hand, DeepConv-DilatedNet uses a popular fully convolution architecture with computation shared on the entire image. Then, Soft-NMS is used to screen boxes and ensure sample quality. Also, K-Means++ is used to generate anchor boxes to improve the localization accuracy. The algorithm obtained 39.23% Mean Average Precision (mAP) on the X-ray image dataset from the Radiological Society of North America (RSNA) and got 38.02% Mean Average Precision (mAP) on the ChestX-ray14 dataset, surpassing other detection algorithms. So, in this paper, an improved algorithm that can provide doctors with location information of pneumonia lesions is proposed.
Automatic prediction of COVID- 19 from chest images using modified ResNet50.
Authors: MarwaElpeltagy, HanySallam
Journal: Multimedia tools and applications

Recently coronavirus 2019 (COVID-2019), discovered in Wuhan city of China in December 2019 announced as world pandemic by the World Health Organization (WHO). It has catastrophic impacts on daily lives, public health, and the global economy. The detection of coronavirus (COVID- 19) is now a critical task for medical specialists. Laboratory methods for detecting the virus such as Polymerase Chain Reaction, antigens, and antibodies have pros and cons represented in time required to obtain results, accuracy, cost and suitability of the test to phase of infection. The need for accurate, fast, and cheap auxiliary diagnostic tools has become a necessity as there are no accurate automated toolkits available. Other medical investigations such as chest X-ray and Computerized Tomography scans are imaging techniques that play an important role in the diagnosis of COVID- 19 virus. Application of advanced artificial intelligence techniques for processing radiological imaging can be helpful for the accurate detection of this virus. However, Due to the small dataset available for COVID- 19, transfer learning from pre-trained convolution neural networks, CNNs can be used as a promising solution for diagnosis of coronavirus. Transfer learning becomes an effective mechanism by transferring knowledge from generic object recognition tasks to domain-specific tasks. Hence, the main contribution of this paper is to exploit the pre-trained deep learning CNN architectures as a cornerstone to enhance and build up an automated tool for detection and diagnosis of COVID- 19 in chest X-Ray and Computerized Tomography images. The main idea is to make use of their convolutional neural network structure and its learned weights on large datasets such as ImageNet. Moreover, a modification to ResNet50 is proposed to classify the patients as COVID infected or not. This modification includes adding three new layers, named,
Determination of COVID-19 pneumonia based on generalized convolutional neural network model from chest X-ray images.
Authors: AdiAlhudhaif, KemalPolat, OnurKaraman
Journal: Expert systems with applications

X-ray units have become one of the most advantageous candidates for triaging the new Coronavirus disease COVID-19 infected patients thanks to its relatively low radiation dose, ease of access, practical, reduced prices, and quick imaging process. This research intended to develop a reliable convolutional-neural-network (CNN) model for the classification of COVID-19 from chest X-ray views. Moreover, it is aimed to prevent bias issues due to the database. Transfer learning-based CNN model was developed by using a sum of 1,218 chest X-ray images (CXIs) consisting of 368 COVID-19 pneumonia and 850 other pneumonia cases by pre-trained architectures, including DenseNet-201, ResNet-18, and SqueezeNet. The chest X-ray images were acquired from publicly available databases, and each individual image was carefully selected to prevent any bias problem. A stratified 5-fold cross-validation approach was utilized with a ratio of 90% for training and 10% for the testing (unseen folds), in which 20% of training data was used as a validation set to prevent overfitting problems. The binary classification performances of the proposed CNN models were evaluated by the testing data. The activation mapping approach was implemented to improve the causality and visuality of the radiograph. The outcomes demonstrated that the proposed CNN model built on DenseNet-201 architecture outperformed amongst the others with the highest accuracy, precision, recall, and F1-scores of 94.96%, 89.74%, 94.59%, and 92.11%, respectively. The results indicated that the reliable diagnosis of COVID-19 pneumonia from CXIs based on the CNN model opens the door to accelerate triage, save critical time, and prioritize resources besides assisting the radiologists.
FBSED based automatic diagnosis of COVID-19 using X-ray and CT images.
Authors: Pradeep KumarChaudhary, Ram BilasPachori
Journal: Computers in biology and medicine

This work introduces the Fourier-Bessel series expansion-based decomposition (FBSED) method, which is an implementation of the wavelet packet decomposition approach in the Fourier-Bessel series expansion domain. The proposed method has been used for the diagnosis of pneumonia caused by the 2019 novel coronavirus disease (COVID-19) using chest X-ray image (CXI) and chest computer tomography image (CCTI). The FBSED method is used to decompose CXI and CCTI into sub-band images (SBIs). The SBIs are then used to train various pre-trained convolutional neural network (CNN) models separately using a transfer learning approach. The combination of SBI and CNN is termed as one channel. Deep features from each channel are fused to get a feature vector. Different classifiers are used to classify pneumonia caused by COVID-19 from other viral and bacterial pneumonia and healthy subjects with the extracted feature vector. The different combinations of channels have also been analyzed to make the process computationally efficient. For CXI and CCTI databases, the best performance has been obtained with only one and four channels, respectively. The proposed model was evaluated using 5-fold and 10-fold cross-validation processes. The average accuracy for the CXI database was 100% for both 5-fold and 10-fold cross-validation processes, and for the CCTI database, it is 97.6% for the 5-fold cross-validation process. Therefore, the proposed method may be used by radiologists to rapidly diagnose patients with COVID-19.